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Nag S, Banerjee C, Goyal M, Siddiqui AA, Saha D, Mazumder S, Debsharma S, Pramanik S, Saha SJ, De R, Bandyopadhyay U. Plasmodium falciparum Alba6 exhibits DNase activity and participates in stress response. iScience 2024; 27:109467. [PMID: 38558939 PMCID: PMC10981135 DOI: 10.1016/j.isci.2024.109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Alba domain proteins, owing to their functional plasticity, play a significant role in organisms. Here, we report an intrinsic DNase activity of PfAlba6 from Plasmodium falciparum, an etiological agent responsible for human malignant malaria. We identified that tyrosine28 plays a critical role in the Mg2+ driven 5'-3' DNase activity of PfAlba6. PfAlba6 cleaves both dsDNA as well as ssDNA. We also characterized PfAlba6-DNA interaction and observed concentration-dependent oligomerization in the presence of DNA, which is evident from size exclusion chromatography and single molecule AFM-imaging. PfAlba6 mRNA expression level is up-regulated several folds following heat stress and treatment with artemisinin, indicating a possible role in stress response. PfAlba6 has no human orthologs and is expressed in all intra-erythrocytic stages; thus, this protein can potentially be a new anti-malarial drug target.
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Affiliation(s)
- Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Manish Goyal
- Department of Molecular & Cell Biology, School of Dental Medicine, Boston University Medical Campus, Boston, MA, USA
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal 712258, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shubhra Jyoti Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal 700135, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal 700091, India
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Markwalter CF, Menya D, Wesolowski A, Esimit D, Lokoel G, Kipkoech J, Freedman E, Sumner KM, Abel L, Ambani G, Meredith HR, Taylor SM, Obala AA, O'Meara WP. Plasmodium falciparum importation does not sustain malaria transmission in a semi-arid region of Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000807. [PMID: 36962553 PMCID: PMC10021402 DOI: 10.1371/journal.pgph.0000807] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022]
Abstract
Human movement impacts the spread and transmission of infectious diseases. Recently, a large reservoir of Plasmodium falciparum malaria was identified in a semi-arid region of northwestern Kenya historically considered unsuitable for malaria transmission. Understanding the sources and patterns of transmission attributable to human movement would aid in designing and targeting interventions to decrease the unexpectedly high malaria burden in the region. Toward this goal, polymorphic parasite genes (ama1, csp) in residents and passengers traveling to Central Turkana were genotyped by amplicon deep sequencing. Genotyping and epidemiological data were combined to assess parasite importation. The contribution of travel to malaria transmission was estimated by modelling case reproductive numbers inclusive and exclusive of travelers. P. falciparum was detected in 6.7% (127/1891) of inbound passengers, including new haplotypes which were later detected in locally-transmitted infections. Case reproductive numbers approximated 1 and did not change when travelers were removed from transmission networks, suggesting that transmission is not fueled by travel to the region but locally endemic. Thus, malaria is not only prevalent in Central Turkana but also sustained by local transmission. As such, interrupting importation is unlikely to be an effective malaria control strategy on its own, but targeting interventions locally has the potential to drive down transmission.
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Affiliation(s)
| | - Diana Menya
- School of Public Health, Moi University College of Health Sciences, Eldoret, Kenya
| | - Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Daniel Esimit
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Gilchrist Lokoel
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Joseph Kipkoech
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Elizabeth Freedman
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kelsey M Sumner
- Duke University School of Medicine, Durham, North Carolina, United States of America
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - George Ambani
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Hannah R Meredith
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Steve M Taylor
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wendy P O'Meara
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
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Mohamed NS, AbdElbagi H, Elsadig AR, Ahmed AE, Mohammed YO, Elssir LT, Elnour MAB, Ali Y, Ali MS, Altahir O, Abubakr M, Siddig EE, Ahmed A, Omer RA. Assessment of genetic diversity of Plasmodium falciparum circumsporozoite protein in Sudan: the RTS,S leading malaria vaccine candidate. Malar J 2021; 20:436. [PMID: 34758827 PMCID: PMC8579544 DOI: 10.1186/s12936-021-03971-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Abstract
Background The currently used malaria vaccine, RTS,S, is designed based on the Plasmodium falciparum circumsporozoite protein (PfCSP). The pfcsp gene, besides having different polymorphic patterns, can vary between P. falciparum isolates due to geographical origin and host immune response. Such aspects are essential when considering the deployment of the RTS,S vaccine in a certain region. Therefore, this study assessed the genetic diversity of P. falciparum in Sudan based on the pfcsp gene by investigating the diversity at the N-terminal, central repeat, and the C-terminal regions. Methods A cross-sectional molecular study was conducted; P. falciparum isolates were collected from different health centres in Khartoum State between January and December 2019. During the study period, a total of 261 febrile patients were recruited. Malaria diagnosis was made by expert microscopists using Giemsa-stained thick and thin blood films. DNA samples were examined by the semi-nested polymerase chain reaction (PCR). Single clonal infection of the confirmed P. falciparum cases, were used to amplify the pfcsp gene. The amplified amplicons of pfcsp have been sequenced using the Sanger dideoxy method. The obtained sequences of pfcsp nucleotide diversity parameters including the numbers of haplotypes (Hap), haplotypes diversity (Hapd), the average number of nucleotide differences between two sequences (p), and the numbers of segregating sites (S) were obtained. The haplotype networks were constructed using the online tcsBU software. Natural selection theory was also tested on pfcsp using Fuand Li’s D, Fuand Li’s F statistics, and Tajima’s D test using DnaSP. Results In comparison with the different pfcsp reference strains, the Sudanese isolates showed high similarity with other African isolates. The results of the N-terminal region showed the presence of 2 different haplotypes with a Hapd of 0.425 ± 0.00727. The presence of the unique insertion of NNNGDNGREGKDEDKRDGNN was reported. The KLKQP motif was conserved in all the studied isolates. At the central repeat region, 11 haplotypes were seen with a Hapd of 0.779 ± 0.00097. The analysis of the genetic diversity in the C-terminal region showed the presence of 10 haplotypes with a Hapd of 0.457 ± 0.073. Several non-synonymous amino acids changes were also seen at the Th2R and the Th3R T-cell epitope regions including T317K, E317K, Q318E, K321N, I322K, T322K, R322K, K324Q, I327L, G352N, S354P, R355K, N356D, Q357E, and E361A. Conclusions In this study, the results indicated a high conservation at the pfcsp gene. This may further contribute in understanding the genetic polymorphisms of P. falciparum prior to the deployment of the RTS,S vaccine in Sudan.
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Affiliation(s)
- Nouh Saad Mohamed
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan. .,Molecular Biology Unit, Sirius Training and Research Centre, Khartoum, Sudan.
| | - Hanadi AbdElbagi
- Molecular Biology Unit, Sirius Training and Research Centre, Khartoum, Sudan
| | | | | | - Yassir Osman Mohammed
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan
| | - Lubna Taj Elssir
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan
| | - Mohammed-Ahmed B Elnour
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan
| | - Yousif Ali
- Health Emergencies and Epidemics Control General Directorate, Sudan Federal Ministry of Health, Khartoum, Sudan
| | - Mohamed S Ali
- Faculty of Medicine, EL-Neelain University, Khartoum, Sudan
| | - Omnia Altahir
- Department of Parasitology and Medical Entomology, Tropical Medicine Research Institute, National Centre for Research, Khartoum, Sudan
| | - Mustafa Abubakr
- Department of the Integrated Vector Management (IVM), Federal Ministry of Health, Khartoum, Sudan
| | | | - Ayman Ahmed
- Molecular Biology Unit, Sirius Training and Research Centre, Khartoum, Sudan
| | - Rihab Ali Omer
- Pediatric Epidemiology, Clinic and Polyclinic for Child and Adolescent Medicine, Medical Faculty, University of Leipzig, Leipzig, Germany
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Sumner KM, Freedman E, Mangeni JN, Obala AA, Abel L, Edwards JK, Emch M, Meshnick SR, Pence BW, Prudhomme-O'Meara W, Taylor SM. Exposure to diverse Plasmodium falciparum genotypes shapes the risk of symptomatic malaria in incident and persistent infections: A longitudinal molecular epidemiologic study in Kenya. Clin Infect Dis 2021; 73:1176-1184. [PMID: 33904907 DOI: 10.1093/cid/ciab357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Repeated exposure to malaria infections could protect against symptomatic progression, as people develop adaptive immunity to infections acquired over time. METHODS We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared to asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of two polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual's successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria. RESULTS After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared to infections with only recurrent haplotypes [odds ratio (OR): 3.24, 95% confidence interval (CI): 1.20 to 8.78], but infections with both new and recurrent haplotypes [OR: 0.64, 95% CI: 0.15 to 2.65] did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes [OR: 0.77, 95% CI: 0.21 to 2.75] had no association with symptomatic malaria compared to infections with only persistent haplotypes. Results were similar for pfama1. CONCLUSIONS These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared to infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.
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Affiliation(s)
- Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Jessie K Edwards
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Department of Geography, University of North Carolina, Chapel Hill NC, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Brian W Pence
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Wendy Prudhomme-O'Meara
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya.,Duke Global Health Institute, Duke University, Durham NC, USA
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,Duke Global Health Institute, Duke University, Durham NC, USA
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5
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Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. mSystems 2021; 6:6/2/e01081-20. [PMID: 33688018 PMCID: PMC8561664 DOI: 10.1128/msystems.01081-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterized in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AU content of Plasmodium RNA, but also the limitations of short-read sequencing in deciphering complex splicing events. In this study, we utilized the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or nearly full-length transcripts with comparable quantification to Illumina sequencing. By comparing these data with available gene models, we find widespread alternative splicing, particularly intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This study highlights a strategy in using long-read sequencing to understand splicing events at the whole-transcript level and has implications in the future interpretation of transcriptome sequencing studies. IMPORTANCE We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
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The repertoire of serine rhomboid proteases of piroplasmids of importance to animal and human health. Int J Parasitol 2021; 51:455-462. [PMID: 33610524 DOI: 10.1016/j.ijpara.2020.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Babesia, Theileria and Cytauxzoon are tick-borne apicomplexan protozoans of the order Piroplasmida, notorious for the diseases they cause in livestock, pets and humans. Host cell invasion is their Achilles heel, allowing for the development of drug or vaccine-based therapies. In other apicomplexans, cleavage of the transmembrane domain of adhesins by the serine rhomboid proteinase ROM4 is required for successful completion of invasion. In this study, we record and classify the rhomboid repertoire encoded in the genomes of 10 piroplasmid species pertaining to the lineages Babesia sensu stricto (s.s., Clade VI), Theileria sensu stricto (Clade IV), Theileria equi (Clade IV), Cytauxzoon felis (Clade IIIb) and Babesia microti (Clade I), as defined by Schnittger et al. (2012). Fifty-six piroplasmid rhomboid-like proteins were assigned by phylogenetic analysis and bidirectional best hit to the ROM4, ROM6, ROM7 or ROM8 groups, and their crucial motifs for conformation and function were identified. Forty-four of these rhomboids had either been incorrectly classified or misannotated. Babesia s.s. encode five or three ROM4 proteinase paralogs, whereas the remaining piroplasmids encode two ROM4 paralogs. All piroplasmids encode a single ROM6, ROM7 and ROM8. Thus, an increased paralog number of ROM4 is the only feature distinguishing Babesia s.s. from other piroplasmid lineages. Piroplasmid ROM6 is related to the mammalian mitochondrial rhomboid and, accordingly, N-terminal mitochondrial targeting signal sequences was found in some cases. ROM6 is the only rhomboid encoded by piroplasmids that is ubiquitous in other organisms. ROM8 represents a pseudoproteinase that is highly conserved between studied piroplasmids, suggesting that it is important in regulatory functions. ROM4, ROM6, ROM7 and ROM8 are exclusively present in Aconoidasida, which comprises piroplasmids and Plasmodium, suggesting a relevant functional role in erythrocyte invasion. The correct classification and designation of piroplasmid rhomboids presented in this study facilitates an informed choice for future in-depth study of their functions.
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Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections. Nat Commun 2021; 12:909. [PMID: 33568678 PMCID: PMC7875998 DOI: 10.1038/s41467-021-21269-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/15/2021] [Indexed: 01/30/2023] Open
Abstract
Malaria control may be enhanced by targeting reservoirs of Plasmodium falciparum transmission. One putative reservoir is asymptomatic malaria infections and the scale of their contribution to transmission in natural settings is not known. We assess the contribution of asymptomatic malaria to onward transmission using a 14-month longitudinal cohort of 239 participants in a high transmission site in Western Kenya. We identify P. falciparum in asymptomatically- and symptomatically-infected participants and naturally-fed mosquitoes from their households, genotype all parasites using deep sequencing of the parasite genes pfama1 and pfcsp, and use haplotypes to infer participant-to-mosquito transmission through a probabilistic model. In 1,242 infections (1,039 in people and 203 in mosquitoes), we observe 229 (pfcsp) and 348 (pfama1) unique parasite haplotypes. Using these to link human and mosquito infections, compared with symptomatic infections, asymptomatic infections more than double the odds of transmission to a mosquito among people with both infection types (Odds Ratio: 2.56; 95% Confidence Interval (CI): 1.36-4.81) and among all participants (OR 2.66; 95% CI: 2.05-3.47). Overall, 94.6% (95% CI: 93.1-95.8%) of mosquito infections likely resulted from asymptomatic infections. In high transmission areas, asymptomatic infections are the major contributor to mosquito infections and may be targeted as a component of transmission reduction.
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8
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Florin-Christensen M, Rodriguez AE, Suárez CE, Ueti MW, Delgado FO, Echaide I, Schnittger L. N-Glycosylation in Piroplasmids: Diversity within Simplicity. Pathogens 2021; 10:50. [PMID: 33429911 PMCID: PMC7826898 DOI: 10.3390/pathogens10010050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
N-glycosylation has remained mostly unexplored in Piroplasmida, an order of tick-transmitted pathogens of veterinary and medical relevance. Analysis of 11 piroplasmid genomes revealed three distinct scenarios regarding N-glycosylation: Babesia sensu stricto (s.s.) species add one or two N-acetylglucosamine (NAcGlc) molecules to proteins; Theileria equi and Cytauxzoon felis add (NAcGlc)2-mannose, while B. microti and Theileria s.s. synthesize dolichol-P-P-NAcGlc and dolichol-P-P-(NAcGlc)2 without subsequent transfer to proteins. All piroplasmids possess the gene complement needed for the synthesis of the N-glycosylation substrates, dolichol-P and sugar nucleotides. The oligosaccharyl transferase of Babesia species, T. equi and C. felis, is predicted to be composed of only two subunits, STT3 and Ost1. Occurrence of short N-glycans in B. bovis merozoites was experimentally demonstrated by fluorescence microscopy using a NAcGlc-specific lectin. In vitro growth of B. bovis was significantly impaired by tunicamycin, an inhibitor of N-glycosylation, indicating a relevant role for N-glycosylation in this pathogen. Finally, genes coding for N-glycosylation enzymes and substrate biosynthesis are transcribed in B. bovis blood and tick stages, suggesting that this pathway is biologically relevant throughout the parasite life cycle. Elucidation of the role/s exerted by N-glycans will increase our understanding of these successful parasites, for which improved control measures are needed.
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Affiliation(s)
- Monica Florin-Christensen
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Anabel E. Rodriguez
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Carlos E. Suárez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Massaro W. Ueti
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Fernando O. Delgado
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Ignacio Echaide
- Estación Experimental Agrícola INTA-Rafaela, Santa Fe, Provincia de Buenos Aires S2300, Argentina;
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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9
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Podgorski RM, Goff KA, Penney TP, Maness NJ, Keating J, Yukich JO, Marx PA. DNA analysis reveals non-falciparum malaria in the Democratic Republic of the Congo. Acta Trop 2020; 212:105557. [PMID: 32479838 DOI: 10.1016/j.actatropica.2020.105557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND The World Health Organization (WHO) attributes the entirety of malaria infection and transmission in the Democratic Republic of the Congo (DRC) to Plasmodium falciparum, one of the several species of malaria known to infect humans. Recent studies have put forth some evidence that transmission of Plasmodium vivax may also be occurring in the DRC. As interventions and treatments differ between malaria species, it is crucial to maintain the most accurate understanding of malaria species diversity in each region. METHODS Blood samples were taken from aymptomatic children 0-5 years old living in three regions of the DRC in 2014. For this study, samples were taken from a larger pool of samples, collected as part of a population-based survey in three regions. Plasmodium infection was screened for using nested polymerase chain reaction (PCR) assays and species were confirmed by cloning and DNA sequencing. RESULTS Of 336 samples screened by PCR, 62.2% (n=209) initially tested positive for P. falciparum and 14.6% (n=49) initially tested positive for P. vivax. Sanger sequencing was performed on PCR-positive Plasmodium samples to confirm identity of Plasmodium species. Sequencing showed Plasmodium malariae in one blood sample and Plasmodium ovale in another sample. Plasmodium vivax was detected in 12/65 cases (18.5%). Overall, 14/65 sequenced cases (21.5%) were infected with a non-falciparum malaria. 330bp 18s P. vivax DNA sequences were obtained. CONCLUSIONS This study reveals Plasmodium vivax and other non-falciparum malaria across several regions of the DRC, and enforces the importance of further testing and more precise diagnostics when testing for and treating malaria in the DRC. Here, we find a higher proportion of cases of P. vivax malaria than found in previous studies. This is the most robust DNA sequencing of Plasmodium vivax in the DRC to date.
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Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates. Sci Rep 2020; 10:20220. [PMID: 33214620 PMCID: PMC7677368 DOI: 10.1038/s41598-020-77001-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
A variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles during parasite development. NEDD8 is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulates diverse cellular processes. Although neddylation is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. We characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Ala/Gly76Ala) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 (rub1Δ) or NEDD8 conjugating E2 enzyme (ubc12Δ). The PfNEDD8 immunoprecipitate also contained S. cerevisiae cullin cdc53, further substantiating cullins as physiological substrates of PfNEDD8. Our findings lay ground for investigation of specific roles and drug target potential of neddylation in malaria parasites.
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11
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Arisue N, Palacpac NMQ, Tougan T, Horii T. Characteristic features of the SERA multigene family in the malaria parasite. Parasit Vectors 2020; 13:170. [PMID: 32252804 PMCID: PMC7132891 DOI: 10.1186/s13071-020-04044-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/27/2020] [Indexed: 02/28/2023] Open
Abstract
Serine repeat antigen (SERA) is conserved among species of the genus Plasmodium. Sera genes form a multigene family and are generally tandemly clustered on a single chromosome. Although all Plasmodium species encode multiple sera genes, the number varies between species. Among species, the members share similar sequences and gene organization. SERA possess a central papain-like cysteine protease domain, however, in some members, the active site cysteine residue is substituted with a serine. Recent studies implicate this gene family in a number of aspects in parasite biology and induction of protective immune response. This review summarizes the current understanding on this important gene family in several Plasmodium species. The Plasmodium falciparum (Pf)-sera family, for example, consists of nine gene members. Unlike other multigene families in Plasmodium species, Pf-sera genes do not exhibit antigenic variation. Pf-sera5 nucleotide diversity is also low. Moreover, although Pf-sera5 is highly transcribed during the blood stage of malaria infection, and a large amount is released into the host blood following schizont rupture, in malaria endemic countries the sero-positive rates for Pf-SERA5 are low, likely due to Pf-SERA5 binding of host proteins to avoid immune recognition. As an antigen, the N-terminal 47 kDa domain of Pf-SERA5 is a promising vaccine candidate currently undergoing clinical trials. Pf-SERA5 and Pf-SERA6, as well as P. berghei (Pb)-SERA3, and Pb-SERA5, have been investigated for their roles in parasite egress. Two P. yoelii SERA, which have a serine residue at the protease active center, are implicated in parasite virulence. Overall, these studies provide insight that during the evolution of the Plasmodium parasite, the sera gene family members have increased by gene duplication, and acquired various functions that enable the parasite to survive and successfully maintain infection in the host.![]()
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Affiliation(s)
- Nobuko Arisue
- Research Center for Infectious Disease Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Nirianne M Q Palacpac
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takahiro Tougan
- Research Center for Infectious Disease Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshihiro Horii
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
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12
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Biosynthesis of heme O in intraerythrocytic stages of Plasmodium falciparum and potential inhibitors of this pathway. Sci Rep 2019; 9:19261. [PMID: 31848371 PMCID: PMC6917786 DOI: 10.1038/s41598-019-55506-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/29/2019] [Indexed: 12/26/2022] Open
Abstract
A number of antimalarial drugs interfere with the electron transport chain and heme-related reactions; however, the biosynthesis of heme derivatives in Plasmodium parasites has not been fully elucidated. Here, we characterized the steps that lead to the farnesylation of heme. After the identification of a gene encoding heme O synthase, we identified heme O synthesis in blood stage parasites through the incorporation of radioactive precursors. The presence of heme O synthesis in intraerythrocytic stages of Plasmodium falciparum was confirmed by mass spectrometry. Inabenfide and uniconazole-P appeared to interfere in heme synthesis, accordingly, parasite growth was also affected by the addition of these drugs. We conclude that heme O synthesis occurs in blood stage-P. falciparum and this pathway could be a potential target for antimalarial drugs.
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13
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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14
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Yu L, Shen Z, Liu Q, Zhan X, Luo X, An X, Sun Y, Li M, Wang S, Nie Z, Ao Y, Zhao Y, Peng G, Mamoun CB, He L, Zhao J. Crystal structures of Babesia microti lactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis. FASEB J 2019; 33:13669-13682. [PMID: 31585506 DOI: 10.1096/fj.201901259r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The tick- and transfusion-transmitted human pathogen Babesia microti infects host erythrocytes to cause the pathologic symptoms associated with human babesiosis, an emerging disease with worldwide distribution and potentially fatal clinical outcome. Drugs currently recommended for the treatment of babesiosis are associated with a high failure rate and significant adverse events, highlighting the urgent need for more-effective and safer babesiosis therapies. Unlike other apicomplexan parasites, B. microti lacks a canonical lactate dehydrogenase (LDH) but instead expresses a unique enzyme, B. microti LDH (BmLDH), acquired through evolution by horizontal transfer from a mammalian host. Here, we report the crystal structures of BmLDH in apo state and ternary complex (enzyme-NADH-oxamate) solved at 2.79 and 1.89 Å. Analysis of these structures reveals that upon binding to the coenzyme and substrate, the active pocket of BmLDH undergoes a major conformational change from an opened and disordered to a closed and stabilized state. Biochemical assays using wild-type and mutant B. microti and human LDHs identified Arg99 as a critical residue for the catalytic activity of BmLDH but not its human counterpart. Interestingly, mutation of Arg99 to Ala had no impact on the overall structure and affinity of BmLDH to NADH but dramatically altered the closure of the enzyme's active pocket. Together, these structural and biochemical data highlight significant differences between B. microti and human LDH enzymes and suggest that BmLDH could be a suitable target for the development of selective antibabesial inhibitors.-Yu, L., Shen, Z., Liu, Q., Zhan, X., Luo, X., An, X., Sun, Y., Li, M., Wang, S., Nie, Z., Ao, Y., Zhao, Y., Peng, G., Ben Mamoun, C., He, L., Zhao, J. Crystal structures of Babesia microti lactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis.
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Affiliation(s)
- Long Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Qin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Xueyan Zhan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Xiaoyin Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Xiaomeng An
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Yali Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Muxiao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Sen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Zheng Nie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Yangsiqi Ao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Yangnan Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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15
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Bruske E, Otto TD, Frank M. Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance. Malar J 2018; 17:376. [PMID: 30348135 PMCID: PMC6198375 DOI: 10.1186/s12936-018-2503-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background Plasmodium falciparum exhibits a high degree of inter-isolate genetic diversity in its variant surface antigen (VSA) families: P. falciparum erythrocyte membrane protein 1, repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR). The role of recombination for the generation of this diversity is a subject of ongoing research. Here the genome of E5, a sibling of the 3D7 genome strain is presented. Short and long read whole genome sequencing (WGS) techniques (Ilumina, Pacific Bioscience) and a set of 84 microsatellites (MS) were employed to characterize the 3D7 and non-3D7 parts of the E5 genome. This is the first time that VSA genes in sibling parasites were analysed with long read sequencing technology. Results Of the 5733 E5 genes only 278 genes, mostly var and rifin/stevor genes, had no orthologues in the 3D7 genome. WGS and MS analysis revealed that chromosomal crossovers occurred at a rate of 0–3 per chromosome. var, stevor and rifin genes were inherited within the respective non-3D7 or 3D7 chromosomal context. 54 of the 84 MS PCR fragments correctly identified the respective MS as 3D7- or non-3D7 and this correlated with var and rifin/stevor gene inheritance in the adjacent chromosomal regions. E5 had 61 var and 189 rifin/stevor genes. One large non-chromosomal recombination event resulted in a new var gene on chromosome 14. The remainder of the E5 3D7-type subtelomeric and central regions were identical to 3D7. Conclusions The data show that the rifin/stevor and var gene families represent the most diverse compartments of the P. falciparum genome but that the majority of var genes are inherited without alterations within their respective parental chromosomal context. Furthermore, MS genotyping with 54 MS can successfully distinguish between two sibling progeny of a natural P. falciparum cross and thus can be used to investigate identity by descent in field isolates. Electronic supplementary material The online version of this article (10.1186/s12936-018-2503-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ellen Bruske
- Institute of Tropical Medicine, University of Tuebingen, Wilhelmstr. 27, 72074, Tuebingen, Germany
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. .,Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tuebingen, Wilhelmstr. 27, 72074, Tuebingen, Germany.
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16
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Bader A, Cockroft SL. Simultaneous G-Quadruplex DNA Logic. Chemistry 2018; 24:4820-4824. [DOI: 10.1002/chem.201800756] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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17
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Cerón-Romero MA, Nwaka E, Owoade Z, Katz LA. PhyloChromoMap, a Tool for Mapping Phylogenomic History along Chromosomes, Reveals the Dynamic Nature of Karyotype Evolution in Plasmodium falciparum. Genome Biol Evol 2018; 10:553-561. [PMID: 29365145 PMCID: PMC5800058 DOI: 10.1093/gbe/evy017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 11/22/2022] Open
Abstract
The genome of Plasmodium falciparum, the causative agent of malaria in Africa, has been extensively studied since it was first fully sequenced in 2002. However, many open questions remain, including understanding the chromosomal context of molecular evolutionary changes (e.g., relationship between chromosome map and phylogenetic conservation, patterns of gene duplication, and patterns of selection). Here, we present PhyloChromoMap, a method that generates a phylogenomic map of chromosomes from a custom-built bioinformatics pipeline. Using P. falciparum 3D7 as a model, we analyze 2,116 genes with homologs in up to 941 diverse eukaryotic, bacterial and archaeal lineages. We estimate the level of conservation along chromosomes based on conservation across clades, and identify “young” regions (i.e., those with recent or fast evolving genes) that are enriched in subtelomeric regions as compared with internal regions. We also demonstrate that patterns of molecular evolution for paralogous genes differ significantly depending on their location as younger paralogs tend to be found in subtelomeric regions whereas older paralogs are enriched in internal regions. Combining these observations with analyses of synteny, we demonstrate that subtelomeric regions are actively shuffled among chromosome ends, which is consistent with the hypothesis that these regions are prone to ectopic recombination. We also assess patterns of selection by comparing dN/dS ratios of gene family members in subtelomeric versus internal regions, and we include the important antigenic gene family var. These analyses illustrate the highly dynamic nature of the karyotype of P. falciparum, and provide a method for exploring genome dynamics in other lineages.
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Affiliation(s)
- Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
| | - Esther Nwaka
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Zuliat Owoade
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
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18
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Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W. Evolutionary Dynamics of Cryptophyte Plastid Genomes. Genome Biol Evol 2017; 9:1859-1872. [PMID: 28854597 PMCID: PMC5534331 DOI: 10.1093/gbe/evx123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2017] [Indexed: 12/14/2022] Open
Abstract
Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch. placoidea, Cryptomonas curvata, and Storeatula sp. CCMP1868 share a number of features including synteny and gene content with the previously sequenced genomes of Cryptomonas paramecium, Rhodomonas salina, Teleaulax amphioxeia, and Guillardia theta. Our analysis of these plastid genomes reveals examples of gene loss and intron insertion. In particular, the chlB/chlL/chlN genes, which encode light-independent (dark active) protochlorophyllide oxidoreductase (LIPOR) proteins have undergone recent gene loss and pseudogenization in cryptophytes. Comparison of phylogenetic trees based on plastid and nuclear genome data sets show the introduction, via secondary endosymbiosis, of a red algal derived plastid in a lineage of chlorophyll-c containing algae. This event was followed by additional rounds of eukaryotic endosymbioses that spread the red lineage plastid to diverse groups such as haptophytes and stramenopiles.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Christa E Moore
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Gangman Yi
- Department of Multimedia Engineering, Dongkuk University, Seoul, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, Korea
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19
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Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding. Genetics 2017; 206:1237-1250. [PMID: 28468906 PMCID: PMC5500127 DOI: 10.1534/genetics.117.200303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant Arabidopsis thaliana and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6-14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1-98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies.
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20
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Guizetti J, Barcons-Simon A, Scherf A. Trans-acting GC-rich non-coding RNA at var expression site modulates gene counting in malaria parasite. Nucleic Acids Res 2016; 44:9710-9718. [PMID: 27466391 PMCID: PMC5175341 DOI: 10.1093/nar/gkw664] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/14/2022] Open
Abstract
Monoallelic expression of the var multigene family enables immune evasion of the malaria parasite Plasmodium falciparum in its human host. At a given time only a single member of the 60-member var gene family is expressed at a discrete perinuclear region called the 'var expression site'. However, the mechanism of var gene counting remains ill-defined. We hypothesize that activation factors associating specifically with the expression site play a key role in this process. Here, we investigate the role of a GC-rich non-coding RNA (ncRNA) gene family composed of 15 highly homologous members. GC-rich genes are positioned adjacent to var genes in chromosome-central gene clusters but are absent near subtelomeric var genes. Fluorescence in situ hybridization demonstrates that GC-rich ncRNA localizes to the perinuclear expression site of central and subtelomeric var genes in trans. Importantly, overexpression of distinct GC-rich ncRNA members disrupts the gene counting process at the single cell level and results in activation of a specific subset of var genes in distinct clones. We identify the first trans-acting factor targeted to the elusive perinuclear var expression site and open up new avenues to investigate ncRNA function in antigenic variation of malaria and other protozoan pathogens.
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Affiliation(s)
- Julien Guizetti
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France .,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
| | - Anna Barcons-Simon
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France.,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France .,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
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21
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Buskes MJ, Harvey KL, Prinz B, Crabb BS, Gilson PR, Wilson DJD, Abbott BM. Exploration of 3-methylisoquinoline-4-carbonitriles as protein kinase A inhibitors of Plasmodium falciparum. Bioorg Med Chem 2016; 24:2389-2396. [PMID: 27112453 DOI: 10.1016/j.bmc.2016.03.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/16/2016] [Accepted: 03/27/2016] [Indexed: 11/29/2022]
Abstract
A series of isoquinolines have been evaluated in a homology model of Plasmodium falciparum Protein Kinase A (PfPKA) using molecular dynamics. Synthesis of these compounds was then undertaken to investigate their structure-activity relationships. One compound was found to inhibit parasite growth in an in vitro assay and provides a lead to further develop 3-methylisoquinoline-4-carbonitriles as antimalarial compounds. Development of a potent and selective PfPKA inhibitor would provide a useful tool to shed further insight into the mechanisms enabling malaria parasites to establish infection.
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Affiliation(s)
- Melissa J Buskes
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Katherine L Harvey
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Boris Prinz
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Brendan S Crabb
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia; Monash University, Melbourne, Victoria 3800, Australia; University of Melbourne, Melbourne 3010, Australia
| | - Paul R Gilson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia; Monash University, Melbourne, Victoria 3800, Australia
| | - David J D Wilson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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Hoo R, Zhu L, Amaladoss A, Mok S, Natalang O, Lapp SA, Hu G, Liew K, Galinski MR, Bozdech Z, Preiser PR. Integrated analysis of the Plasmodium species transcriptome. EBioMedicine 2016; 7:255-66. [PMID: 27322479 PMCID: PMC4909483 DOI: 10.1016/j.ebiom.2016.04.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/09/2016] [Accepted: 04/11/2016] [Indexed: 01/18/2023] Open
Abstract
The genome sequence available for different Plasmodium species is a valuable resource for understanding malaria parasite biology. However, comparative genomics on its own cannot fully explain all the species-specific differences which suggests that other genomic aspects such as regulation of gene expression play an important role in defining species-specific characteristics. Here, we developed a comprehensive approach to measure transcriptional changes of the evolutionary conserved syntenic orthologs during the intraerythrocytic developmental cycle across six Plasmodium species. We show significant transcriptional constraint at the mid-developmental stage of Plasmodium species while the earliest stages of parasite development display the greatest transcriptional variation associated with critical functional processes. Modeling of the evolutionary relationship based on changes in transcriptional profile reveal a phylogeny pattern of the Plasmodium species that strictly follows its mammalian hosts. In addition, the work shows that transcriptional conserved orthologs represent potential future targets for anti-malaria intervention as they would be expected to carry out key essential functions within the parasites. This work provides an integrated analysis of orthologous transcriptome, which aims to provide insights into the Plasmodium evolution thereby establishing a framework to explore complex pathways and drug discovery in Plasmodium species with broad host range. Comparison of variations in mRNA abundance across six different Plasmodium species. Transcriptional conservation and divergence of Plasmodium syntenic orthologs. Pattern of Plasmodium transcriptome evolution are established. Transcriptionally conserved orthologs represent attractive intervention targets.
Malaria remains a major public health concern despite global efforts in the fight against this disease. The intraerythrocytic stage of the malaria parasites is currently in the spotlight for anti-malarial intervention and vaccine targets. The primary goal of this study is to generate a comprehensive and directly comparable transcriptome dataset across multiple Plasmodium species originating from different hosts. We establish that specific pathways and intraerythrocytic stages are more transcriptionally diverged than others, reflecting transcriptional evolutionary diversity. We further propose a panel of transcriptionally conserved genes as potential drug targets.
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Affiliation(s)
- Regina Hoo
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anburaj Amaladoss
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Onguma Natalang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Stacey A Lapp
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guangan Hu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kingsley Liew
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore.
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore.
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Abstract
Thyroglobulin (Tg) is a vertebrate secretory protein synthesized in the thyrocyte endoplasmic reticulum (ER), where it acquires N-linked glycosylation and conformational maturation (including formation of many disulfide bonds), leading to homodimerization. Its primary functions include iodide storage and thyroid hormonogenesis. Tg consists largely of repeating domains, and many tyrosyl residues in these domains become iodinated to form monoiodo- and diiodotyrosine, whereas only a small portion of Tg structure is dedicated to hormone formation. Interestingly, evolutionary ancestors, dependent upon thyroid hormone for development, synthesize thyroid hormones without the complete Tg protein architecture. Nevertheless, in all vertebrates, Tg follows a strict pattern of region I, II-III, and the cholinesterase-like (ChEL) domain. In vertebrates, Tg first undergoes intracellular transport through the secretory pathway, which requires the assistance of thyrocyte ER chaperones and oxidoreductases, as well as coordination of distinct regions of Tg, to achieve a native conformation. Curiously, regions II-III and ChEL behave as fully independent folding units that could function as successful secretory proteins by themselves. However, the large Tg region I (bearing the primary T4-forming site) is incompetent by itself for intracellular transport, requiring the downstream regions II-III and ChEL to complete its folding. A combination of nonsense mutations, frameshift mutations, splice site mutations, and missense mutations in Tg occurs spontaneously to cause congenital hypothyroidism and thyroidal ER stress. These Tg mutants are unable to achieve a native conformation within the ER, interfering with the efficiency of Tg maturation and export to the thyroid follicle lumen for iodide storage and hormonogenesis.
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Affiliation(s)
- Bruno Di Jeso
- Laboratorio di Patologia Generale (B.D.J.), Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy; and Division of Metabolism, Endocrinology, and Diabetes (P.A.), University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Peter Arvan
- Laboratorio di Patologia Generale (B.D.J.), Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy; and Division of Metabolism, Endocrinology, and Diabetes (P.A.), University of Michigan Medical School, Ann Arbor, Michigan 48105
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24
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Liu P, Robbins AH, Marzahn MR, McClung SH, Yowell CA, Stevens SM, Dame JB, Dunn BM. Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei. PLoS One 2015; 10:e0141758. [PMID: 26510189 PMCID: PMC4624963 DOI: 10.1371/journal.pone.0141758] [Citation(s) in RCA: 4] [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: 06/03/2015] [Accepted: 10/12/2015] [Indexed: 01/17/2023] Open
Abstract
The rodent malaria parasite Plasmodium berghei is a practical model organism for experimental studies of human malaria. Plasmepsins are a class of aspartic proteinase isoforms that exert multiple pathological effects in malaria parasites. Plasmepsins residing in the food vacuole (FV) of the parasite hydrolyze hemoglobin in red blood cells. In this study, we cloned PbPM4, the FV plasmepsin gene of P. berghei that encoded an N-terminally truncated pro-segment and the mature enzyme from genomic DNA. We over-expressed this PbPM4 zymogen as inclusion bodies (IB) in Escherichia coli, and purified the protein following in vitro IB refolding. Auto-maturation of the PbPM4 zymogen to mature enzyme was carried out at pH 4.5, 5.0, and 5.5. Interestingly, we found that the PbPM4 zymogen exhibited catalytic activity regardless of the presence of the pro-segment. We determined the optimal catalytic conditions for PbPM4 and studied enzyme kinetics on substrates and inhibitors of aspartic proteinases. Using combinatorial chemistry-based peptide libraries, we studied the active site preferences of PbPM4 at subsites S1, S2, S3, S1’, S2’ and S3’. Based on these results, we designed and synthesized a selective peptidomimetic compound and tested its inhibition of PbPM4, seven FV plasmepsins from human malaria parasites, and human cathepsin D (hcatD). We showed that this compound exhibited a >10-fold selectivity to PbPM4 and human malaria parasite plasmepsin 4 orthologs versus hcatD. Data from this study furthesr our understanding of enzymatic characteristics of the plasmepsin family and provides leads for anti-malarial drug design.
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Affiliation(s)
- Peng Liu
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (PL); (BMD)
| | - Arthur H. Robbins
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Melissa R. Marzahn
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Scott H. McClung
- Protein Core, Interdisciplinary Center for Biotechnology Research, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Charles A. Yowell
- Department of Infectious Diseases and Pathology, University of Florida, College of Veterinary Medicine, Gainesville, Florida, United States of America
| | - Stanley M. Stevens
- Protein Core, Interdisciplinary Center for Biotechnology Research, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - John B. Dame
- Department of Infectious Diseases and Pathology, University of Florida, College of Veterinary Medicine, Gainesville, Florida, United States of America
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (PL); (BMD)
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25
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Mailu BM, Li L, Arthur J, Nelson TM, Ramasamy G, Fritz-Wolf K, Becker K, Gardner MJ. Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites. J Biol Chem 2015; 290:29629-41. [PMID: 26318454 DOI: 10.1074/jbc.m115.655100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 01/25/2023] Open
Abstract
The malaria parasite Plasmodium falciparum apicoplast indirect aminoacylation pathway utilizes a non-discriminating glutamyl-tRNA synthetase to synthesize Glu-tRNA(Gln) and a glutaminyl-tRNA amidotransferase to convert Glu-tRNA(Gln) to Gln-tRNA(Gln). Here, we show that Plasmodium falciparum and other apicomplexans possess a unique heterodimeric glutamyl-tRNA amidotransferase consisting of GatA and GatB subunits (GatAB). We localized the P. falciparum GatA and GatB subunits to the apicoplast in blood stage parasites and demonstrated that recombinant GatAB converts Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro. We demonstrate that the apicoplast GatAB-catalyzed reaction is essential to the parasite blood stages because we could not delete the Plasmodium berghei gene encoding GatA in blood stage parasites in vivo. A phylogenetic analysis placed the split between Plasmodium GatB, archaeal GatE, and bacterial GatB prior to the phylogenetic divide between bacteria and archaea. Moreover, Plasmodium GatA also appears to have emerged prior to the bacterial-archaeal phylogenetic divide. Thus, although GatAB is found in Plasmodium, it emerged prior to the phylogenetic separation of archaea and bacteria.
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Affiliation(s)
- Boniface M Mailu
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Ling Li
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Jen Arthur
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Todd M Nelson
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Gowthaman Ramasamy
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Karin Fritz-Wolf
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and the Max-Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Katja Becker
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and
| | - Malcolm J Gardner
- From the Center for Infectious Disease Research, Seattle, Washington 98109, the Department of Global Health, University of Washington, Seattle, Washington 98195,
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26
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Han JH, Li J, Wang B, Lee SK, Nyunt MH, Na S, Park JH, Han ET. Identification of Immunodominant B-cell Epitope Regions of Reticulocyte Binding Proteins in Plasmodium vivax by Protein Microarray Based Immunoscreening. THE KOREAN JOURNAL OF PARASITOLOGY 2015; 53:403-11. [PMID: 26323838 PMCID: PMC4566507 DOI: 10.3347/kjp.2015.53.4.403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022]
Abstract
Plasmodium falciparum can invade all stages of red blood cells, while Plasmodium vivax can invade only reticulocytes. Although many P. vivax proteins have been discovered, their functions are largely unknown. Among them, P. vivax reticulocyte binding proteins (PvRBP1 and PvRBP2) recognize and bind to reticulocytes. Both proteins possess a C-terminal hydrophobic transmembrane domain, which drives adhesion to reticulocytes. PvRBP1 and PvRBP2 are large (> 326 kDa), which hinders identification of the functional domains. In this study, the complete genome information of the P. vivax RBP family was thoroughly analyzed using a prediction server with bioinformatics data to predict B-cell epitope domains. Eleven pvrbp family genes that included 2 pseudogenes and 9 full or partial length genes were selected and used to express recombinant proteins in a wheat germ cell-free system. The expressed proteins were used to evaluate the humoral immune response with vivax malaria patients and healthy individual serum samples by protein microarray. The recombinant fragments of 9 PvRBP proteins were successfully expressed; the soluble proteins ranged in molecular weight from 16 to 34 kDa. Evaluation of the humoral immune response to each recombinant PvRBP protein indicated a high antigenicity, with 38-88% sensitivity and 100% specificity. Of them, N-terminal parts of PvRBP2c (PVX_090325-1) and PvRBP2 like partial A (PVX_090330-1) elicited high antigenicity. In addition, the PvRBP2-like homologue B (PVX_116930) fragment was newly identified as high antigenicity and may be exploited as a potential antigenic candidate among the PvRBP family. The functional activity of the PvRBP family on merozoite invasion remains unknown.
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Affiliation(s)
- Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Jian Li
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Parasitology, College of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Bo Wang
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Myat Htut Nyunt
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.,Department of Medical Research, Yangon, Myanmar
| | - Sunghun Na
- Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Jeong-Hyun Park
- Department of Anatomy, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
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27
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Wei G, Zhao Y, Zhang Q, Pan W. Dual regulatory effects of non-coding GC-rich elements on the expression of virulence genes in malaria parasites. INFECTION GENETICS AND EVOLUTION 2015; 36:490-499. [PMID: 26299885 DOI: 10.1016/j.meegid.2015.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 01/19/2023]
Abstract
As the primary virulence factor of falciparum malaria, var genes harboring mutually exclusive expression pattern lead to antigenic variation and immune evasion of this pathogen in human host. Although various mechanisms contribute to silence of var genes, little is known of transcriptional activation pathways of a single var gene and maintenance of its active state with other silent var loci. Here, we report a monoallelic expression pattern of the non-coding GC-elements flanking chromosomal internal var genes, and transcript from the active one was required for activation of the var gene in the same array. Meanwhile, GFP reporter assays revealed a repressive effect on the adjacent gene induced by DNA motifs of the insulator-like GC-element, which was linked to heterochromatin subnuclear localization. Taken together, these data for the first time provide experimental evidence of the dual cis- and trans-acting regulatory functions of the GC-elements in both silence and activation of var genes, which would advance our understanding of the complex regulatory network of the virulence gene family in P. falciparum.
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Affiliation(s)
- Guiying Wei
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China
| | - Yuemeng Zhao
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China
| | - Qingfeng Zhang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China.
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China; Department of Tropical Infectious Diseases, Second Military Medical University, 800 Xiang Yin Road, Shanghai 200433, China.
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28
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Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J. Representing virus-host interactions and other multi-organism processes in the Gene Ontology. BMC Microbiol 2015; 15:146. [PMID: 26215368 PMCID: PMC4517558 DOI: 10.1186/s12866-015-0481-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/10/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. METHODS To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. CONCLUSIONS Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.
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Affiliation(s)
- R E Foulger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - D Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - B K McIntosh
- Department of Biochemistry and Biophysics, Texas Agrilife Research, Texas A&M University, College Station, TX, 77843, USA.
| | - C Hulo
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Masson
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - S Poux
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - J Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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29
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Kim JI, Yoon HS, Yi G, Kim HS, Yih W, Shin W. The Plastid Genome of the Cryptomonad Teleaulax amphioxeia. PLoS One 2015; 10:e0129284. [PMID: 26047475 PMCID: PMC4457928 DOI: 10.1371/journal.pone.0129284] [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: 01/05/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022] Open
Abstract
Teleaulax amphioxeia is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellate Dinophysis caudata through the ciliate Mesodinium rubrum in the marine food web. To better understand the genomic characteristics of T. amphioxeia, we have sequenced and analyzed its plastid genome. The plastid genome sequence of T. amphioxeia is similar to that of Rhodomonas salina, and they share significant synteny. This sequence exhibits less similarity to that of Guillardia theta, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome of T. amphioxeia is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (dnaX) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred in R. salina. On the other hand, the psbN gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Gangman Yi
- Department of Computer Science, Gangneung-Wonju National University, Wonju, Korea
| | - Hyung Seop Kim
- Department of Marine Biotechnology, Kunsan National University, Kunsan, Korea
| | - Wonho Yih
- Department of Marine Biotechnology, Kunsan National University, Kunsan, Korea
- * E-mail: (WY); (WS)
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, Korea
- * E-mail: (WY); (WS)
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30
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Ouattara A, Kone A, Adams M, Fofana B, Maiga AW, Hampton S, Coulibaly D, Thera MA, Diallo N, Dara A, Sagara I, Gil JP, Bjorkman A, Takala-Harrison S, Doumbo OK, Plowe CV, Djimde AA. Polymorphisms in the K13-propeller gene in artemisinin-susceptible Plasmodium falciparum parasites from Bougoula-Hameau and Bandiagara, Mali. Am J Trop Med Hyg 2015; 92:1202-6. [PMID: 25918205 DOI: 10.4269/ajtmh.14-0605] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/09/2014] [Indexed: 12/16/2022] Open
Abstract
Artemisinin-resistant Plasmodium falciparum malaria has been documented in southeast Asia and may already be spreading in that region. Molecular markers are important tools for monitoring the spread of antimalarial drug resistance. Recently, single-nucleotide polymorphisms (SNPs) in the PF3D7_1343700 kelch propeller (K13-propeller) domain were shown to be associated with artemisinin resistance in vivo and in vitro. The prevalence and role of K13-propeller mutations are poorly known in sub-Saharan Africa. K13-propeller mutations were genotyped by direct sequencing of nested polymerase chain reaction (PCR) amplicons from dried blood spots of pre-treatment falciparum malaria infections collected before and after the use of artemisinin-based combination therapy (ACT) as first-line therapy in Mali. Although K13-propeller mutations previously associated with delayed parasite clearance in Cambodia were not identified, 26 K13-propeller mutations were identified in both recent samples and pre-ACT infections. Parasite clearance time was comparable between infections with non-synonymous K13-propeller mutations and infections with the reference allele. These findings suggest that K13-propeller mutations are present in artemisinin-sensitive parasites and that they preceded the wide use of ACTs in Mali.
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Affiliation(s)
- Amed Ouattara
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Aminatou Kone
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Matthew Adams
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Bakary Fofana
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Amelia Walling Maiga
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Shay Hampton
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Drissa Coulibaly
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Mahamadou A Thera
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Nouhoum Diallo
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Antoine Dara
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Issaka Sagara
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Jose Pedro Gil
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Anders Bjorkman
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Shannon Takala-Harrison
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Ogobara K Doumbo
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Christopher V Plowe
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
| | - Abdoulaye A Djimde
- Department of Epidemiology of Parasitic Diseases, University of Science, Techniques and Technologies of Bamako, Bamako, Mali; Vanderbilt University Medical Center, Nashville, Tennessee; Howard Hughes Medical Institute, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska University Hospital/Karolinska Institutet, Stockholm, Sweden; Drug Resistance and Pharmacogenetics, Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal; The Harpur College of Arts and Sciences, Binghamton University, The State University of New York, Binghamton, New York
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Chia WN, Goh YS, Rénia L. Novel approaches to identify protective malaria vaccine candidates. Front Microbiol 2014; 5:586. [PMID: 25452745 PMCID: PMC4233905 DOI: 10.3389/fmicb.2014.00586] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/17/2014] [Indexed: 12/17/2022] Open
Abstract
Efforts to develop vaccines against malaria have been the focus of substantial research activities for decades. Several categories of candidate vaccines are currently being developed for protection against malaria, based on antigens corresponding to the pre-erythrocytic, blood stage, or sexual stages of the parasite. Long lasting sterile protection from Plasmodium falciparum sporozoite challenge has been observed in human following vaccination with whole parasite formulations, clearly demonstrating that a protective immune response targeting predominantly the pre-erythrocytic stages can develop against malaria. However, most of vaccine candidates currently being investigated, which are mostly subunits vaccines, have not been able to induce substantial (>50%) protection thus far. This is due to the fact that the antigens responsible for protection against the different parasite stages are still yet to be known and relevant correlates of protection have remained elusive. For a vaccine to be developed in a timely manner, novel approaches are required. In this article, we review the novel approaches that have been developed to identify the antigens for the development of an effective malaria vaccine.
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Affiliation(s)
- Wan Ni Chia
- Singapore Immunology Network, Agency for Science, Technology and Research Singapore, Singapore ; Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
| | - Yun Shan Goh
- Singapore Immunology Network, Agency for Science, Technology and Research Singapore, Singapore
| | - Laurent Rénia
- Singapore Immunology Network, Agency for Science, Technology and Research Singapore, Singapore ; Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
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32
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Vembar SS, Scherf A, Siegel TN. Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression. Curr Opin Microbiol 2014; 20:153-61. [PMID: 25022240 PMCID: PMC4157322 DOI: 10.1016/j.mib.2014.06.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/15/2014] [Accepted: 06/20/2014] [Indexed: 11/15/2022]
Abstract
The eukaryotic unicellular pathogen Plasmodium falciparum tightly regulates gene expression, both during development and in adaptation to dynamic host environments. This regulation is evident in the mutually exclusive expression of members of clonally variant virulence multigene families. While epigenetic regulators have been selectively identified at active or repressed virulence genes, their specific recruitment remains a mystery. In recent years, noncoding RNAs (ncRNAs) have emerged as lynchpins of eukaryotic gene regulation; by binding to epigenetic regulators, they provide target specificity to otherwise non-specific enzyme complexes. Not surprisingly, there is great interest in understanding the role of ncRNA in P. falciparum, in particular, their contribution to the mutually exclusive expression of virulence genes. The current repertoire of P. falciparum ncRNAs includes, but is not limited to, subtelomeric ncRNAs, virulence gene-associated ncRNAs and natural antisense RNA transcripts. Continued improvement in high-throughput sequencing methods is sure to expand this repertoire. Here, we summarize recent advances in P. falciparum ncRNA biology, with an emphasis on ncRNA-mediated epigenetic modes of gene regulation.
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Affiliation(s)
- Shruthi S Vembar
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France; CNRS URA2581, Paris, France
| | - Artur Scherf
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France; CNRS URA2581, Paris, France
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, University of Wuerzburg, Josef-Schneider-Str. 2/Bau D15, 97080 Wuerzburg, Germany.
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Butler CL, Lucas O, Wuchty S, Xue B, Uversky VN, White M. Identifying novel cell cycle proteins in Apicomplexa parasites through co-expression decision analysis. PLoS One 2014; 9:e97625. [PMID: 24841368 PMCID: PMC4026381 DOI: 10.1371/journal.pone.0097625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/22/2014] [Indexed: 11/26/2022] Open
Abstract
Hypothetical proteins comprise roughly half of the predicted gene complement of Toxoplasma gondii and Plasmodium falciparum and represent the largest class of uniquely functioning proteins in these parasites. Following the idea that functional relationships can be informed by the timing of gene expression, we devised a strategy to identify the core set of apicomplexan cell division cycling genes with important roles in parasite division, which includes many uncharacterized proteins. We assembled an expanded list of orthologs from the T. gondii and P. falciparum genome sequences (2781 putative orthologs), compared their mRNA profiles during synchronous replication, and sorted the resulting set of dual cell cycle regulated orthologs (744 total) into protein pairs conserved across many eukaryotic families versus those unique to the Apicomplexa. The analysis identified more than 100 ortholog gene pairs with unknown function in T. gondii and P. falciparum that displayed co-conserved mRNA abundance, dynamics of cyclical expression and similar peak timing that spanned the complete division cycle in each parasite. The unknown cyclical mRNAs encoded a diverse set of proteins with a wide range of mass and showed a remarkable conservation in the internal organization of ordered versus disordered structural domains. A representative sample of cyclical unknown genes (16 total) was epitope tagged in T. gondii tachyzoites yielding the discovery of new protein constituents of the parasite inner membrane complex, key mitotic structures and invasion organelles. These results demonstrate the utility of using gene expression timing and dynamic profile to identify proteins with unique roles in Apicomplexa biology.
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Affiliation(s)
- Carrie L. Butler
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Olivier Lucas
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Stefan Wuchty
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bin Xue
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Michael White
- Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Florida Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, United States of America
- * E-mail:
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Diversity and population structure of Plasmodium falciparum in Thailand based on the spatial and temporal haplotype patterns of the C-terminal 19-kDa domain of merozoite surface protein-1. Malar J 2014; 13:54. [PMID: 24521474 PMCID: PMC3931489 DOI: 10.1186/1475-2875-13-54] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/27/2014] [Indexed: 11/21/2022] Open
Abstract
Background The 19-kDa C-terminal region of the merozoite surface protein-1 of the human malaria parasite Plasmodium falciparum (PfMSP-119) constitutes the major component on the surface of merozoites and is considered as one of the leading candidates for asexual blood stage vaccines. Because the protein exhibits a level of sequence variation that may compromise the effectiveness of a vaccine, the global sequence diversity of PfMSP-119 has been subjected to extensive research, especially in malaria endemic areas. In Thailand, PfMSP-119 sequences have been derived from a single parasite population in Tak province, located along the Thailand-Myanmar border, since 1995. However, the extent of sequence variation and the spatiotemporal patterns of the MSP-119 haplotypes along the Thai borders with Laos and Cambodia are unknown. Methods Sixty-three isolates of P. falciparum from five geographically isolated populations along the Thai borders with Myanmar, Laos and Cambodia in three transmission seasons between 2002 and 2008 were collected and culture-adapted. The msp-1 gene block 17 was sequenced and analysed for the allelic diversity, frequency and distribution patterns of PfMSP-119 haplotypes in individual populations. The PfMSP-119 haplotype patterns were then compared between parasite populations to infer the population structure and genetic differentiation of the malaria parasite. Results Five conserved polymorphic positions, which accounted for five distinct haplotypes, of PfMSP-119 were identified. Differences in the prevalence of PfMSP-119 haplotypes were detected in different geographical regions, with the highest levels of genetic diversity being found in the Kanchanaburi and Ranong provinces along the Thailand-Myanmar border and Trat province located at the Thailand-Cambodia border. Despite this variability, the distribution patterns of individual PfMSP-119 haplotypes seemed to be very similar across the country and over the three malarial transmission seasons, suggesting that gene flow may operate between parasite populations circulating in Thailand and the three neighboring countries. Conclusion The major MSP-119 haplotypes of P. falciparum populations in all endemic populations during three transmission seasons in Thailand were identified, providing basic information on the common haplotypes of MSP-119 that is of use for malaria vaccine development and inferring the population structure of P. falciparum populations in Thailand.
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Jaron KS, Moravec JC, Martínková N. SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. Bioinformatics 2013; 30:1081-1086. [PMID: 24371153 DOI: 10.1093/bioinformatics/btt727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead. RESULTS We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition. AVAILABILITY AND IMPLEMENTATION Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research-data-analysis-tools-sighunt are implemented in C and R and are platform-independent. CONTACT 376090@mail.muni.cz or martinkova@ivb.cz.
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Affiliation(s)
- Kamil S Jaron
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jiří C Moravec
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Natália Martínková
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Malaria proteomics: insights into the parasite-host interactions in the pathogenic space. J Proteomics 2013; 97:107-25. [PMID: 24140976 DOI: 10.1016/j.jprot.2013.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 06/23/2013] [Accepted: 10/08/2013] [Indexed: 11/23/2022]
Abstract
Proteomics is improving malaria research by providing global information on relevant protein sets from the parasite and the host in connection with its cellular structures and specific functions. In the last decade, reports have described biologically significant elements in the proteome of Plasmodium, which are selectively targeted and quantified, allowing for sensitive and high-throughput comparisons. The identification of molecules by which the parasite and the host react during the malaria infection is crucial to the understanding of the underlying pathogenic mechanisms. Hence, proteomics is playing a major role by defining the elements within the pathogenic space between both organisms that change across the parasite life cycle in association with the host transformation and response. Proteomics has identified post-translational modifications in the parasite and the host that are discussed in terms of functional interactions in malaria parasitism. Furthermore, the contribution of proteomics to the investigation of immunogens for potential vaccine candidates is summarized. The malaria-specific technological advances in proteomics are particularly suited now for identifying host-parasite interactions that could lead to promising targets for therapy, diagnosis or prevention. In this review, we examine the knowledge gained on the biology, pathogenesis, immunity and diagnosis of Plasmodium infection from recent proteomic studies. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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37
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Mailu BM, Ramasamay G, Mudeppa DG, Li L, Lindner SE, Peterson MJ, DeRocher AE, Kappe SHI, Rathod PK, Gardner MJ. A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. J Biol Chem 2013; 288:32539-32552. [PMID: 24072705 DOI: 10.1074/jbc.m113.507467] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related organisms possess a relict plastid known as the apicoplast. Apicoplast protein synthesis is a validated drug target in malaria because antibiotics that inhibit translation in prokaryotes also inhibit apicoplast protein synthesis and are sometimes used for malaria prophylaxis or treatment. We identified components of an indirect aminoacylation pathway for Gln-tRNA(Gln) biosynthesis in Plasmodium that we hypothesized would be essential for apicoplast protein synthesis. Here, we report our characterization of the first enzyme in this pathway, the apicoplast glutamyl-tRNA synthetase (GluRS). We expressed the recombinant P. falciparum enzyme in Escherichia coli, showed that it is nondiscriminating because it glutamylates both apicoplast tRNA(Glu) and tRNA(Gln), determined its kinetic parameters, and demonstrated its inhibition by a known bacterial GluRS inhibitor. We also localized the Plasmodium berghei ortholog to the apicoplast in blood stage parasites but could not delete the PbGluRS gene. These data show that Gln-tRNA(Gln) biosynthesis in the Plasmodium apicoplast proceeds via an essential indirect aminoacylation pathway that is reminiscent of bacteria and plastids.
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Affiliation(s)
- Boniface M Mailu
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | | | - Devaraja G Mudeppa
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Ling Li
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Scott E Lindner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Megan J Peterson
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Amy E DeRocher
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Stefan H I Kappe
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Pradipsinh K Rathod
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Malcolm J Gardner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195.
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Hoen R, Novoa EM, López A, Camacho N, Cubells L, Vieira P, Santos M, Marin-Garcia P, Bautista JM, Cortés A, Ribas de Pouplana L, Royo M. Selective inhibition of an apicoplastic aminoacyl-tRNA synthetase from Plasmodium falciparum. Chembiochem 2013; 14:499-509. [PMID: 23444099 DOI: 10.1002/cbic.201200620] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 01/13/2023]
Abstract
The resistance of malaria parasites to available drugs continues to grow, and this makes the need for new antimalarial therapies pressing. Aminoacyl-tRNA synthetases (ARSs) are essential enzymes and well-established antibacterial targets and so constitute a promising set of targets for the development of new antimalarials. Despite their potential as drug targets, apicoplastic ARSs remain unexplored. We have characterized the lysylation system of Plasmodium falciparum, and designed, synthesized, and tested a set of inhibitors based on the structure of the natural substrate intermediate: lysyl-adenylate. Here we demonstrate that selective inhibition of apicoplastic ARSs is feasible and describe new compounds that that specifically inhibit Plasmodium apicoplastic lysyl-tRNA synthetase and show antimalarial activities in the micromolar range.
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Affiliation(s)
- Rob Hoen
- Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
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Evans L, Gowers D, Firman K, Youell J. Enhanced purification and characterization of the PfeIF4A (PfH45) helicase from Plasmodium falciparum using a codon-optimised clone. Protein Expr Purif 2012; 85:1-8. [PMID: 22750398 DOI: 10.1016/j.pep.2012.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/14/2012] [Accepted: 06/18/2012] [Indexed: 11/26/2022]
Abstract
With the intention of investigating the DNA strand displacement properties of Plasmodium falciparum helicase PfeIF4A (formerly known as PfH45) a codon-optimized gene for expression in Escherichia coli has been produced. Several histidine-containing proteins with intrinsic helicase activity were captured from the bacterial sonicate by initial Ni(2+)-chromatography. Heparin and size-exclusion steps were subsequently required for unambiguous PfeIF4A purification. This strategy generated an active recombinant protein of significantly improved yield in comparison to previously published studies (~4.2 mg/g wet weight of cells). Helicase unwinding assays confirmed a bipolar activity, but revealed a preference for unwinding a free 3'-end, with a rate of displacement in the 3'-5' direction 2-fold higher than that in the 5'-3' direction. DNA constructs with two, three or four blunt ends were not unwound. Studies confirmed the enzyme to be Mg(2+)-dependent, optimally active at 37°C and had a background ATP turnover rate of 23.16±1.74 pmol/min, which in the presence of single- or double-stranded DNA doubled to 42.92±3.21 pmol/min.
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Affiliation(s)
- Luke Evans
- IBBS Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire, United Kingdom
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40
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Iwanaga S, Kato T, Kaneko I, Yuda M. Centromere plasmid: a new genetic tool for the study of Plasmodium falciparum. PLoS One 2012; 7:e33326. [PMID: 22479383 PMCID: PMC3316556 DOI: 10.1371/journal.pone.0033326] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 02/07/2012] [Indexed: 11/19/2022] Open
Abstract
The introduction of transgenes into Plasmodium falciparum, a highly virulent human malaria parasite, has been conducted either by single crossover recombination or by using episomal plasmids. However, these techniques remain insufficient because of the low transfection efficiency and the low frequency of recombination. To improve the genetic manipulation of P. falciparum, we developed the centromere plasmid as a new genetic tool. First, we attempted to clone all of the predicted centromeres from P. falciparum into E. coli cells but failed because of the high A/T contents of these sequences. To overcome this difficulty, we identified the common sequence features of the centromere of Plasmodium spp. and designed a small centromere that retained those features. The centromere plasmid constructed with the small centromere sequence, pFCEN, segregated into daughter parasites with approximately 99% efficiency, resulting in the stable maintenance of this plasmid in P. falciparum even in the absence of drug selection. This result demonstrated that the small centromere sequence harboured in pFCEN could function as an actual centromere in P. falciparum. In addition, transgenic parasites were more rapidly generated when using pFCEN than when using the control plasmid, which did not contain the centromere sequence. Furthermore, in contrast to the control plasmid, pFCEN did not form concatemers and, thus, was maintained as a single copy over multiple cell divisions. These unique properties of the pFCEN plasmid will solve the current technical limitations of the genetic manipulation of P. falciparum, and thus, this plasmid will become a standard genetic tool for the study of this parasite.
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Affiliation(s)
- Shiroh Iwanaga
- Mie University, School of Medicine, Tsu, Japan
- * E-mail: (SI); (MY)
| | | | | | - Masao Yuda
- Mie University, School of Medicine, Tsu, Japan
- * E-mail: (SI); (MY)
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Iwanaga S, Kaneko I, Yuda M. A high-coverage artificial chromosome library for the genome-wide screening of drug-resistance genes in malaria parasites. Genome Res 2012; 22:985-92. [PMID: 22426943 PMCID: PMC3337443 DOI: 10.1101/gr.124164.111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The global spread of drug-resistant parasites is a serious problem for the treatment of malaria. Although identifying drug-resistance genes is crucial for the efforts against resistant parasites, an effective approach has not yet been developed. Here, we report a robust method for identifying resistance genes from parasites by using a Plasmodium artificial chromosome (PAC). Large genomic DNA fragments (10–50 kb) from the drug-resistant rodent malaria parasite Plasmodium berghei were ligated into the PAC and directly introduced into the drug-sensitive (i.e., wild-type) parasite by electroporation, resulting in a PAC library that encompassed the whole genomic sequence of the parasite. Subsequently, the transformed parasites that acquired resistance were selected by screening with the drug, and the resistance gene in the PAC was successfully identified. Furthermore, the drug-resistance gene was identified from a PAC library that was made from the pyrimethamine-resistant parasite Plasmodium chabaudi, further demonstrating the utility of our method. This method will promote the identification of resistance genes and contribute to the global fight against drug-resistant parasites.
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Affiliation(s)
- Shiroh Iwanaga
- School of Medicine, Mie University, Tsu City, Mie, Japan.
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HOLROYD N, SANCHEZ-FLORES A. Producing parasitic helminth reference and draft genomes at the Wellcome Trust Sanger Institute. Parasite Immunol 2012; 34:100-7. [DOI: 10.1111/j.1365-3024.2011.01311.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Prole DL, Taylor CW. Identification of intracellular and plasma membrane calcium channel homologues in pathogenic parasites. PLoS One 2011; 6:e26218. [PMID: 22022573 PMCID: PMC3194816 DOI: 10.1371/journal.pone.0026218] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 09/22/2011] [Indexed: 11/29/2022] Open
Abstract
Ca2+ channels regulate many crucial processes within cells and their abnormal activity can be damaging to cell survival, suggesting that they might represent attractive therapeutic targets in pathogenic organisms. Parasitic diseases such as malaria, leishmaniasis, trypanosomiasis and schistosomiasis are responsible for millions of deaths each year worldwide. The genomes of many pathogenic parasites have recently been sequenced, opening the way for rational design of targeted therapies. We analyzed genomes of pathogenic protozoan parasites as well as the genome of Schistosoma mansoni, and show the existence within them of genes encoding homologues of mammalian intracellular Ca2+ release channels: inositol 1,4,5-trisphosphate receptors (IP3Rs), ryanodine receptors (RyRs), two-pore Ca2+ channels (TPCs) and intracellular transient receptor potential (Trp) channels. The genomes of Trypanosoma, Leishmania and S. mansoni parasites encode IP3R/RyR and Trp channel homologues, and that of S. mansoni additionally encodes a TPC homologue. In contrast, apicomplexan parasites lack genes encoding IP3R/RyR homologues and possess only genes encoding TPC and Trp channel homologues (Toxoplasma gondii) or Trp channel homologues alone. The genomes of parasites also encode homologues of mammalian Ca2+influx channels, including voltage-gated Ca2+ channels and plasma membrane Trp channels. The genome of S. mansoni also encodes Orai Ca2+ channel and STIM Ca2+ sensor homologues, suggesting that store-operated Ca2+ entry may occur in this parasite. Many anti-parasitic agents alter parasite Ca2+ homeostasis and some are known modulators of mammalian Ca2+ channels, suggesting that parasite Ca2+ channel homologues might be the targets of some current anti-parasitic drugs. Differences between human and parasite Ca2+ channels suggest that pathogen-specific targeting of these channels may be an attractive therapeutic prospect.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
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Abstract
In vertebrates, the thyroglobulin (Tg) gene product must be exported to the lumen of thyroid follicles for thyroid hormone synthesis. In toto, Tg is composed of multiple type-1 repeats connected by linker and hinge (altogether considered as "region I," nearly 1,200 residues); regions II-III (~720 residues); and cholinesterase-like (ChEL) domain (~570 residues). Regions II-III and ChEL rapidly acquire competence for secretion, yet regions I-II-III require 20 min to become a partially mature disulfide isomer; stabilization of a fully oxidized form requires ChEL. Transition from partially mature to mature Tg occurs as a discrete "jump" in mobility by nonreducing SDS-PAGE, suggesting formation of at most a few final pairings of Cys residues that may be separated by significant intervening primary sequence. Using two independent approaches, we have investigated which portion of Tg is engaged in this late stage of its maturation. First, we demonstrate that this event is linked to oxidation involving region I. Introduction of the Tg-C1245R mutation in the hinge (identical to that causing human goitrous hypothyroidism) inhibits this maturation, although the Cys-1245 partner remains unidentified. Second, we find that Tg truncated after its fourth type-1 repeat is a fully independent secretory protein. Together, the data indicate that final acquisition of secretory competence includes conformational maturation in the interval between linker and hinge segments of region I.
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Affiliation(s)
- Jaemin Lee
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
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Pole JCM, McCaughan F, Newman S, Howarth KD, Dear PH, Edwards PAW. Single-molecule analysis of genome rearrangements in cancer. Nucleic Acids Res 2011; 39:e85. [PMID: 21525129 PMCID: PMC3141271 DOI: 10.1093/nar/gkr227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Rearrangements of the genome can be detected by microarray methods and massively parallel sequencing, which identify copy-number alterations and breakpoint junctions, but these techniques are poorly suited to reconstructing the long-range organization of rearranged chromosomes, for example, to distinguish between translocations and insertions. The single-DNA-molecule technique HAPPY mapping is a method for mapping normal genomes that should be able to analyse genome rearrangements, i.e. deviations from a known genome map, to assemble rearrangements into a long-range map. We applied HAPPY mapping to cancer cell lines to show that it could identify rearrangement of genomic segments, even in the presence of normal copies of the genome. We could distinguish a simple interstitial deletion from a copy-number loss at an inversion junction, and detect a known translocation. We could determine whether junctions detected by sequencing were on the same chromosome, by measuring their linkage to each other, and hence map the rearrangement. Finally, we mapped an uncharacterized reciprocal translocation in the T-47D breast cancer cell line to about 2 kb and hence cloned the translocation junctions. We conclude that HAPPY mapping is a versatile tool for determining the structure of rearrangements in the human genome.
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Affiliation(s)
- Jessica C M Pole
- Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK
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Otto TD, Sanders M, Berriman M, Newbold C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010; 26:1704-7. [PMID: 20562415 PMCID: PMC2894513 DOI: 10.1093/bioinformatics/btq269] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 04/23/2010] [Accepted: 05/19/2010] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. RESULTS Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. AVAILABILITY The software is available at http://icorn.sourceforge.net
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Affiliation(s)
- Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.
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Cserti-Gazdewich CM. Plasmodium falciparum malaria and carbohydrate blood group evolution. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1751-2824.2010.01380.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Cox D, McConkey S. The role of platelets in the pathogenesis of cerebral malaria. Cell Mol Life Sci 2010; 67:557-68. [PMID: 20091081 PMCID: PMC11115904 DOI: 10.1007/s00018-009-0211-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 11/05/2009] [Indexed: 01/31/2023]
Abstract
Malaria is a major cause of morbidity and mortality in the developing world and cerebral malaria is responsible for the majority of malaria-associated deaths. There is a strong association between thrombocytopenia and outcome in malaria, suggesting a role for platelets in the pathogenesis of malaria. This thrombocytopenia is likely due to platelet activation possibly through an interaction between PfEMP1 on plasmodium and CD36 on platelets. Platelet activation by plasmodium has two potential consequences. It can lead to the formation of micro-aggregates of infected red blood cells and platelets which can occlude blood vessels and it also leads to binding to and activation of the endothelium.
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Affiliation(s)
- Dermot Cox
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland.
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Dutta S, Sullivan JS, Grady KK, Haynes JD, Komisar J, Batchelor AH, Soisson L, Diggs CL, Heppner DG, Lanar DE, Collins WE, Barnwell JW. High antibody titer against apical membrane antigen-1 is required to protect against malaria in the Aotus model. PLoS One 2009; 4:e8138. [PMID: 19997632 PMCID: PMC2780715 DOI: 10.1371/journal.pone.0008138] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 10/23/2009] [Indexed: 11/19/2022] Open
Abstract
A Plasmodium falciparum 3D7 strain Apical Membrane Antigen-1 (AMA1) vaccine, formulated with AS02A adjuvant, slowed parasite growth in a recent Phase 1/2a trial, however sterile protection was not observed. We tested this AS02A, and a Montanide ISA720 (ISA) formulation of 3D7 AMA1 in Aotus monkeys. The 3D7 parasite does not invade Aotus erythrocytes, hence two heterologous strains, FCH/4 and FVO, were used for challenge, FCH/4 AMA1 being more homologous to 3D7 than FVO AMA1. Following three vaccinations, the monkeys were challenged with 50,000 FCH/4 or 10,000 FVO parasites. Three of the six animals in the AMA+ISA group were protected against FCH/4 challenge. One monkey did not become parasitemic, another showed only a short period of low level parasitemia that self-cured, and a third animal showed a delay before exhibiting its parasitemic phase. This is the first protection shown in primates with a recombinant P. falciparum AMA1 without formulation in Freund's complete adjuvant. No animals in the AMA+AS02A group were protected, but this group exhibited a trend towards reduced growth rate. A second group of monkeys vaccinated with AMA+ISA vaccine was not protected against FVO challenge, suggesting strain-specificity of AMA1-based protection. Protection against FCH/4 strain correlated with the quantity of induced antibodies, as the protected animals were the only ones to have in vitro parasite growth inhibitory activity of >70% at 1∶10 serum dilution; immuno-fluorescence titers >8,000; ELISA titers against full-length AMA1 >300,000 and ELISA titer against AMA1 domains1+2 >100,000. A negative correlation between log ELISA titer and day 11 cumulative parasitemia (Spearman rank r = −0.780, p value = 0.0001), further confirmed the relationship between antibody titer and protection. High titers of cross-strain inhibitory antibodies against AMA1 are therefore critical to confer solid protection, and the Aotus model can be used to down-select future AMA1 formulations, prior to advanced human trials.
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Affiliation(s)
- Sheetij Dutta
- Department of Epitope Mapping, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail: (SD); (JWB)
| | - JoAnn S. Sullivan
- Malaria Branch, Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Katharine K. Grady
- Malaria Branch, Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - J. David Haynes
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jack Komisar
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Adrian H. Batchelor
- Department of Epitope Mapping, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Lorraine Soisson
- Malaria Vaccine Development Program, United States Agency for International Development, Washington, D. C., United States of America
| | - Carter L. Diggs
- Malaria Vaccine Development Program, United States Agency for International Development, Washington, D. C., United States of America
| | - D. Gray Heppner
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - David E. Lanar
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - William E. Collins
- Malaria Branch, Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John W. Barnwell
- Malaria Branch, Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (SD); (JWB)
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Wuchty S, Adams JH, Ferdig MT. A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome. Proteomics 2009; 9:1841-9. [PMID: 19333996 DOI: 10.1002/pmic.200800383] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We derive a map of protein interactions in the parasite Plasmodium falciparum from conserved interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Escherichia coli and pool them with experimental interaction data. The application of a clique-percolation algorithm allows us to find overlapping clusters, strongly correlated with yeast specific conserved protein complexes. Such clusters contain core activities that govern gene expression, largely dominated by components of protein production and degradation processes as well as RNA metabolism. A critical role of protein hubs in the interactome of P. falciparum is supported by their appearance in multiple clusters and the tendencies of their interactions to reach into many distinct protein clusters. Parasite proteins with a human ortholog tend to appear in single complexes. Annotating each protein with the stage where it is maximally expressed we observe a high level of cluster integrity in the ring stage. While we find no signal in the trophozoite phase, expression patterns are reversed in the schizont phase, implying a preponderance of parasite specific functions in this late, invasive schizont stage. As such, the inference of potential protein interactions and their analysis contributes to our understanding of the parasite, indicating basic pathways and processes as unique targets for therapeutic intervention.
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Affiliation(s)
- Stefan Wuchty
- Northwestern Institute of Complexity, Northwestern University, Evanston, IL 60201, USA.
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