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Pavlovic Djuranovic S, Erath J, Andrews RJ, Bayguinov PO, Chung JJ, Chalker DL, Fitzpatrick JAJ, Moss WN, Szczesny P, Djuranovic S. Plasmodium falciparum translational machinery condones polyadenosine repeats. eLife 2020; 9:e57799. [PMID: 32469313 PMCID: PMC7295572 DOI: 10.7554/elife.57799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/28/2020] [Indexed: 01/04/2023] Open
Abstract
Plasmodium falciparum is a causative agent of human malaria. Sixty percent of mRNAs from its extremely AT-rich (81%) genome harbor long polyadenosine (polyA) runs within their ORFs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate polyA runs cause ribosome stalling and frameshifting, triggering mRNA surveillance pathways and attenuating protein synthesis. Here, we show that P. falciparum is an exception to this rule. We demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately translated in P. falciparum cells. We show that polyA runs do not elicit any response from No Go Decay (NGD) or result in the production of frameshifted proteins. This is in stark contrast to what we observe in human cells or T. thermophila, an organism with similar AT-content. Finally, using stalling reporters we show that Plasmodium cells evolved not to have a fully functional NGD pathway.
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Affiliation(s)
| | - Jessey Erath
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
| | - Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
| | - Joyce J Chung
- Department of Biology, Washington UniversitySt LouisUnited States
| | | | - James AJ Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
- Department of Neuroscience, Washington University School of MedicineSt. LouisUnited States
- Department of Biomedical Engineering, Washington UniversitySt LouisUnited States
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Pawel Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Department of BioinformaticsWarsawPoland
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
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Garzón-Ospina D, Buitrago SP, Ramos AE, Patarroyo MA. Identifying Potential Plasmodium vivax Sporozoite Stage Vaccine Candidates: An Analysis of Genetic Diversity and Natural Selection. Front Genet 2018; 9:10. [PMID: 29422913 PMCID: PMC5788960 DOI: 10.3389/fgene.2018.00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022] Open
Abstract
Parasite antigen genetic diversity represents a great obstacle when designing a vaccine against malaria caused by Plasmodium vivax. Selecting vaccine candidate antigens has been focused on those fulfilling a role in invasion and which are conserved, thus avoiding specific-allele immune responses. Most antigens described to date belong to the blood stage, thereby blocking parasite development within red blood cells, whilst studying antigens from other stages has been quite restricted. Antigens from different parasite stages are required for developing a completely effective vaccine; thus, pre-erythrocyte stage antigens able to block the first line of infection becoming established should also be taken into account. However, few antigens from this stage have been studied to date. Several P. falciparum sporozoite antigens are involved in invasion. Since 77% of genes are orthologous amongst Plasmodium parasites, P. vivax sporozoite antigen orthologs to those of P. falciparum might be present in its genome. Although these genes might have high genetic diversity, conserved functionally-relevant regions (ideal for vaccine development) could be predicted by comparing genetic diversity patterns and evolutionary rates. This study was thus aimed at searching for putative P. vivax sporozoite genes so as to analyse their genetic diversity for determining their potential as vaccine candidates. Several DNA sequence polymorphism estimators were computed at each locus. The evolutionary force (drift, selection and recombination) drawing the genetic diversity pattern observed was also determined by using tests based on polymorphism frequency spectrum as well as the type of intra- and inter-species substitutions. Likewise, recombination was assessed both indirectly and directly. The results showed that sporozoite genes were more conserved than merozoite genes evaluated to date. Putative domains implied in cell traversal, gliding motility and hepatocyte interaction had a negative selection signal, being conserved amongst different species in the genus. PvP52, PvP36, PvSPATR, PvPLP1, PvMCP1, PvTLP, PvCelTOS, and PvMB2 antigens or functionally restricted regions within them would thus seem promising vaccine candidates and could be used when designing a pre-erythrocyte and/or multi-stage vaccine against P. vivax to avoid allele-specific immune responses that could reduce vaccine efficacy.
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Affiliation(s)
- Diego Garzón-Ospina
- Molecular Biology and Immunology Laboratory, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,PhD Programme in Biomedical and Biological Sciences, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Sindy P Buitrago
- Molecular Biology and Immunology Laboratory, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | - Andrea E Ramos
- Molecular Biology and Immunology Laboratory, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Laboratory, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res 2011; 21:487-93. [PMID: 21209072 DOI: 10.1101/gr.113985.110] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.
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Affiliation(s)
- Szymon M Kiełbasa
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, Berlin D-14195, Germany
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Nguyen TV, Sacci JB, de la Vega P, John CC, James AA, Kang AS. Characterization of immunoglobulin G antibodies to Plasmodium falciparum sporozoite surface antigen MB2 in malaria exposed individuals. Malar J 2009; 8:235. [PMID: 19852802 PMCID: PMC2772840 DOI: 10.1186/1475-2875-8-235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 10/23/2009] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND MB2 protein is a sporozoite surface antigen on the human malaria parasite Plasmodium falciparum. MB2 was identified by screening a P. falciparum sporozoite cDNA expression library using immune sera from a protected donor immunized via the bites of P. falciparum-infected irradiated mosquitoes. It is not known whether natural exposure to P. falciparum also induces the anti-MB2 response and if this response differs from that in protected individuals immunized via the bites of P. falciparum infected irradiated mosquitoes. The anti-MB2 antibody response may be part of a robust protective response against the sporozoite. METHODS Fragments of polypeptide regions of MB2 were constructed as recombinant fusions sandwiched between glutathione S-transferase and a hexa histidine tag for bacterial expression. The hexa histidine tag affinity purified proteins were used to immunize rabbits and the polyclonal sera evaluated in an in vitro inhibition of sporozoite invasion assay. The proteins were also used in immunoblots with sera from a limited number of donors immunized via the bites of P. falciparum infected irradiated mosquitoes and plasma and serum obtained from naturally exposed individuals in Kenya. RESULTS Rabbit polyclonal antibodies targeting the non-repeat region of the basic domain of MB2 inhibited sporozoites entry into HepG2-A16 cells in vitro. Analysis of serum from five human volunteers that were immunized via the bites of P. falciparum infected irradiated mosquitoes that developed immunity and were completely protected against subsequent challenge with non-irradiated parasite also had detectable levels of antibody against MB2 basic domain. In contrast, in three volunteers not protected, anti-MB2 antibodies were below the level of detection. Sera from protected volunteers preferentially recognized a non-repeat region of the basic domain of MB2, whereas plasma from naturally-infected individuals also had antibodies that recognize regions of MB2 that contain a repeat motif in immunoblots. Sequence analysis of eleven field isolates and four laboratory strains showed that these antigenic regions of the basic domain of the MB2 gene are highly conserved in parasites obtained from different parts of the world. Moreover, anti-MB2 antibodies also were detected in the plasma of 83% of the individuals living in a malaria endemic area of Kenya (n = 41). CONCLUSION A preliminary analysis of the human humoral response against MB2 indicates that it may be an additional highly conserved target for immune intervention at the pre-erythrocytic stage of P. falciparum life cycle.
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Affiliation(s)
- Thanh V Nguyen
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- NeoGenomics California, 6 Morgan, Suite 150, Irvine, CA 92618, USA
| | - John B Sacci
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Room 324 660 W Redwood Street, Baltimore, MD 21201, USA
| | - Patricia de la Vega
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Room 324 660 W Redwood Street, Baltimore, MD 21201, USA
- Department of Cell Mediated Immunity, Division of Malaria Vaccine Development, US Military Malaria Vaccine Program, Walter Reed Army Institute of Research, USA
| | - Chandy C John
- Global Pediatrics Program and Division of Pediatric Infectious Diseases, University of MN Medical School, 420 Delaware Street, SE, MMC #296, 850-Mayo, Minneapolis, MN 55455, USA
| | - Anthony A James
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-3900, USA
| | - Angray S Kang
- The School of Life Sciences, Department of Molecular and Applied Biosciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK
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Correia CF, Balaj PO, Scuderi D, Maitre P, Ohanessian G. Vibrational Signatures of Protonated, Phosphorylated Amino Acids in the Gas Phase. J Am Chem Soc 2008; 130:3359-70. [DOI: 10.1021/ja073868z] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Catarina F. Correia
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, and the Laboratoire de Chimie Physique, Université Paris-Sud 11, CNRS, 91405 Orsay CEDEX, France
| | - Petru O. Balaj
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, and the Laboratoire de Chimie Physique, Université Paris-Sud 11, CNRS, 91405 Orsay CEDEX, France
| | - Debora Scuderi
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, and the Laboratoire de Chimie Physique, Université Paris-Sud 11, CNRS, 91405 Orsay CEDEX, France
| | - Philippe Maitre
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, and the Laboratoire de Chimie Physique, Université Paris-Sud 11, CNRS, 91405 Orsay CEDEX, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France, and the Laboratoire de Chimie Physique, Université Paris-Sud 11, CNRS, 91405 Orsay CEDEX, France
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