51
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Karamysheva ZN, Tikhonova EB, Grozdanov PN, Huffman JC, Baca KR, Karamyshev A, Denison RB, MacDonald CC, Zhang K, Karamyshev AL. Polysome Profiling in Leishmania, Human Cells and Mouse Testis. J Vis Exp 2018. [PMID: 29683462 DOI: 10.3791/57600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Proper protein expression at the right time and in the right amounts is the basis of normal cell function and survival in a fast-changing environment. For a long time, the gene expression studies were dominated by research on the transcriptional level. However, the steady-state levels of mRNAs do not correlate well with protein production, and the translatability of mRNAs varies greatly depending on the conditions. In some organisms, like the parasite Leishmania, the protein expression is regulated mostly at the translational level. Recent studies demonstrated that protein translation dysregulation is associated with cancer, metabolic, neurodegenerative and other human diseases. Polysome profiling is a powerful method to study protein translation regulation. It allows to measure the translational status of individual mRNAs or examine translation on a genome-wide scale. The basis of this technique is the separation of polysomes, ribosomes, their subunits and free mRNAs during centrifugation of a cytoplasmic lysate through a sucrose gradient. Here, we present a universal polysome profiling protocol used on three different models - parasite Leishmania major, cultured human cells and animal tissues. Leishmania cells freely grow in suspension and cultured human cells grow in adherent monolayer, while mouse testis represents an animal tissue sample. Thus, the technique is adapted to all of these sources. The protocol for the analysis of polysomal fractions includes detection of individual mRNA levels by RT-qPCR, proteins by Western blot and analysis of ribosomal RNAs by electrophoresis. The method can be further extended by examination of mRNAs association with the ribosome on a transcriptome level by deep RNA-seq and analysis of ribosome-associated proteins by mass spectroscopy of the fractions. The method can be easily adjusted to other biological models.
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Affiliation(s)
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Petar N Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - James C Huffman
- Department of Biological Sciences, Texas Tech University; CISER (Center for the Integration of STEM Education & Research), Texas Tech University
| | - Kristen R Baca
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center; CISER (Center for the Integration of STEM Education & Research), Texas Tech University
| | - Alexander Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - R Brian Denison
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Clinton C MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center
| | - Kai Zhang
- Department of Biological Sciences, Texas Tech University
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center;
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52
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Vindu A, Dandewad V, Seshadri V. Identification of human Phosphatidyl Inositol 5-Phosphate 4-Kinase as an RNA binding protein that is imported into Plasmodium falciparum. Biochem Biophys Res Commun 2018. [PMID: 29518392 DOI: 10.1016/j.bbrc.2018.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum is a causative agent for malaria and has a complex life cycle in human and mosquito hosts. Translation repression of specific set of mRNA has been reported in gametocyte stages of this parasite. A conserved element present in the 3'UTR of some of these transcripts was identified. Biochemical studies have identified components of the RNA storage and/or translation inhibitor complex but it is not yet clear how the complex is specifically recruited on the RNA targeted for translation regulation. We used the 3'UTR region of translationally regulated transcripts to identify Phosphatidyl-inositol 5-phosphate 4-kinase (PIP4K2A) as the protein that associates with these RNAs. We further show that recombinant PIP4K2A has the RNA binding activity and can associate specifically with Plasmodium 3'UTR RNAs. Immunostainings show that hPIP4K2A is imported into the Plasmodium parasite from RBC. These results identify a novel RNA binding role for PIP4K2A that may play a role in Plasmodium propagation.
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Affiliation(s)
- Arya Vindu
- National Centre for Cell Science, University of Pune Campus, Ganeshkhind, Pune, 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vishal Dandewad
- National Centre for Cell Science, University of Pune Campus, Ganeshkhind, Pune, 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vasudevan Seshadri
- National Centre for Cell Science, University of Pune Campus, Ganeshkhind, Pune, 411007, India.
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53
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Mahanta A, Ganguli P, Barah P, Sarkar RR, Sarmah N, Phukan S, Bora M, Baruah S. Integrative Approaches to Understand the Mastery in Manipulation of Host Cytokine Networks by Protozoan Parasites with Emphasis on Plasmodium and Leishmania Species. Front Immunol 2018. [PMID: 29527208 PMCID: PMC5829655 DOI: 10.3389/fimmu.2018.00296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Diseases by protozoan pathogens pose a significant public health concern, particularly in tropical and subtropical countries, where these are responsible for significant morbidity and mortality. Protozoan pathogens tend to establish chronic infections underscoring their competence at subversion of host immune processes, an important component of disease pathogenesis and of their virulence. Modulation of cytokine and chemokine levels, their crosstalks and downstream signaling pathways, and thereby influencing recruitment and activation of immune cells is crucial to immune evasion and subversion. Many protozoans are now known to secrete effector molecules that actively modulate host immune transcriptome and bring about alterations in host epigenome to alter cytokine levels and signaling. The complexity of multi-dimensional events during interaction of hosts and protozoan parasites ranges from microscopic molecular levels to macroscopic ecological and epidemiological levels that includes disrupting metabolic pathways, cell cycle (Toxoplasma and Theileria sp.), respiratory burst, and antigen presentation (Leishmania spp.) to manipulation of signaling hubs. This requires an integrative systems biology approach to combine the knowledge from all these levels to identify the complex mechanisms of protozoan evolution via immune escape during host-parasite coevolution. Considering the diversity of protozoan parasites, in this review, we have focused on Leishmania and Plasmodium infections. Along with the biological understanding, we further elucidate the current efforts in generating, integrating, and modeling of multi-dimensional data to explain the modulation of cytokine networks by these two protozoan parasites to achieve their persistence in host via immune escape during host-parasite coevolution.
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Affiliation(s)
- Anusree Mahanta
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India.,Institute of Stem Cell Biology and Regenerative Medicine, Bengaluru, India
| | - Piyali Ganguli
- Chemical Engineering and Process Development, CSIR- National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Ram Rup Sarkar
- Chemical Engineering and Process Development, CSIR- National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NCL Campus, Pune, India
| | - Neelanjana Sarmah
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Saurav Phukan
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Mayuri Bora
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Shashi Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
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54
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Cooper C, Keatley S, Northover A, Gofton AW, Brigg F, Lymbery AJ, Pallant L, Clode PL, Thompson RCA. Next generation sequencing reveals widespread trypanosome diversity and polyparasitism in marsupials from Western Australia. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:58-67. [PMID: 29988778 PMCID: PMC6031965 DOI: 10.1016/j.ijppaw.2018.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/29/2017] [Accepted: 01/16/2018] [Indexed: 01/22/2023]
Abstract
In Western Australia a number of indigenous Trypanosoma spp. infect susceptible native marsupials, such as the woylie (Bettongia penicillata), brushtail possum (Trichosurus vulpecula), and chuditch (Dasyurus geoffroii). Two genotypes of Trypanosoma copemani (identified as G1 and G2) have been found in the woylie, and G2 has been implicated in the decline of this host species, making its presence of particular interest. Here we used targeted amplicon next generation sequencing (NGS) of the Trypanosoma 18S rDNA loci on 70 Trypanosoma-positive marsupial blood samples, to identify T. copemani genotypes and multiple Trypanosoma infections (polyparasitism) in woylies and cohabiting species in Western Australia. Polyparasitism with Trypanosoma spp. was found in 50% of the wildlife sampled, and within species diversity was high, with 85 zero-radius operational taxonomic units (ZOTUs) identified in nine putative parasite species. Trypanosoma copemani was assigned 17 ZOTUs and was identified in 80% of samples. The most abundant ZOTU isolated (63%) differed slightly from the published genotype of G1, and G2 was the second most abundant ZOTU (14%). Trypanosome diversity was significantly greater in woylies than in brushtail possums, and parasite community composition also differed significantly between these host species. One novel Trypanosoma spp. genotype (Trypanosoma sp. ANU2) was found in 20% of samples. A species of Crithidia was detected in a woylie, and two avian trypanosomes (Trypanosoma avium and Trypanosoma sp. AAT) were identified in woylies for the first time. Extensive trypanosome diversity and polyparasitism in south Western Australia. A significant difference between trypanosomes infecting woylies and brushtail possums. Evidence that the current species-level taxonomy of Australian trypanosomes may need revision.
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Affiliation(s)
- Crystal Cooper
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Stirling HWY, Crawley, WA 6009, Australia
| | - Sarah Keatley
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Amy Northover
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Alex W Gofton
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Frances Brigg
- State Agriculture and Biotechnology Institute, School of Veterinary and Life Sciences, Murdoch University, WA 6150, Australia
| | - Alan J Lymbery
- Fish Health Unit, School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia
| | - Louise Pallant
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Peta L Clode
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Stirling HWY, Crawley, WA 6009, Australia
| | - R C Andrew Thompson
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
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55
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Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, LE Roch KG, Fonseca LL, Voit EO. Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria. Parasitology 2018; 145:85-100. [PMID: 28712361 PMCID: PMC5798396 DOI: 10.1017/s0031182017001135] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 02/08/2023]
Abstract
Antigenic variation in malaria was discovered in Plasmodium knowlesi studies involving longitudinal infections of rhesus macaques (M. mulatta). The variant proteins, known as the P. knowlesi Schizont Infected Cell Agglutination (SICA) antigens and the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) antigens, expressed by the SICAvar and var multigene families, respectively, have been studied for over 30 years. Expression of the SICA antigens in P. knowlesi requires a splenic component, and specific antibodies are necessary for variant antigen switch events in vivo. Outstanding questions revolve around the role of the spleen and the mechanisms by which the expression of these variant antigen families are regulated. Importantly, the longitudinal dynamics and molecular mechanisms that govern variant antigen expression can be studied with P. knowlesi infection of its mammalian and vector hosts. Synchronous infections can be initiated with established clones and studied at multi-omic levels, with the benefit of computational tools from systems biology that permit the integration of datasets and the design of explanatory, predictive mathematical models. Here we provide an historical account of this topic, while highlighting the potential for maximizing the use of P. knowlesi - macaque model systems and summarizing exciting new progress in this area of research.
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Affiliation(s)
- M R Galinski
- Emory Vaccine Center,Yerkes National Primate Research Center,Emory University,Atlanta,GA,USA
| | - S A Lapp
- Emory Vaccine Center,Yerkes National Primate Research Center,Emory University,Atlanta,GA,USA
| | - M S Peterson
- Emory Vaccine Center,Yerkes National Primate Research Center,Emory University,Atlanta,GA,USA
| | - F Ay
- La Jolla Institute for Allergy and Immunology,La Jolla,CA 92037,USA
| | - C J Joyner
- Emory Vaccine Center,Yerkes National Primate Research Center,Emory University,Atlanta,GA,USA
| | - K G LE Roch
- Department of Cell Biology & Neuroscience,Center for Disease and Vector Research,Institute for Integrative Genome Biology,University of California Riverside,CA 92521,USA
| | - L L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering,Georgia Institute of Technology and Emory University,Atlanta,Georgia,30332-2000,USA
| | - E O Voit
- The Wallace H. Coulter Department of Biomedical Engineering,Georgia Institute of Technology and Emory University,Atlanta,Georgia,30332-2000,USA
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56
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Abstract
Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen's biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources ( http://eupathdb.org ) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpathogenic species. EuPathDB integrates preanalyzed data with advanced search capabilities, data visualization, analysis tools and a comprehensive record system in a graphical interface that does not require prior computational skills. This chapter describes guiding concepts common across EuPathDB sites and illustrates the powerful data mining capabilities of some of the available tools and features.
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57
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Rono MK, Nyonda MA, Simam JJ, Ngoi JM, Mok S, Kortok MM, Abdullah AS, Elfaki MM, Waitumbi JN, El-Hassan IM, Marsh K, Bozdech Z, Mackinnon MJ. Adaptation of Plasmodium falciparum to its transmission environment. Nat Ecol Evol 2017; 2:377-387. [PMID: 29255304 DOI: 10.1038/s41559-017-0419-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022]
Abstract
Success in eliminating malaria will depend on whether parasite evolution outpaces control efforts. Here, we show that Plasmodium falciparum parasites (the deadliest of the species causing human malaria) found in low-transmission-intensity areas have evolved to invest more in transmission to new hosts (reproduction) and less in within-host replication (growth) than parasites found in high-transmission areas. At the cellular level, this adaptation manifests as increased production of reproductive forms (gametocytes) early in the infection at the expense of processes associated with multiplication inside red blood cells, especially membrane transport and protein trafficking. At the molecular level, this manifests as changes in the expression levels of genes encoding epigenetic and translational machinery. Specifically, expression levels of the gene encoding AP2-G-the transcription factor that initiates reproduction-increase as transmission intensity decreases. This is accompanied by downregulation and upregulation of genes encoding HDAC1 and HDA1-two histone deacetylases that epigenetically regulate the parasite's replicative and reproductive life-stage programmes, respectively. Parasites in reproductive mode show increased reliance on the prokaryotic translation machinery found inside the plastid-derived organelles. Thus, our dissection of the parasite's adaptive regulatory architecture has identified new potential molecular targets for malaria control.
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Affiliation(s)
- Martin K Rono
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Bioscience Research Centre, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mary A Nyonda
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
| | | | - Joyce M Ngoi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sachel Mok
- Columbia University Medical Center, New York, NY, USA
| | - Moses M Kortok
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Mohammed M Elfaki
- Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Gizan, Jazan, Saudi Arabia
| | - John N Waitumbi
- Walter Reed Army Institute of Research/Kenya Medical Research Institute, Kisumu, Kenya
| | - Ibrahim M El-Hassan
- Faculty of Public Health and Tropical Medicine, Jazan University, Gizan, Jazan, Saudi Arabia
| | - Kevin Marsh
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
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58
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Hassan MA, Vasquez JJ, Guo-Liang C, Meissner M, Nicolai Siegel T. Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii. BMC Genomics 2017; 18:961. [PMID: 29228904 PMCID: PMC5725899 DOI: 10.1186/s12864-017-4362-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/01/2017] [Indexed: 11/17/2022] Open
Abstract
Background The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite that is shielded from the cytosolic host immune factors by a parasitophorous vacuole, the brief entry into the extracellular space is likely to exert enormous stress. Due to its role in cellular stress response, we hypothesize that translational control plays an important role in regulating gene expression in Toxoplasma during the lytic cycle. Unlike transcriptional profiles, insights into genome-wide translational profiles of Toxoplasma gondii are lacking. Methods We have performed genome-wide ribosome profiling, coupled with high throughput RNA sequencing, in intracellular and extracellular Toxoplasma gondii parasites to investigate translational control during the lytic cycle. Results Although differences in transcript abundance were mostly mirrored at the translational level, we observed significant differences in the abundance of ribosome footprints between the two parasite stages. Furthermore, our data suggest that mRNA translation in the parasite is potentially regulated by mRNA secondary structure and upstream open reading frames. Conclusion We show that most of the Toxoplasma genes that are dysregulated during the lytic cycle are translationally regulated. Electronic supplementary material The online version of this article (10.1186/s12864-017-4362-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Musa A Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, UK. .,The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Juan J Vasquez
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Present address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chew Guo-Liang
- Computational Biology Program, Basic Sciences and Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, WA, 98105, USA
| | - Markus Meissner
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany
| | - T Nicolai Siegel
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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59
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Gajbhiye S, Patra P, Yadav MK. New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species. Acta Trop 2017; 176:29-33. [PMID: 28751162 DOI: 10.1016/j.actatropica.2017.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023]
Abstract
Codon usage bias is due to the non-random usage of synonymous codons for coding amino acids. The synonymous sites are under weak selection, and codon usage bias is maintained by the equilibrium in mutational bias, genetic drift and selection pressure. The differential codon usage choices are also relevant to human infecting Plasmodium species. Recently, P. knowlesi switches its natural host, long-tailed macaques, and starts infecting humans. This review focuses on the comparative analysis of codon usage choices among human infecting P. falciparum and P. vivax along with P. knowlesi species taking their coding sequence data. The variation in GC content, amino acid frequencies, effective number of codons and other factors plays a crucial role in determining synonymous codon choices. Within species codon choices are more similar for P. vivax and P. knowlesi in comparison with P. falciparum species. This study suggests that synonymous codon choice modulates the gene expression level, mRNA stability, ribosome speed, protein folding, translation efficiency and its accuracy in Plasmodium species, and provides a valuable information regarding the codon usage pattern to facilitate gene cloning as well as expression and transfection studies for malaria causing species.
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60
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Plasmodium falciparum Calcium-Dependent Protein Kinase 2 Is Critical for Male Gametocyte Exflagellation but Not Essential for Asexual Proliferation. mBio 2017; 8:mBio.01656-17. [PMID: 29042501 PMCID: PMC5646254 DOI: 10.1128/mbio.01656-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Drug development efforts have focused mostly on the asexual blood stages of the malaria parasite Plasmodium falciparum. Except for primaquine, which has its own limitations, there are no available drugs that target the transmission of the parasite to mosquitoes. Therefore, there is a need to validate new parasite proteins that can be targeted for blocking transmission. P. falciparum calcium-dependent protein kinases (PfCDPKs) play critical roles at various stages of the parasite life cycle and, importantly, are absent in the human host. These features mark them as attractive drug targets. In this study, using CRISPR/Cas9 we successfully knocked out PfCDPK2 from blood-stage parasites, which was previously thought to be an indispensable protein. The growth rate of the PfCDPK2 knockout (KO) parasites was similar to that of wild-type parasites, confirming that PfCDPK2 function is not essential for the asexual proliferation of the parasite in vitro. The mature male and female gametocytes of PfCDPK2 KO parasites become round after induction. However, they fail to infect female Anopheles stephensi mosquitoes due to a defect(s) in male gametocyte exflagellation and possibly in female gametes. Despite reductions in the number of deaths it causes, malaria continues to be a leading infectious disease of the developing world. For effective control and elimination of malaria, multiple stages of the parasite need to be targeted. One such stage includes the transmission of the parasite to mosquitoes. Here, we demonstrate the successful knockout of PfCDPK2, which was previously thought to be indispensable for parasite growth in red blood cells. The PfCDPK2 KO parasites are incapable of establishing an infection in mosquitoes. Therefore, our study suggests that targeting PfCDPK2 may be a good strategy to control malaria transmission in countries with high transmission. Moreover, molecular understanding of the signaling pathway of PfCDPK2 may provide additional targets for malaria control.
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61
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Translational Control in the Latency of Apicomplexan Parasites. Trends Parasitol 2017; 33:947-960. [PMID: 28942109 DOI: 10.1016/j.pt.2017.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 01/07/2023]
Abstract
Apicomplexan parasites Toxoplasma gondii and Plasmodium spp. use latent stages to persist in the host, facilitate transmission, and thwart treatment of infected patients. Therefore, it is important to understand the processes driving parasite differentiation to and from quiescent stages. Here, we discuss how a family of protein kinases that phosphorylate the eukaryotic initiation factor-2 (eIF2) function in translational control and drive differentiation. This translational control culminates in reprogramming of the transcriptome to facilitate parasite transition towards latency. We also discuss how eIF2 phosphorylation contributes to the maintenance of latency and provides a crucial role in the timing of reactivation of latent parasites towards proliferative stages.
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62
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Muñoz EE, Hart KJ, Walker MP, Kennedy MF, Shipley MM, Lindner SE. ALBA4 modulates its stage-specific interactions and specific mRNA fates during Plasmodium yoelii growth and transmission. Mol Microbiol 2017; 106:266-284. [PMID: 28787542 DOI: 10.1111/mmi.13762] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2017] [Indexed: 12/20/2022]
Abstract
Transmission of the malaria parasite occurs in an unpredictable moment, when a mosquito takes a blood meal. Plasmodium has therefore evolved strategies to prepare for transmission, including translationally repressing and protecting mRNAs needed to establish the infection. However, mechanisms underlying these critical controls are not well understood, including whether Plasmodium changes its translationally repressive complexes and mRNA targets in different stages. Efforts to understand this have been stymied by severe technical limitations due to substantial mosquito contamination of samples. Here using P. yoelii, for the first time we provide a proteomic comparison of a protein complex across asexual blood, sexual and sporozoite stages, along with a transcriptomic comparison of the mRNAs that are affected in these stages. We find that the Apicomplexan-specific ALBA4 RNA-binding protein acts to regulate development of the parasite's transmission stages, and that ALBA4 associates with both stage-specific and stage-independent partners to produce opposing mRNA fates. These efforts expand our understanding and ability to interrogate both sexual and sporozoite transmission stages and the molecular preparations they evolved to perpetuate their infectious cycle.
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Affiliation(s)
- Elyse E Muñoz
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Kevin J Hart
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Michael P Walker
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Mark F Kennedy
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Mackenzie M Shipley
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, University Park, PA, USA
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63
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Lu X, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch K. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2017; 45:7825-7840. [PMID: 28531310 PMCID: PMC5737683 DOI: 10.1093/nar/gkx464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
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MESH Headings
- Animals
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Genes, Protozoan
- Humans
- Malaria, Falciparum/blood
- Malaria, Falciparum/parasitology
- Plasmodium falciparum/genetics
- Plasmodium falciparum/growth & development
- Plasmodium falciparum/pathogenicity
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Xueqing Maggie Lu
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Michael Lee
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Evelien M. Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Karine G. Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
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64
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Barbosa AD, Gofton AW, Paparini A, Codello A, Greay T, Gillett A, Warren K, Irwin P, Ryan U. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS). PLoS One 2017; 12:e0181279. [PMID: 28704541 PMCID: PMC5509321 DOI: 10.1371/journal.pone.0181279] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/28/2017] [Indexed: 01/19/2023] Open
Abstract
Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2–39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2–39.8%), T. gilletti (25%, 95% CI: 18.7–32.3%), T. copemani (27.4%, 95% CI: 20.8–34.8%) and T. vegrandis (10.1%, 95% CI: 6.0–15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0–3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1–9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21–35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2–9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the natural genetic diversity of Trypanosoma communities infecting koalas and constitutes a benchmark for future clinical and epidemiological studies required to quantify the contribution of trypanosome infections on koala survival rates.
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Affiliation(s)
- Amanda D. Barbosa
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Distrito Federal, Brazil
- * E-mail:
| | - Alexander W. Gofton
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Annachiara Codello
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Telleasha Greay
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
- School of Veterinary Science, University of Queensland, Saint Lucia, Australia
| | - Kristin Warren
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Peter Irwin
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
| | - Una Ryan
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Perth, Western Australia
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65
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Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 2017; 33:364-377. [PMID: 28065669 PMCID: PMC5410391 DOI: 10.1016/j.pt.2016.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022]
Abstract
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined. Finally, we address the use of epigenetic processes as targets for novel antimalarial therapies. Collectively, these topics highlight the unique biology of P. falciparum, and contribute to our understanding of mechanisms regulating gene expression in this deadly parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M Lu
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
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66
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Painter HJ, Carrasquilla M, Llinás M. Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum. Genome Res 2017; 27:1074-1086. [PMID: 28416533 PMCID: PMC5453321 DOI: 10.1101/gr.217356.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
To capture the transcriptional dynamics within proliferating cells, methods to differentiate nascent transcription from preexisting mRNAs are desired. One approach is to label newly synthesized mRNA transcripts in vivo through the incorporation of modified pyrimidines. However, the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine deaminase/uracil phosphoribosyltransferase (FCU). We show that expression of FCU allows for the direct incorporation of thiol-modified pyrimidines into nascent mRNAs. Using developmental stage-specific promoters to express FCU-GFP enables the biosynthetic capture and in-depth analysis of mRNA dynamics from subpopulations of cells undergoing differentiation. We demonstrate the utility of this method by examining the transcriptional dynamics of the sexual gametocyte stage transition, a process that is essential to malaria transmission between hosts. Using the pfs16 gametocyte-specific promoter to express FCU-GFP in 3D7 parasites, we found that sexual stage commitment is governed by transcriptional reprogramming and stabilization of a subset of essential gametocyte transcripts. We also measured mRNA dynamics in F12 gametocyte-deficient parasites and demonstrate that the transcriptional program required for sexual commitment and maturation is initiated but likely aborted due to the absence of the PfAP2-G transcriptional regulator and a lack of gametocyte-specific mRNA stabilization. Biosynthetic labeling of Plasmodium mRNAs is incredibly versatile, can be used to measure transcriptional dynamics at any stage of parasite development, and will allow for future applications to comprehensively measure RNA-protein interactions in the malaria parasite.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuela Carrasquilla
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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67
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Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum. Sci Rep 2017; 7:723. [PMID: 28389662 PMCID: PMC5429705 DOI: 10.1038/s41598-017-00801-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 11/08/2022] Open
Abstract
Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism. Particularly, asparagine homorepeats are generally encoded by locally clustered GU wobble AAT codons, we demonstrated that this GU wobble-rich codon context is the determining factor that causes reduction of protein level. Moreover, insertion of clustered AAT codons also causes destabilization of the transcripts. Interestingly, more frequent asparagine homorepeats insertion is seen in single-exon genes, suggesting transcripts of these genes may have been programmed for rapid mRNA decay to compensate for the inefficiency of mRNA surveillance regulation on intronless genes. To our knowledge, this is the first study that addresses P. falciparum codon usage in vitro and provides new insights on translational regulation and genome evolution of this parasite.
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68
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Untranslated regions of mRNA and their role in regulation of gene expression in protozoan parasites. J Biosci 2017; 42:189-207. [PMID: 28229978 DOI: 10.1007/s12038-016-9660-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protozoan parasites are one of the oldest living entities in this world that throughout their existence have shown excellent resilience to the odds of survival and have adapted beautifully to ever changing rigors of the environment. In view of the dynamic environment encountered by them throughout their life cycle, and in establishing pathogenesis, it is unsurprising that modulation of gene expression plays a fundamental role in their survival. In higher eukaryotes, untranslated regions (UTRs) of transcripts are one of the crucial regulators of gene expression (influencing mRNA stability and translation efficiency). Parasitic protozoan genome studies have led to the characterization (in silico, in vitro and in vivo) of a large number of their genes. Comparison of higher eukaryotic UTRs with parasitic protozoan UTRs reveals the existence of several similar and dissimilar facets of the UTRs. This review focuses on the elements of UTRs of medically important protozoan parasites and their regulatory role in gene expression. Such information may be useful to researchers in designing gene targeting strategies linked with perturbation of host-parasite relationships leading to control of specific parasites.
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69
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Oyelade J, Isewon I, Oladipupo F, Aromolaran O, Uwoghiren E, Ameh F, Achas M, Adebiyi E. Clustering Algorithms: Their Application to Gene Expression Data. Bioinform Biol Insights 2016; 10:237-253. [PMID: 27932867 PMCID: PMC5135122 DOI: 10.4137/bbi.s38316] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/05/2016] [Accepted: 09/09/2016] [Indexed: 12/17/2022] Open
Abstract
Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure.
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Affiliation(s)
- Jelili Oyelade
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Funke Oladipupo
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Olufemi Aromolaran
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Efosa Uwoghiren
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Faridah Ameh
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Moses Achas
- Department of Computer Science and Information Technology, Bells University of Technology, Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
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70
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Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ, Spruill D, Wang H, Warrenfeltz S, Zheng J. EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res 2016; 45:D581-D591. [PMID: 27903906 PMCID: PMC5210576 DOI: 10.1093/nar/gkw1105] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/28/2016] [Indexed: 12/26/2022] Open
Abstract
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions.
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Affiliation(s)
- Cristina Aurrecoechea
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ana Barreto
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evelina Y Basenko
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - John Brestelli
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian P Brunk
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shon Cade
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Crouch
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Ryan Doherty
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dave Falke
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Steve Fischer
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bindu Gajria
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar S Harb
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA .,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Heiges
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | | | - Sufen Hu
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Iodice
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica C Kissinger
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Cris Lawrence
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Li
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deborah F Pinney
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jane A Pulman
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Achchuthan Shanmugasundram
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Fatima Silva-Franco
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sascha Steinbiss
- Wellcome Trust Sanger Institute, Parasite Genomics, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Christian J Stoeckert
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Spruill
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Haiming Wang
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Susanne Warrenfeltz
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Jie Zheng
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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71
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Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics 2016; 108:224-231. [PMID: 27789319 DOI: 10.1016/j.ygeno.2016.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022]
Abstract
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from other Plasmodium species. A distinct predominance of quadruplexes was observed in nuclear and organellar genes that participate in antigenic variation, pathogenesis, DNA/RNA regulation, metabolic and protein quality control processes. Data also suggested association of quadruplexes with SNPs and DNA methylation. Furthermore, analysis of steady state mRNA (RNA-seq) and polysome-associated mRNA (Ribosome profiling) data revealed stage-specific differences in translational efficiency of quadruplex harboring genes. Taken together, our findings hint towards existence of regulatory dynamics associated with quadruplexes that may modulate translational efficiency of quadruplex harboring genes to provide survival advantage to the parasite against host immune response and antimalarial drug pressure.
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Affiliation(s)
- Deeksha Bhartiya
- ICMR-Institute of Cytology and Preventive Oncology, Noida 201301, Uttar Pradesh, India
| | - Vandna Chawla
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Sourav Ghosh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India
| | - Ravi Shankar
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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72
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Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol 2016; 33:3108-3132. [PMID: 27604222 PMCID: PMC5100048 DOI: 10.1093/molbev/msw189] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Clara S Chan
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert M Waterhouse
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, Geneva, Switzerland.,Swiss Institute of Bioinformatics, rue Michel-Servet 1, Geneva, Switzerland
| | | | | | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
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73
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Abstract
Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.
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Affiliation(s)
- Sebastian Kirchner
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - B Joanne Power
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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Wang C, Adapa SR, Gibbons J, Sutton S, Jiang RHY. Punctuated chromatin states regulate Plasmodium falciparum antigenic variation at the intron and 2 kb upstream regions. BMC Genomics 2016; 17:652. [PMID: 27538502 PMCID: PMC4990864 DOI: 10.1186/s12864-016-3005-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/10/2016] [Indexed: 11/27/2022] Open
Abstract
Background Understanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few var genes exhibit high expression levels. However, the global regulation of var expression and the relationship between epigenetic and genetic control remains to be established. Result We have systematically reanalyzed the existing genomic data including chromatin configurations and gene expressions; and for the first time used robust statistical methods to show that the intron and 2 kb upstream regions of each endogenous var gene always maintain high chromatin accessibility, with high potential to bind transcription factors (TFs). The levels of transcripts for different var gene family members are associated with this chromatin accessibility. Any given var gene thus shows punctuated chromatin states throughout the asexual life cycle. This is demonstrated by three independent transcript datasets. Chromatin accessibility in the var intron and 2 kb upstream regions are also positively correlated with their GC content, suggesting the level of var genes silencing might be encoded in their intron sequences. Interestingly, both var intron and 2 kb upstream regions exhibit higher chromatin accessibility when the genes have relatively lower transcription levels, suggesting a punctuated repressive function for these regulatory elements. Conclusion By integrating and analyzing epigenomic, genomic and transcriptomic data, our work reveals a novel distal element in var control. We found dynamic modulations of specific epigenetic marks around the var intron and distal upstream regions are involved in the general var gene expression patterns in malarial antigenic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3005-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengqi Wang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Justin Gibbons
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Stephen Sutton
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
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75
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Gissot M, Hovasse A, Chaloin L, Schaeffer-Reiss C, Van Dorsselaer A, Tomavo S. An evolutionary conserved zinc finger protein is involved inToxoplasma gondiimRNA nuclear export. Cell Microbiol 2016; 19. [DOI: 10.1111/cmi.12644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/20/2016] [Accepted: 07/02/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Mathieu Gissot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille; U1019, UMR 8204, CIIL, Centre d'Infection et d'Immunité de Lille; F-59000 Lille France
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Laurent Chaloin
- CPBS, CNRS UMR 5236; Université de Montpellier; Montpellier France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, CNRS; Université de Strasbourg; Strasbourg France
| | - Stanislas Tomavo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille; U1019, UMR 8204, CIIL, Centre d'Infection et d'Immunité de Lille; F-59000 Lille France
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76
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Bunnik EM, Batugedara G, Saraf A, Prudhomme J, Florens L, Le Roch KG. The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. Genome Biol 2016; 17:147. [PMID: 27381095 PMCID: PMC4933991 DOI: 10.1186/s13059-016-1014-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/20/2016] [Indexed: 02/08/2023] Open
Abstract
Background Gene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional control of gene expression, while at least part of Plasmodium’s genome is controlled by post-transcriptional mechanisms. To generate insights into the mechanisms that regulate gene expression at the post-transcriptional level, we undertook complementary computational, comparative genomics, and experimental approaches to identify and characterize mRNA-binding proteins (mRBPs) in P. falciparum. Results Close to 1000 RNA-binding proteins are identified by hidden Markov model searches, of which mRBPs encompass a relatively large proportion of the parasite proteome as compared to other eukaryotes. Several abundant mRNA-binding domains are enriched in apicomplexan parasites, while strong depletion of mRNA-binding domains involved in RNA degradation is observed. Next, we experimentally capture 199 proteins that interact with mRNA during the blood stages, 64 of which with high confidence. These captured mRBPs show a significant overlap with the in silico identified candidate RBPs (p < 0.0001). Among the experimentally validated mRBPs are many known translational regulators active in other stages of the parasite’s life cycle, such as DOZI, CITH, PfCELF2, Musashi, and PfAlba1–4. Finally, we also detect several proteins with an RNA-binding domain abundant in Apicomplexans (RAP domain) that is almost exclusively found in apicomplexan parasites. Conclusions Collectively, our results provide the most complete comparative genomics and experimental analysis of mRBPs in P. falciparum. A better understanding of these regulatory proteins will not only give insight into the intricate parasite life cycle but may also provide targets for novel therapeutic strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1014-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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77
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Serum stress responsive gene EhslncRNA of Entamoeba histolytica is a novel long noncoding RNA. Sci Rep 2016; 6:27476. [PMID: 27273618 PMCID: PMC4895391 DOI: 10.1038/srep27476] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
Non coding RNAs are known to play important roles in regulating gene expression at the transcriptional and posttranscriptional levels in metazoans. There is very little information available about non coding RNAs in protists such as Entamoeba histolytica. Antisense and micro RNAs have been reported in E. histolytica, however no long non coding RNAs has been reported yet. Here, we report our findings on an in vitro serum stress-inducible gene EhslncRNA, a member of B1 transmembrane kinase family of E. histolytica. EhslncRNA encodes a transcript of 2.6 kb and sequence analysis revealed that there is no ORF >150 bp within this transcript. The transcript was found to be polyadenylated and mainly associated with monosomes in the cytoplasm under serum starvation. In normal proliferating cells this RNA is mainly present in the nucleus. The promoter element was mapped between 437 to 346 nucleotides upstream of transcriptional start site and has both positive and negative regulatory elements. Deletion of the negative element converted the promoter to serum inducible type. Oxygen and heat stress also increased expression levels of EhslncRNA. These observations suggest that EhslncRNA may be a long non coding RNA and likely to help cells withstand stressful conditions in the host.
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78
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Vembar SS, Droll D, Scherf A. Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems-wide studies pave the way. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:772-792. [PMID: 27230797 PMCID: PMC5111744 DOI: 10.1002/wrna.1365] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 11/10/2022]
Abstract
The malaria parasite Plasmodium spp. varies the expression profile of its genes depending on the host it resides in and its developmental stage. Virtually all messenger RNA (mRNA) is expressed in a monocistronic manner, with transcriptional activation regulated at the epigenetic level and by specialized transcription factors. Furthermore, recent systems-wide studies have identified distinct mechanisms of post-transcriptional and translational control at various points of the parasite lifecycle. Taken together, it is evident that 'just-in-time' transcription and translation strategies coexist and coordinate protein expression during Plasmodium development, some of which we review here. In particular, we discuss global and specific mechanisms that control protein translation in blood stages of the human malaria parasite Plasmodium falciparum, once a cytoplasmic mRNA has been generated, and its crosstalk with mRNA decay and storage. We also focus on the widespread translational delay observed during the 48-hour blood stage lifecycle of P. falciparum-for over 30% of transcribed genes, including virulence factors required to invade erythrocytes-and its regulation by cis-elements in the mRNA, RNA-processing enzymes and RNA-binding proteins; the first-characterized amongst these are the DNA- and RNA-binding Alba proteins. More generally, we conclude that translational regulation is an emerging research field in malaria parasites and propose that its elucidation will not only shed light on the complex developmental program of this parasite, but may also reveal mechanisms contributing to drug resistance and define new targets for malaria intervention strategies. WIREs RNA 2016, 7:772-792. doi: 10.1002/wrna.1365 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.
| | - Dorothea Droll
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
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79
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Apicomplexa-specific tRip facilitates import of exogenous tRNAs into malaria parasites. Proc Natl Acad Sci U S A 2016; 113:4717-22. [PMID: 27071116 DOI: 10.1073/pnas.1600476113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The malaria-causing Plasmodium parasites are transmitted to vertebrates by mosquitoes. To support their growth and replication, these intracellular parasites, which belong to the phylum Apicomplexa, have developed mechanisms to exploit their hosts. These mechanisms include expropriation of small metabolites from infected host cells, such as purine nucleotides and amino acids. Heretofore, no evidence suggested that transfer RNAs (tRNAs) could also be exploited. We identified an unusual gene in Apicomplexa with a coding sequence for membrane-docking and structure-specific tRNA binding. This Apicomplexa protein-designated tRip (tRNA import protein)-is anchored to the parasite plasma membrane and directs import of exogenous tRNAs. In the absence of tRip, the fitness of the parasite stage that multiplies in the blood is significantly reduced, indicating that the parasite may need host tRNAs to sustain its own translation and/or as regulatory RNAs. Plasmodium is thus the first example, to our knowledge, of a cell importing exogenous tRNAs, suggesting a remarkable adaptation of this parasite to extend its reach into host cell biology.
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80
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Parsons M, Myler PJ. Illuminating Parasite Protein Production by Ribosome Profiling. Trends Parasitol 2016; 32:446-457. [PMID: 27061497 DOI: 10.1016/j.pt.2016.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/25/2016] [Accepted: 03/04/2016] [Indexed: 12/29/2022]
Abstract
While technologies for global enumeration of transcript abundance are well-developed, those that assess protein abundance require tailoring to penetrate to low-abundance proteins. Ribosome profiling circumvents this challenge by measuring global protein production via sequencing small mRNA fragments protected by the assembled ribosome. This powerful approach is now being applied to protozoan parasites including trypanosomes and Plasmodium. It has been used to identify new protein-coding sequences (CDSs) and clarify the boundaries of previously annotated CDSs in Trypanosoma brucei. Ribosome profiling has demonstrated that translation efficiencies vary widely between genes and, for trypanosomes at least, for the same gene across stages. The ribosomal proteins are themselves subjected to translational control, suggesting a means of reinforcing global translational regulation.
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Affiliation(s)
- Marilyn Parsons
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North STE 500, Seattle, WA 98109 USA; Department of Global Health, Box 357965, University of Washington, Seattle, WA 98195, USA.
| | - Peter J Myler
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North STE 500, Seattle, WA 98109 USA; Department of Global Health, Box 357965, University of Washington, Seattle, WA 98195, USA; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
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81
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Adjalley SH, Chabbert CD, Klaus B, Pelechano V, Steinmetz LM. Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum. Cell Rep 2016; 14:2463-75. [PMID: 26947071 DOI: 10.1016/j.celrep.2016.02.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/09/2015] [Accepted: 02/01/2016] [Indexed: 12/20/2022] Open
Abstract
A comprehensive map of transcription start sites (TSSs) across the highly AT-rich genome of P. falciparum would aid progress toward deciphering the molecular mechanisms that underlie the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single-nucleotide resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcription unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.
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Affiliation(s)
- Sophie H Adjalley
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christophe D Chabbert
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Vicent Pelechano
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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82
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Vermeulen ET, Lott MJ, Eldridge MDB, Power ML. Evaluation of next generation sequencing for the analysis of Eimeria communities in wildlife. J Microbiol Methods 2016; 124:1-9. [PMID: 26944624 DOI: 10.1016/j.mimet.2016.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/31/2022]
Abstract
Next-generation sequencing (NGS) techniques are well-established for studying bacterial communities but not yet for microbial eukaryotes. Parasite communities remain poorly studied, due in part to the lack of reliable and accessible molecular methods to analyse eukaryotic communities. We aimed to develop and evaluate a methodology to analyse communities of the protozoan parasite Eimeria from populations of the Australian marsupial Petrogale penicillata (brush-tailed rock-wallaby) using NGS. An oocyst purification method for small sample sizes and polymerase chain reaction (PCR) protocol for the 18S rRNA locus targeting Eimeria was developed and optimised prior to sequencing on the Illumina MiSeq platform. A data analysis approach was developed by modifying methods from bacterial metagenomics and utilising existing Eimeria sequences in GenBank. Operational taxonomic unit (OTU) assignment at a high similarity threshold (97%) was more accurate at assigning Eimeria contigs into Eimeria OTUs but at a lower threshold (95%) there was greater resolution between OTU consensus sequences. The assessment of two amplification PCR methods prior to Illumina MiSeq, single and nested PCR, determined that single PCR was more sensitive to Eimeria as more Eimeria OTUs were detected in single amplicons. We have developed a simple and cost-effective approach to a data analysis pipeline for community analysis of eukaryotic organisms using Eimeria communities as a model. The pipeline provides a basis for evaluation using other eukaryotic organisms and potential for diverse community analysis studies.
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Affiliation(s)
- Elke T Vermeulen
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Matthew J Lott
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Mark D B Eldridge
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; Australian Museum Research Institute, Australian Museum, 6 College Street, Sydney, NSW 2010, Australia.
| | - Michelle L Power
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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83
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Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva. BMC Genomics 2016; 17:128. [PMID: 26896950 PMCID: PMC4761415 DOI: 10.1186/s12864-016-2444-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/08/2016] [Indexed: 11/23/2022] Open
Abstract
Background Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annotation now available for this parasite, offer an unprecedented opportunity to characterize the genomic features associated with gene regulation in this species. Our previous analyses revealed a T. parva genome even more gene-dense than previously thought, with many adjacent loci overlapping each other, not only at the level of untranslated sequences (UTRs) but even in coding sequences. Results Despite this compactness, Theileria intergenic regions show a pattern of size distribution indicative of monocistronic gene transcription. Three previously described motifs are conserved among Theileria species and highly prevalent in promoter regions near or at the transcription start sites. We found novel motifs at many transcription termination sites, as well as upstream of parasite genes thought to be critical for host transformation. Adjacent genes that could be regulated by antisense transcription from an overlapping transcriptional unit are syntenic between T. parva and P. falciparum at a frequency higher than expected by chance, suggesting the presence of common, and evolutionary old, regulatory mechanisms in the phylum Apicomplexa. Conclusions We propose a model of transcription with conserved sense and antisense transcription from a few taxonomically ubiquitous and several species-specific promoter motifs. Interestingly, the gene networks regulated by conserved promoters are themselves, in most cases, not conserved between species or genera. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2444-5) contains supplementary material, which is available to authorized users.
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84
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Kumar M, Srinivas V, Patankar S. Upstream AUGs and upstream ORFs can regulate the downstream ORF in Plasmodium falciparum. Malar J 2015; 14:512. [PMID: 26692187 PMCID: PMC4687322 DOI: 10.1186/s12936-015-1040-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Upstream open reading frames (uORFs) and upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flanking ORFs. Methods A bioinformatics approach was used to detect uATGs associated with different genes in the parasite. To study the effect of some of these uAUGs on the expression of the downstream ORF, promoters and 5′ leaders containing uAUGs and uORFs were cloned upstream of a luciferase reporter gene. Luciferase assays were carried out in transient transfection experiments to assess the effects of uAUGs and mutations on reporter expression. Results The average number of uATGs and uORFs seen in P. falciparum coding sequences (CDS) is expectedly high compared to other less biased genomes. Certain genes, including the var gene family contain the maximum number of uATGs and uORFs in the parasite. They possess ~5 times more uORFs and ~4.5 times more uAUGs within 100 bases upstream of the start codons than other CDS of the parasite. A 60 bp upstream region containing three ORFs and five ATGs from var gene PF3D7_0400100 and a gene of unknown function (PF3D7_0517100) when cloned upstream of the luciferase start codon, driven by the hsp86 promoter, resulted in loss of luciferase activity. This was restored when all the ATGs present in the −60 bp were mutated to TTGs. Point mutations in the ATGs showed that even one AUG was sufficient to repress the luciferase gene. Conclusions Overall, this work indicates that the P. falciparum genome has a large number of uATGs and uORFs that can repress the expression of flanking ORFs. The role of AUGs in translation initiation suggests that this repression is mediated by preventing the translation initiation complex from reaching the main AUG of the downstream ORF. How the P. falciparum ribosome is able to bypass these uAUGs and uORFs for highly expressed genes remains a question for future research. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-1040-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mayank Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Vivek Srinivas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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85
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LaMonte G, Walzer KA, Lacsina J, Nicchitta C, Chi JT. Methods to Investigate the Regulatory Role of Small RNAs and Ribosomal Occupancy of Plasmodium falciparum. J Vis Exp 2015:e53214. [PMID: 26709459 DOI: 10.3791/53214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The genetic variation responsible for the sickle cell allele (HbS) enables erythrocytes to resist infection by the malaria parasite, P. falciparum. The molecular basis of this resistance, which is known to be multifactorial, remains incompletely understood. Recent studies found that the differential expression of erythrocyte microRNAs, once translocated into malaria parasites, affect both gene regulation and parasite growth. These miRNAs were later shown to inhibit mRNA translation by forming a chimeric RNA transcript via 5' RNA fusion with discreet subsets of parasite mRNAs. Here, the techniques that were used to study the functional role and putative mechanism underlying erythrocyte microRNAs on the gene regulation and translational potential of P. falciparum, including the transfection of modified synthetic microRNAs into host erythrocytes, will be detailed. Finally, a polysome gradient method is used to determine the extent of translation of these transcripts. Together, these techniques allowed us to demonstrate that the dysregulated levels of erythrocyte microRNAs contribute to cell-intrinsic malaria resistance of sickle erythrocytes.
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Affiliation(s)
- Gregory LaMonte
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Center for Genomic and Computational Biology, Duke University School of Medicine
| | - Katelyn A Walzer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Center for Genomic and Computational Biology, Duke University School of Medicine
| | - Joshua Lacsina
- Department of Cell Biology, Duke University School of Medicine
| | | | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Center for Genomic and Computational Biology, Duke University School of Medicine;
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86
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Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. BMC Genomics 2015; 16:1005. [PMID: 26607328 PMCID: PMC4658763 DOI: 10.1186/s12864-015-2214-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/13/2015] [Indexed: 12/26/2022] Open
Abstract
Background Plasmodium falciparum, the deadliest malaria-causing parasite, has an extremely AT-rich (80.7 %) genome. Because of high AT-content, sequence-based annotation of genes and functional elements remains challenging. In order to better understand the regulatory network controlling gene expression in the parasite, a more complete genome annotation as well as analysis tools adapted for AT-rich genomes are needed. Recent studies on genome-wide nucleosome positioning in eukaryotes have shown that nucleosome landscapes exhibit regular characteristic patterns at the 5’- and 3’-end of protein and non-protein coding genes. In addition, nucleosome depleted regions can be found near transcription start sites. These unique nucleosome landscape patterns may be exploited for the identification of novel genes. In this paper, we propose a computational approach to discover novel putative genes based exclusively on nucleosome positioning data in the AT-rich genome of P. falciparum. Results Using binary classifiers trained on nucleosome landscapes at the gene boundaries from two independent nucleosome positioning data sets, we were able to detect a total of 231 regions containing putative genes in the genome of Plasmodium falciparum, of which 67 highly confident genes were found in both data sets. Eighty-eight of these 231 newly predicted genes exhibited transcription signal in RNA-Seq data, indicative of active transcription. In addition, 20 out of 21 selected gene candidates were further validated by RT-PCR, and 28 out of the 231 genes showed significant matches using BLASTN against an expressed sequence tag (EST) database. Furthermore, 108 (47 %) out of the 231 putative novel genes overlapped with previously identified but unannotated long non-coding RNAs. Collectively, these results provide experimental validation for 163 predicted genes (70.6 %). Finally, 73 out of 231 genes were found to be potentially translated based on their signal in polysome-associated RNA-Seq representing transcripts that are actively being translated. Conclusion Our results clearly indicate that nucleosome positioning data contains sufficient information for novel gene discovery. As distinct nucleosome landscapes around genes are found in many other eukaryotic organisms, this methodology could be used to characterize the transcriptome of any organism, especially when coupled with other DNA-based gene finding and experimental methods (e.g., RNA-Seq). Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2214-9) contains supplementary material, which is available to authorized users.
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87
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Shaw PJ, Kaewprommal P, Piriyapongsa J, Wongsombat C, Yuthavong Y, Kamchonwongpaisan S. Estimating mRNA lengths from Plasmodium falciparum genes by Virtual Northern RNA-seq analysis. Int J Parasitol 2015; 46:7-12. [PMID: 26548960 DOI: 10.1016/j.ijpara.2015.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/21/2015] [Accepted: 09/28/2015] [Indexed: 11/16/2022]
Abstract
Accurate gene models are essential for understanding parasite biology. However, transcript structure information is lacking for most parasite genes. Here, we describe "Virtual Northern" analysis of the malaria parasite Plasmodium falciparum to address this issue. RNA-seq libraries were made from size-fractionated RNA. Transcript sizes for 3052 genes were inferred from the read counts in each library. The data show that for almost half of the transcripts, the combined untranslated regions are more than twice the length of the open reading frame. Furthermore, we identified novel polycistronic, or gene overlapping, transcripts that suggest revisions to current gene models are needed.
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Affiliation(s)
- Philip J Shaw
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Pavita Kaewprommal
- Biostatistics and Bioinformatics Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- Biostatistics and Bioinformatics Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Chayaphat Wongsombat
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Yongyuth Yuthavong
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Sumalee Kamchonwongpaisan
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
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88
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Abstract
During the asexual replication cycle of the malaria parasite Plasmodium falciparum, the RNA-binding protein PfAlba1 binds and stabilizes a subset of transcripts for translation at a later time point. Please see related Research article: http://www.genomebiology.com/2015/16/1/212
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Affiliation(s)
- Evelien M Bunnik
- Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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89
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Sun M, Li W, Blomqvist K, Das S, Hashem Y, Dvorin JD, Frank J. Dynamical features of the Plasmodium falciparum ribosome during translation. Nucleic Acids Res 2015; 43:10515-24. [PMID: 26432834 PMCID: PMC4666399 DOI: 10.1093/nar/gkv991] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/19/2015] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it proliferates, multiplies and finally spreads to new erythrocytes. Development of drugs targeting the ribosome, the site of protein synthesis, requires specific knowledge of its structure and work cycle, and, critically, the ways they differ from those in the human host. Here, we present five cryo-electron microscopy (cryo-EM) reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution. Atomic models were built from these density maps by flexible fitting. Significantly, our study has taken advantage of new capabilities of cryo-EM, in visualizing several structures co-existing in the sample at once, at a resolution sufficient for building atomic models. We have discovered structural and dynamic features that differentiate the ribosomes of P. falciparum from those of mammalian system. Prompted by the absence of RACK1 on the ribosome in our and an earlier study we confirmed that RACK1 does not specifically co-purify with the 80S fraction in schizonts. More extensive studies, using cryo-EM methodology, of translation in the parasite will provide structural knowledge that may lead to development of novel anti-malarials.
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Affiliation(s)
- Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Karin Blomqvist
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sanchaita Das
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN, Université de Strasbourg, Strasbourg 67084, France
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
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90
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Vembar SS, Macpherson CR, Sismeiro O, Coppée JY, Scherf A. The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages. Genome Biol 2015; 16:212. [PMID: 26415947 PMCID: PMC4587749 DOI: 10.1186/s13059-015-0771-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Transcriptome-wide ribosome occupancy studies have suggested that during the intra-erythrocytic lifecycle of Plasmodium falciparum, select mRNAs are post-transcriptionally regulated. A subset of these encodes parasite virulence factors required for invading host erythrocytes, and are currently being developed as vaccine candidates. However, the molecular mechanisms that govern post-transcriptional regulation are currently unknown. Results We explore the previously identified DNA/RNA-binding protein PfAlba1, which localizes to multiple foci in the cytoplasm of P. falciparum trophozoites. We establish that PfAlba1 is essential for asexual proliferation, and subsequently investigate parasites overexpressing epitope-tagged PfAlba1 to identify its RNA targets and effects on mRNA homeostasis and translational regulation. Using deep sequencing of affinity-purified PfAlba1-associated RNAs, we identify 1193 transcripts that directly bind to PfAlba1 in trophozoites. For 105 such transcripts, 43 % of which are uncharacterized and 13 % of which encode erythrocyte invasion components, the steady state levels significantly change at this stage, evidencing a role for PfAlba1 in maintaining mRNA homeostasis. Additionally, we discover that binding of PfAlba1 to four erythrocyte invasion mRNAs, Rap1, RhopH3, CDPK1, and AMA1, is linked to translation repression in trophozoites whereas release of these mRNAs from a PfAlba1 complex in mature stages correlates with protein synthesis. Conclusions We show that PfAlba1 binds to a sub-population of asexual stage mRNAs and fine-tunes the timing of translation. This mode of post-transcriptional regulation may be especially important for P. falciparum erythrocyte invasion components that have to be assembled into apical secretory organelles in a highly time-dependent manner towards the end of the parasite’s asexual lifecycle. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0771-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, UMR 1201, Paris, 75015, France.
| | - Cameron Ross Macpherson
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, UMR 1201, Paris, 75015, France
| | - Odile Sismeiro
- Plate-forme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Jean-Yves Coppée
- Plate-forme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, UMR 1201, Paris, 75015, France.
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91
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Hallée S, Richard D. Evidence that the Malaria Parasite Plasmodium falciparum Putative Rhoptry Protein 2 Localizes to the Golgi Apparatus throughout the Erythrocytic Cycle. PLoS One 2015; 10:e0138626. [PMID: 26375591 PMCID: PMC4574476 DOI: 10.1371/journal.pone.0138626] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022] Open
Abstract
Invasion of a red blood cell by Plasmodium falciparum merozoites is an essential step in the malaria lifecycle. Several of the proteins involved in this process are stored in the apical complex of the merozoite, a structure containing secretory organelles that are released at specific times during invasion. The molecular players involved in erythrocyte invasion thus represent potential key targets for both therapeutic and vaccine-based strategies to block parasite development. In our quest to identify and characterize new effectors of invasion, we investigated the P. falciparum homologue of a P. berghei protein putatively localized to the rhoptries, the Putative rhoptry protein 2 (PbPRP2). We show that in P. falciparum, the protein colocalizes extensively with the Golgi apparatus across the asexual erythrocytic cycle. Furthermore, imaging of merozoites caught at different times during invasion show that PfPRP2 is not secreted during the process instead staying associated with the Golgi apparatus. Our evidence therefore suggests that PfPRP2 is a Golgi protein and that it is likely not a direct effector in the process of merozoite invasion.
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Affiliation(s)
- Stéphanie Hallée
- Centre de recherche en infectiologie, CHU-Université Laval, Quebec City, Quebec, Canada
| | - Dave Richard
- Centre de recherche en infectiologie, CHU-Université Laval, Quebec City, Quebec, Canada
- * E-mail:
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92
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Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:381-400. [PMID: 26306749 PMCID: PMC4679367 DOI: 10.1002/wsbm.1311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug‐resistant parasites necessitates that the research community take an active role in understanding host–parasite infection biology in order to develop improved therapeutics. Recent advances in next‐generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host–parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high‐throughput ‐omic data will undoubtedly generate extraordinary insight into host–parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host–parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies. WIREs Syst Biol Med 2015, 7:381–400. doi: 10.1002/wsbm.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Justine Swann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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93
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Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 2015; 16:454. [PMID: 26070627 PMCID: PMC4465157 DOI: 10.1186/s12864-015-1603-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 11/21/2022] Open
Abstract
Background The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs (lncRNAs) could represent a missing regulatory layer across a broad range of organisms. Results To investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs, six of which we validated experimentally. Conclusions We found that a subset of lncRNAs, including all subtelomeric lncRNAs, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mRNAs, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circRNAs, which is notable given the lack of RNA interference in the organism, and discovered that a highly expressed, five-exon antisense RNA is poised to regulate P. falciparum gametocyte development 1 (PfGDV1), a gene required for early sexual commitment events. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1603-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kate M Broadbent
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA.
| | - Jill C Broadbent
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA. .,Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden.
| | - Dyann Wirth
- Broad Institute, Cambridge, Massachusetts, USA. .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.
| | - John L Rinn
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Pardis C Sabeti
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
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94
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Fang X, Reifman J, Wallqvist A. Modeling metabolism and stage-specific growth of Plasmodium falciparum HB3 during the intraerythrocytic developmental cycle. MOLECULAR BIOSYSTEMS 2015; 10:2526-37. [PMID: 25001103 DOI: 10.1039/c4mb00115j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human malaria parasite Plasmodium falciparum goes through a complex life cycle, including a roughly 48-hour-long intraerythrocytic developmental cycle (IDC) in human red blood cells. A better understanding of the metabolic processes required during the asexual blood-stage reproduction will enhance our basic knowledge of P. falciparum and help identify critical metabolic reactions and pathways associated with blood-stage malaria. We developed a metabolic network model that mechanistically links time-dependent gene expression, metabolism, and stage-specific growth, allowing us to predict the metabolic fluxes, the biomass production rates, and the timing of production of the different biomass components during the IDC. We predicted time- and stage-specific production of precursors and macromolecules for P. falciparum (strain HB3), allowing us to link specific metabolites to specific physiological functions. For example, we hypothesized that coenzyme A might be involved in late-IDC DNA replication and cell division. Moreover, the predicted ATP metabolism indicated that energy was mainly produced from glycolysis and utilized for non-metabolic processes. Finally, we used the model to classify the entire tricarboxylic acid cycle into segments, each with a distinct function, such as superoxide detoxification, glutamate/glutamine processing, and metabolism of fumarate as a byproduct of purine biosynthesis. By capturing the normal metabolic and growth progression in P. falciparum during the IDC, our model provides a starting point for further elucidation of strain-specific metabolic activity, host-parasite interactions, stress-induced metabolic responses, and metabolic responses to antimalarial drugs and drug candidates.
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Affiliation(s)
- Xin Fang
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA.
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95
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Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J, Pain A. Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS One 2015; 10:e0124473. [PMID: 25875305 PMCID: PMC4395442 DOI: 10.1371/journal.pone.0124473] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/02/2015] [Indexed: 11/25/2022] Open
Abstract
Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities.
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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, Jeddah, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Tareq B. Malas
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Ehab Moussa
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Aswini Panigrahi
- Bioscience Core Laboratory (BCL), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Sarah J. Vermont
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Thomas D. Otto
- Parasite Genomics Group, Wellcome Trust Sanger Institute (WTSI), Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan Wastling
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
- * E-mail:
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96
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Caro F, Ahyong V, Betegon M, DeRisi JL. Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages. eLife 2014; 3. [PMID: 25493618 PMCID: PMC4371882 DOI: 10.7554/elife.04106] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022] Open
Abstract
The characterization of the transcriptome and proteome of Plasmodium
falciparum has been a tremendous resource for the understanding of the
molecular physiology of this parasite. However, the translational dynamics that link
steady-state mRNA with protein levels are not well understood. In this study, we
bridge this disconnect by measuring genome-wide translation using ribosome profiling,
through five stages of the P. falciparum blood phase developmental
cycle. Our findings show that transcription and translation are tightly coupled, with
overt translational control occurring for less than 10% of the transcriptome.
Translationally regulated genes are predominantly associated with merozoite egress
functions. We systematically define mRNA 5′ leader sequences, and 3′
UTRs, as well as antisense transcripts, along with ribosome occupancy for each, and
establish that accumulation of ribosomes on 5′ leaders is a common transcript
feature. This work represents the highest resolution and broadest portrait of gene
expression and translation to date for this medically important parasite. DOI:http://dx.doi.org/10.7554/eLife.04106.001 The genome of an organism includes all of the genes or information necessary to
build, maintain, and replicate that organism. However, cells with the same
genome—such as a skin cell and a liver cell from the same person—can
look and behave very differently depending on which of the genes in their genomes
they express, and to what extent. For a gene to be expressed, its DNA is ‘transcribed’ to make an RNA
molecule, which is then ‘translated’ to make a protein. Efforts to
measure the transcription and translation processes in diseased cells, or in the
microorganisms that cause infections, may lead to new treatments and preventative
medicines. Such work is currently ongoing in the global effort to treat and prevent
malaria. Malaria is both preventable and curable, yet over 600,000 people are estimated to die
from this disease each year. The disease is caused by a single-celled parasite called
Plasmodium. Mosquitoes carry the parasites in their salivary
glands, and when a mosquito bites a human, these parasites are injected into the
bloodstream with the mosquito's saliva. Plasmodium parasites then
travel to and infect the liver, before bursting out of this tissue into the
bloodstream. Here, the parasites infect red blood cells and undergo rounds of
replication during which the symptoms of the disease are manifested. It is also
during this bloodstream phase that parasites can develop into forms capable of
infecting another mosquito and continuing the transmission cycle. The genes, RNA molecules, and proteins of the Plasmodium falciparum
parasite—which causes the most serious cases of malaria in humans—have
been cataloged to better understand the biology of this parasite. However, the
processes that control how, and when, an RNA transcript is translated into a protein
are not well understood. Now Caro et al. have uncovered which RNA molecules are being translated, and by how
much, during Plasmodium development within the blood. The
transcription and translation of genes in this parasite were found to be tightly
linked processes; the expression of only a few genes was controlled more by the
translation process than by transcription. These translationally regulated genes were
found mainly to be those that encode proteins involved in the parasite's exit from
the red blood cells and spread throughout the bloodstream. Caro et al. discovered that genetic regulation of the malaria parasite resembles a
preset genetic program, rather than a system that responds to changes and external
signals. As such, these findings suggest that targeting such a genetic program within
Plasmodium and preventing its implementation could prove an
effective strategy to curb the spread of malaria. DOI:http://dx.doi.org/10.7554/eLife.04106.002
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Affiliation(s)
- Florence Caro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Vida Ahyong
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Miguel Betegon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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97
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Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays 2014; 37:182-94. [PMID: 25394267 DOI: 10.1002/bies.201400145] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plasmodium falciparum is the most deadly human malarial parasite, responsible for an estimated 207 million cases of disease and 627,000 deaths in 2012. Recent studies reveal that the parasite actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells and that epigenetics plays an important role in this precise gene regulation. Here, we discuss recent advances in our understanding of three aspects of epigenetic regulation in P. falciparum: changes in histone modifications, nucleosome occupancy and the three-dimensional genome structure. We compare these three aspects of the P. falciparum epigenome to those of other eukaryotes, and show that large-scale compartmentalization is particularly important in determining histone decomposition and gene regulation in P. falciparum. We conclude by presenting a gene regulation model for P. falciparum that combines the described epigenetic factors, and by discussing the implications of this model for the future of malaria research.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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98
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Cui L, Lindner S, Miao J. Translational regulation during stage transitions in malaria parasites. Ann N Y Acad Sci 2014; 1342:1-9. [PMID: 25387887 DOI: 10.1111/nyas.12573] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complicated life cycle of the malaria parasite involves a vertebrate host and a mosquito vector, and translational regulation plays a prominent role in orchestrating the developmental events in the two transition stages: gametocytes and sporozoites. Translational regulation is executed in both global and transcript-specific manners. Plasmodium uses a conserved mechanism involving phosphorylation of eIF2α to repress global protein synthesis during the latent period of sporozoite development in the mosquito salivary glands. Transcript-specific translational regulation is achieved by a network of RNA-binding proteins (RBPs), among which the Dhh1 RNA helicase DOZI and Puf family RBPs are by far the best studied in Plasmodium. While the DOZI complex defines a new P granule with a role in protecting certain gametocyte mRNAs from degradation, the Puf proteins appear to repress expression of mRNAs in both gametocytes and sporozoites. These examples underscore the significance of translational regulation in Plasmodium development.
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99
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Molecular characterization of Plasmodium falciparum Bruno/CELF RNA binding proteins. Mol Biochem Parasitol 2014; 198:1-10. [DOI: 10.1016/j.molbiopara.2014.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 10/13/2014] [Accepted: 10/22/2014] [Indexed: 01/04/2023]
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100
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Faye MD, Graber TE, Holcik M. Assessment of selective mRNA translation in mammalian cells by polysome profiling. J Vis Exp 2014:e52295. [PMID: 25407425 PMCID: PMC4353390 DOI: 10.3791/52295] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Regulation of protein synthesis represents a key control point in cellular response to stress. In particular, discreet RNA regulatory elements were shown to allow to selective translation of specific mRNAs, which typically encode for proteins required for a particular stress response. Identification of these mRNAs, as well as the characterization of regulatory mechanisms responsible for selective translation has been at the forefront of molecular biology for some time. Polysome profiling is a cornerstone method in these studies. The goal of polysome profiling is to capture mRNA translation by immobilizing actively translating ribosomes on different transcripts and separate the resulting polyribosomes by ultracentrifugation on a sucrose gradient, thus allowing for a distinction between highly translated transcripts and poorly translated ones. These can then be further characterized by traditional biochemical and molecular biology methods. Importantly, combining polysome profiling with high throughput genomic approaches allows for a large scale analysis of translational regulation.
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Affiliation(s)
- Mame Daro Faye
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute and Department of Biochemistry, Microbiology and Immunology, University of Ottawa
| | | | - Martin Holcik
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute and Department of Pediatrics, University of Ottawa;
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