1
|
Srivastava SK, Parker C, O'Brien CN, Tucker MS, Thompson PC, Rosenthal BM, Dubey JP, Khan A, Jenkins MC. Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella. Sci Rep 2023; 13:22802. [PMID: 38129566 PMCID: PMC10739835 DOI: 10.1038/s41598-023-50117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, "ERR296879") share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.
Collapse
Affiliation(s)
- Subodh K Srivastava
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Carolyn Parker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Celia N O'Brien
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Matthew S Tucker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Peter C Thompson
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Benjamin M Rosenthal
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Jitender P Dubey
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Asis Khan
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Mark C Jenkins
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
| |
Collapse
|
2
|
Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
Collapse
Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
3
|
Cruz-Bustos T, Dolezal M, Feix AS, Ruttkowski B, Hummel K, Razzazi-Fazeli E, Joachim A. Unravelling the sexual developmental biology of Cystoisospora suis, a model for comparative coccidian parasite studies. Front Cell Infect Microbiol 2023; 13:1271731. [PMID: 37953800 PMCID: PMC10635411 DOI: 10.3389/fcimb.2023.1271731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction The apicomplexan parasite Cystoisospora suis has global significance as an enteropathogen of suckling piglets. Its intricate life cycle entails a transition from an asexual phase to sexual development, ultimately leading to the formation of transmissible oocysts. Methods To advance our understanding of the parasite's cellular development, we complemented previous transcriptome studies by delving into the proteome profiles at five distinct time points of in vitro cultivation through LC/MS-MS analysis. Results A total of 1,324 proteins were identified in the in vitro developmental stages of C. suis, and 1,082 proteins were identified as significantly differentially expressed. Data are available via ProteomeXchange with identifier PXD045050. We performed BLAST, GO enrichment, and KEGG pathway analyses on the up- and downregulated proteins to elucidate correlated events in the C. suis life cycle. Our analyses revealed intriguing metabolic patterns in macromolecule metabolism, DNA- and RNA-related processes, proteins associated with sexual stages, and those involved in cell invasion, reflecting the adaptation of sexual stages to a nutrient-poor and potentially stressful extracellular environment, with a focus on enzymes involved in metabolism and energy production. Discussion These findings have important implications for understanding the developmental biology of C. suis as well as other, related coccidian parasites, such as Eimeria spp. and Toxoplasma gondii. They also support the role of C. suis as a new model for the comparative biology of coccidian tissue cyst stages.
Collapse
Affiliation(s)
- Teresa Cruz-Bustos
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Marlies Dolezal
- Platform for Bioinformatics and Biostatistics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Anna Sophia Feix
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Bärbel Ruttkowski
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karin Hummel
- VetCore Facility (Proteomics), University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility (Proteomics), University of Veterinary Medicine Vienna, Vienna, Austria
| | - Anja Joachim
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
4
|
Goyal M, Simantov K, Dzikowski R. Beyond splicing: serine-arginine proteins as emerging multifaceted regulators of RNA metabolism in malaria parasites. Curr Opin Microbiol 2022; 70:102201. [PMID: 36087463 DOI: 10.1016/j.mib.2022.102201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
The serine-arginine-rich (SR) proteins play an exceptionally important role in eukaryotic gene expression, primarily by regulating constitutive and alternative splicing events. In addition to their primary role as splicing factors, SR proteins have emerged as multifunctional RNA-binding proteins that act as key regulators of almost every step of RNA metabolism. As in higher eukaryotes, Plasmodium parasites encode several SR proteins, which were implicated in pre-mRNA splicing. However, only a few have been characterized and their biological roles remain understudied. Intriguingly, in addition to splicing regulation, unexpected functions of particular SR proteins have been reported in Plasmodium in recent years. Here, we highlight the key characteristics and different noncanonical splicing functions of SR proteins and discuss potential mechanisms, which might be involved in their multifaceted functionality in Plasmodium.
Collapse
Affiliation(s)
- Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| |
Collapse
|
5
|
Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS. A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics 2022; 23:780. [PMID: 36451097 PMCID: PMC9710153 DOI: 10.1186/s12864-022-09017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. RESULTS We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. CONCLUSIONS The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
Collapse
Affiliation(s)
- Johanna Hoshizaki
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie H. Adjalley
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,Micrographia Bio, London, W12 0BZ UK
| | - Vandana Thathy
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS UK ,grid.239585.00000 0001 2285 2675Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY10032 USA
| | - Kim Judge
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew Berriman
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.8756.c0000 0001 2193 314XWellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA UK
| | - Adam J. Reid
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.5335.00000000121885934Present address: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN UK
| | - Marcus C. S. Lee
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| |
Collapse
|
6
|
Mkandawire TT, Sateriale A. The Long and Short of Next Generation Sequencing for Cryptosporidium Research. Front Cell Infect Microbiol 2022; 12:871860. [PMID: 35419299 PMCID: PMC8995782 DOI: 10.3389/fcimb.2022.871860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal parasite Cryptosporidium is a significant cause of severe diarrhoeal disease that can have long term effects. Therapeutic options remain limited despite a significant impact on public health, partly due to various challenges in the field of Cryptosporidium research, including the availability of genomic and transcriptomic data from environmental and clinical isolates. In this review we explore how long read DNA and RNA sequencing technologies have begun to provide novel insights into the biology of the parasite. The increased deployment of these technologies will help researchers address key gaps in the understanding of Cryptosporidium biology, and ultimately drive translational research and better parasite control.
Collapse
|
7
|
Mohammadi MA, Harandi MF, McManus DP, Mansouri M. Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway. Parasit Vectors 2021; 14:574. [PMID: 34772444 PMCID: PMC8587495 DOI: 10.1186/s13071-021-05067-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. METHODS Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. RESULTS At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. CONCLUSIONS The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments.
Collapse
Affiliation(s)
- Mohammad Ali Mohammadi
- Student Research Committee, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
8
|
Ramakrishnan C, Smith NC. Recent achievements and doors opened for coccidian parasite research and development through transcriptomics of enteric sexual stages. Mol Biochem Parasitol 2021; 243:111373. [PMID: 33961917 DOI: 10.1016/j.molbiopara.2021.111373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
The Coccidia is the largest group of parasites within the Apicomplexa, a phylum of unicellular, obligate parasites characterized by the possession of an apical complex of organelles and structures in the asexual stages of their life cycles, as well as by a sexual reproductive phase that occurs enterically in host animals. Coccidian sexual reproduction involves morphologically distinct microgametes and macrogametes that combine to form a diploid zygote and, ultimately, following meiosis and mitosis, haploid, infectious sporozoites, inside sporocysts within an oocyst. Recent transcriptomic analyses have identified genes involved in coccidian sexual stage development and reproduction, including genes encoding for microgamete- and macrogamete-specific proteins with roles in gamete motility, fusion and fertilization, and in the formation of the resilient oocyst wall that allows coccidians to persist for long periods in the environment. Transcriptomics has also provided important clues about the regulation of gene expression in the transformation of parasites from one developmental stage to the next, a complex sequence of events that may involve transcription factors such as the apicomplexan Apetala2 (ApiAP2) family, alternative splicing, regulatory RNAs and MORC (a microrchida homologue and regulator of sexual stage development in Toxoplasma gondii). The molecular dissection of coccidian sexual development and reproduction by transcriptomic analyses may lead to the development of novel transmission-blocking strategies.
Collapse
Affiliation(s)
- Chandra Ramakrishnan
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerland
| | - Nicholas C Smith
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Arora Verasztó H, Logotheti M, Albrecht R, Leitner A, Zhu H, Hartmann MD. Architecture and functional dynamics of the pentafunctional AROM complex. Nat Chem Biol 2020; 16:973-978. [PMID: 32632294 DOI: 10.1038/s41589-020-0587-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.
Collapse
Affiliation(s)
- Harshul Arora Verasztó
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Maria Logotheti
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| |
Collapse
|
11
|
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms. Nat Commun 2020; 11:2763. [PMID: 32488076 PMCID: PMC7265539 DOI: 10.1038/s41467-020-16593-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 05/04/2020] [Indexed: 01/23/2023] Open
Abstract
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of Plasmodium falciparum genes show 24 h rhythms in expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a 24 h transcriptional rhythm and disrupting it in rodent malaria parasites shortens the IDC by 2-3 h; (v) Multiple processes including DNA replication, and the ubiquitin and proteasome pathways, are affected by loss of coordination with host rhythms and by disruption of SR10. Our results reveal malaria parasites are at least partly responsible for scheduling the IDC and coordinating their development with host daily rhythms. The mechanism underlying periodicity of Plasmodium’s intra-erythrocytic developmental cycle (IDC) is unclear. Here, Subudhi et al. show that serpentine receptor 10 (SR10) plays a role in regulating the schedule of the IDC in line with the timing of host daily rhythms.
Collapse
|
12
|
Tretina K, Pelle R, Orvis J, Gotia HT, Ifeonu OO, Kumari P, Palmateer NC, Iqbal SBA, Fry LM, Nene VM, Daubenberger CA, Bishop RP, Silva JC. Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. BMC Genomics 2020; 21:279. [PMID: 32245418 PMCID: PMC7126163 DOI: 10.1186/s12864-020-6683-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/18/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome. RESULTS The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized. CONCLUSIONS The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.
Collapse
Affiliation(s)
- Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hanzel T Gotia
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Olukemi O Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Priti Kumari
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Nicholas C Palmateer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Shaikh B A Iqbal
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay M Fry
- Animal Disease Research Unit, Agricultural Research Service, USDA, Pullman, WA, 99164, USA
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA
| | | | - Claudia A Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Richard P Bishop
- Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| |
Collapse
|
13
|
Matralis AN, Malik A, Penzo M, Moreno I, Almela MJ, Camino I, Crespo B, Saadeddin A, Ghidelli-Disse S, Rueda L, Calderon F, Osborne SA, Drewes G, Böesche M, Fernández-Álvaro E, Martin Hernando JI, Baker DA. Development of Chemical Entities Endowed with Potent Fast-Killing Properties against Plasmodium falciparum Malaria Parasites. J Med Chem 2019; 62:9217-9235. [PMID: 31566384 PMCID: PMC6816013 DOI: 10.1021/acs.jmedchem.9b01099] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
One of the attractive properties of artemisinins is their extremely fast-killing capability, quickly relieving malaria symptoms. Nevertheless, the unique benefits of these medicines are now compromised by the prolonged parasite clearance times and the increasing frequency of treatment failures, attributed to the increased tolerance of Plasmodium falciparum to artemisinin. This emerging artemisinin resistance threatens to undermine the effectiveness of antimalarial combination therapies. Herein, we describe the medicinal chemistry efforts focused on a cGMP-dependent protein kinase (PKG) inhibitor scaffold, leading to the identification of novel chemical entities with very potent, similar to artemisinins, fast-killing potency against asexual blood stages that cause disease, and activity against gametocyte activation that is required for transmission. Furthermore, we confirm that selective PKG inhibitors have a slow speed of kill, while chemoproteomic analysis suggests for the first time serine/arginine protein kinase 2 (SRPK2) targeting as a novel strategy for developing antimalarial compounds with extremely fast-killing properties.
Collapse
Affiliation(s)
- Alexios N Matralis
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain.,Biomedical Sciences Research Center "Alexander Fleming" , Fleming 34 Street , 16672 Vari , Greece
| | - Adnan Malik
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Maria Penzo
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain.,Faculty of Infectious and Tropical Diseases , London School of Hygiene & Tropical Medicine , London WC1E 7HT , U.K
| | - Inmaculada Moreno
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Maria J Almela
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Isabel Camino
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Benigno Crespo
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Anas Saadeddin
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Lourdes Rueda
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Felix Calderon
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Simon A Osborne
- LifeArc, Accelerator Building, Open Innovation Campus , Stevenage SG1 2FX , U.K
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Markus Böesche
- Cellzome GmbH, a GlaxoSmithKline Company , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Elena Fernández-Álvaro
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Jose Ignacio Martin Hernando
- Tres Cantos, Medicines Development Campus, DDW, GlaxoSmithKline , Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - David A Baker
- Faculty of Infectious and Tropical Diseases , London School of Hygiene & Tropical Medicine , London WC1E 7HT , U.K
| |
Collapse
|