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Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites

Achchuthan Shanmugasundram, Faviel F. Gonzalez-Galarza, Jonathan M. Wastling, Olga Vasieva, Andrew R. Jones
2012 Nucleic Acids Research  
The Library of Apicomplexan Metabolic Pathways (LAMP, http://www.llamp.net) is a web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent  ...  intracellular parasites of the phylum Apicomplexa.  ...  Hagai Ginsburg for kindly providing his MPMP annotation data.  ... 
doi:10.1093/nar/gks1139 pmid:23193253 pmcid:PMC3531055 fatcat:z4nfyocjdjchtdvwdhr4kofn6q

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling, Frédéric Bringaud, Peter Bütikofer, Amy M. Cattanach (+29 others)
2014 Nucleic Acids Research  
Here we present a dynamic database, TrypanoCyc (http: //www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan  ...  in which to visualise the metabolism of this important parasite.  ...  Metabolic databases such as Leish-Cyc (7) (for Leishmania), and the Library of Apicomplexan Metabolic Pathways (8) (for apicomplexan parasites) are among the few examples where this information is available  ... 
doi:10.1093/nar/gku944 pmid:25300491 pmcid:PMC4384016 fatcat:mjmzi3ytkzds3lgfmufbua4gom

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Yong H Woo, Hifzur Ansari, Thomas D Otto, Christen M Klinger, Martin Kolisko, Jan Michálek, Alka Saxena, Dhanasekaran Shanmugam, Annageldi Tayyrov, Alaguraj Veluchamy, Shahjahan Ali, Axel Bernal (+31 others)
2015 eLife  
Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism.  ...  The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding  ...  Acknowledgements We thank the KAUST Bioscience Core Laboratory personnel for sequencing specific Illumina libraries used in this project, KAUST Computational Bioscience Research Center for providing computing  ... 
doi:10.7554/elife.06974 pmid:26175406 pmcid:PMC4501334 fatcat:edb2tz2kxjfevitirdhdcw5edm

Multiple independent origins of apicomplexan-like parasites [article]

Varsha Mathur, Martin Kolisko, Elisabeth Hehenberger, Nicholas AT Irwin, Brian S Leander, Arni Kristmundsson, Mark A Freeman, Patrick J Keeling
2019 biorxiv/medrxiv   pre-print
Apicomplexans are a diverse group of globally important parasites, that include pathogens like Plasmodium, the causative agent of malaria.  ...  These findings suggest a predilection in this lineage for both the loss of photosynthesis and the transition to a morphologically similar parasitic lifestyle, resulting in multiple lineages of highly convergent  ...  metabolic pathways [2] .  ... 
doi:10.1101/636183 fatcat:2newkv5ubrgnbgwu4nkqmunyia

Metabolic contributions of an alphaproteobacterial endosymbiont in the apicomplexan Cardiosporidium cionae [article]

Elizabeth S. Hunter, Christopher Paight, Christopher E. Lane
2020 biorxiv/medrxiv   pre-print
A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host.  ...  Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis.  ...  α-Proteobacteria Of the contigs assigned to Rickettsiales, 45 were larger than 1 kb. Reassembly yielded 31 contigs, and manual curation resulted in a final 29 contigs.  ... 
doi:10.1101/2020.10.19.346205 fatcat:spojkn5k5vfwndcp22z73jipuy

Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae

Elizabeth Sage Hunter, Christopher Paight, Christopher E. Lane
2020 Frontiers in Microbiology  
A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host.  ...  Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis.  ...  α-Proteobacteria Of the contigs assigned to Rickettsiales, 45 were larger than 1 kb. Reassembly yielded 31 contigs, and manual curation resulted in a final 29 contigs.  ... 
doi:10.3389/fmicb.2020.580719 pmid:33335517 pmcid:PMC7737231 fatcat:hepruew72vcgtaicjg5ccw22yu

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

Sebastian G. Gornik, Febrimarsa, Andrew M. Cassin, James I. MacRae, Abhinay Ramaprasad, Zineb Rchiad, Malcolm J. McConville, Antony Bacic, Geoffrey I. McFadden, Arnab Pain, Ross F. Waller
2015 Proceedings of the National Academy of Sciences of the United States of America  
Indeed, discovery of nonphotosynthetic plastids in many eukaryotes-notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodiumhighlights the essential metabolic functions  ...  ., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid.  ...  Conclusion Compilation of genomic evidence for plastid-type metabolic pathways that occur in apicomplexans, dinoflagellates, and ciliates provides insights into the pathways that were present in the common  ... 
doi:10.1073/pnas.1423400112 pmid:25902514 pmcid:PMC4426444 fatcat:nkxpgry2b5g3dkajtoo2i24zdm

Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae

Sunil Kumar Dogga, Pavla Bartošová-Sojková, Julius Lukeš, Dominique Soldati-Favre
2015 Protist  
G. janae possesses a partial glideosome and along with it, the metabolic capabilities and adaptions of G. janae might provide cues as to how apicomplexans adjusted to extra-or intra-cytoplasmic niches  ...  This allows re-evaluation of the phylogenetic position of G. janae and sheds light on the emergence of the highly successful obligatory intracellularity of apicomplexan parasites.  ...  We thank Eva Dobaková for RNA isolation and Nicolas Hulo for his expert assistance on the analysis of the transcriptomic data.  ... 
doi:10.1016/j.protis.2015.09.003 pmid:26599727 fatcat:si2kvqtxkfgt7i5noyv7ep46yu

Metabolic reconstruction and analysis for parasite genomes

John W. Pinney, Balázs Papp, Christopher Hyland, Lillian Wambua, David R. Westhead, Glenn A. McConkey
2007 Trends in Parasitology  
The annotation of parasitic genomes is difficult owing to their great divergence and compositional bias, but funds are lacking for complete manual curation of several neglected organisms.  ...  For some industrially significant prokaryotes, the analysis of reconstructed metabolic networks has already proved useful; for example, in increasing the production of a desired metabolic product [10]  ...  We acknowledge funding from the MRC and BBSRC for this work. J.P. and B.P. are supported by the BBSRC and the International Human Frontier Science Program Organization, respectively.  ... 
doi:10.1016/j.pt.2007.08.013 pmid:17950669 fatcat:chzvhyqcqze5tefcyi6monjy6a

Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates)

Ann-Kathrin Ludewig-Klingner, Victoria Michael, Michael Jarek, Henner Brinkmann, Jörn Petersen
2017 Genome Biology and Evolution  
Apicomplexan parasites including the malaria and toxoplasmosis agents were described as the first group of mitochondriate protists devoid of peroxisomes.  ...  Our comparative genome analysis provides unequivocal evidence for the presence of peroxisomes in Toxoplasma gondii and related genera.  ...  This work including the Ph.D. stipend for A.-K. L.  ... 
doi:10.1093/gbe/evx250 pmid:29202176 pmcid:PMC5755239 fatcat:e2v54tfhcje63esbvgsexd6oiy

The origins of apicomplexan sequence innovation

J. Wasmuth, J. Daub, J. M. Peregrin-Alvarez, C. A.M. Finney, J. Parkinson
2009 Genome Research  
To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites.  ...  The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma.  ...  This work was funded by a grant from the Canadian Institutes of Health Research (CIHR #MOP84556) to J.P. and in part by a Research Training award from the Hospital for Sick Children to J.W.  ... 
doi:10.1101/gr.083386.108 pmid:19363216 pmcid:PMC2704437 fatcat:vtsrd4a72ffjxaeygyczqrptd4

Phylogenomics identifies a new major subgroup of apicomplexans, Marosporida class. nov., with extreme apicoplast genome reduction

Varsha Mathur, Waldan K Kwong, Filip Husnik, Nicholas A T Irwin, Árni Kristmundsson, Camino Gestal, Mark Freeman, Patrick J Keeling, Geoff McFadden
2020 Genome Biology and Evolution  
This new lineage of apicomplexans, for which we propose the class Marosporida class nov., occupies a key intermediate position in the apicomplexan phylogeny, and adds a new complexity to the models of  ...  Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism.  ...  V.M. was supported by a University Graduate Fellowship from the University of British Columbia.  ... 
doi:10.1093/gbe/evaa244 pmid:33566096 pmcid:PMC7875001 fatcat:pcj5vzave5arjcjearkm7ke4v4

Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles

Jan Janouškovec, Gita G Paskerova, Tatiana S Miroliubova, Kirill V Mikhailov, Thomas Birley, Vladimir V Aleoshin, Timur G Simdyanov
2019 eLife  
We generated single-cell transcriptomes for all major apicomplexan groups lacking large-scale sequence data.  ...  Environmental sequences of ten novel plastid lineages and structural innovations in plastid proteins confirm that plastids in apicomplexans and their relatives are widespread and share a common, photosynthetic  ...  We thank the staff of the White Sea Biological Station of Lomonosov Moscow State University and the Marine Biological Station of St. Petersburg State University for assistance during field sampling.  ... 
doi:10.7554/elife.49662 pmid:31418692 pmcid:PMC6733595 fatcat:z5xfivvgezhsva2rmhxvqk4pvu

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy

Adam James Reid, Sarah J. Vermont, James A. Cotton, David Harris, Grant A. Hill-Cawthorne, Stephanie Könen-Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam (+12 others)
2012 PLoS Pathogens  
rather it shows a striking preference for highly efficient vertical transmission in cattle.  ...  Toxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts.  ...  Acknowledgments We acknowledge EuPathDB (http://eupathdb.org/) for providing a publicly available repository for all genomic data sources on Toxoplasma.  ... 
doi:10.1371/journal.ppat.1002567 pmid:22457617 pmcid:PMC3310773 fatcat:mgnsnnhqmbd67cmp4oadxopboy

Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates

Jennifer H. Wisecaver, Michael L. Brosnahan, Jeremiah D. Hackett
2013 Genome Biology and Evolution  
The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation.  ...  The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.  ...  They also thank Susan Miller, William Driscoll, and Bonnie Hurwitz for computational and statistical advice.  ... 
doi:10.1093/gbe/evt179 pmid:24259313 pmcid:PMC3879968 fatcat:7yhpyi5735d35nhxbl3wdjfsbe
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