ApicoAP: the first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa.

PloS One
Gokcen CilingirAudrey O T Lau

Abstract

Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for the survival of the parasite, but its unique properties make it an ideal drug target. The majority of apicoplast-associated proteins are nuclear encoded and targeted post-translationally to the organellar lumen via a bipartite signaling mechanism that requires an N-terminal signal and transit peptide (TP). Attempts to define a consensus motif that universally identifies apicoplast TPs have failed. In this study, we propose a generalized rule-based classification model to identify apicoplast-targeted proteins (ApicoTPs) that use a bipartite signaling mechanism. Given a training set specific to an organism, this model, called ApicoAP, incorporates a procedure based on a genetic algorithm to tailor a discriminating rule that exploits the known characteristics of ApicoTPs. Performance of ApicoAP is evaluated for four labeled datasets of Plasmodium falciparum, Plasmodium yoelii, Babesia bovis, and Toxoplasma gondii proteins. ApicoAP improves the classification accuracy of the published dataset for P. falciparum to 94%, originally 90% using PlasmoAP. We present a parametric model...Continue Reading

References

May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jun 6, 1996·Nature·G I McFaddenN Lang-Unnasch
Dec 6, 1997·Nature·M E Fichera, D S Roos
Oct 15, 1998·Proceedings of the National Academy of Sciences of the United States of America·R F WallerG I McFadden
Aug 4, 1999·Trends in Microbiology·G I McFadden, D S Roos
Aug 25, 1999·Current Opinion in Microbiology·D S RoosB Striepen
Sep 28, 2000·Parasitology Today·G G van DoorenG I McFadden
Apr 27, 2002·The Journal of Biological Chemistry·Giel G van DoorenGeoffrey I McFadden
Oct 9, 2002·Genome Research·Lewis Y GeerStephen H Bryant
Feb 1, 2003·Science·Bernardo J FothGeoffrey I McFadden
Apr 15, 2004·Nature Reviews. Microbiology·Stuart A RalphGeoffrey I McFadden
Jun 30, 2004·Journal of Molecular Biology·Jannick Dyrløv BendtsenSøren Brunak
Dec 31, 2005·Nucleic Acids Research·Feng ChenDavid S Roos
Apr 21, 2007·Nature Protocols·Olof EmanuelssonHenrik Nielsen
May 8, 2007·Nucleic Acids Research·Lukas KällErik L L Sonnhammer
Sep 29, 2007·Traffic·Christopher J TonkinGeoffrey I McFadden
Nov 8, 2008·PLoS Computational Biology·Sheila M ReynoldsWilliam Stafford Noble
Apr 7, 2009·Trends in Parasitology·Liting LimGeoffrey I McFadden
Nov 17, 2009·Nucleic Acids Research·Cristina AurrecoecheaHaiming Wang
Jan 20, 2010·Microbes and Infection·Tobias FleigeDominique Soldati-Favre
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Nov 8, 2011·Molecular and Biochemical Parasitology·Marina C CaballeroAudrey O T Lau

❮ Previous
Next ❯

Citations

Oct 8, 2013·Journal of Microbiological Methods·Gokcen CilingirShira L Broschat
Jan 11, 2013·Molecular Biology and Evolution·T A O MendesD C Bartholomeu
Nov 10, 2012·BMC Genomics·Lowell S KappmeyerKelly A Brayton
Sep 22, 2012·Trends in Parasitology·Ben J WoodcroftStuart A Ralph
Dec 20, 2014·BMC Bioinformatics·Soshichiro NaganoJonathan Gardiner Heddle
Jun 10, 2016·Journal of Pharmacopuncture·Avinaba Mukherjee, Gobinda Chandra Sadhukhan
May 23, 2015·Genome Biology and Evolution·Gillian H GileJohn M Archibald
Jun 27, 2015·BioMed Research International·Alexandr V SeliverstovPhilip S Kitsis
Feb 20, 2015·BioMed Research International·Gokcen Cilingir, Shira L Broschat
May 23, 2015·PLoS Computational Biology·Stepan TymoshenkoVassily Hatzimanikatis
Mar 10, 2017·Critical Reviews in Biochemistry and Molecular Biology·Lakshmipuram Seshadri Swapna, John Parkinson
Jan 17, 2020·Molecular Informatics·Subrata PramanikKlaus Heese
May 11, 2020·Cellular Microbiology·Anat FlorentinVasant Muralidharan
Jun 3, 2020·Proceedings of the National Academy of Sciences of the United States of America·Anat FlorentinVasant Muralidharan
Sep 19, 2019·Database : the Journal of Biological Databases and Curation·Rahila SardarDinesh Gupta
Nov 25, 2018·International Journal of Molecular Sciences·Michał BurdukiewiczPaweł Mackiewicz
Dec 16, 2020·Parasitology International·Ying ZhangHonglin Jia

❮ Previous
Next ❯

Software Mentioned

PlasmoAP
ApicoAP
SignalP
CDART ( Conserved Domain Architecture Retrieval Tool )
ApiLoc
EuPathDB
ApicoTP
PATS
ApicoTPs

Related Concepts

Related Feeds

Babesiosis

Babesiosis is caused by parasites of the genus babesia, which are transmitted in nature by the bite of an infected tick. Discover the latest research on babesiosis here.

Babesiosis (ASM)

Babesiosis is caused by parasites of the genus babesia, which are transmitted in nature by the bite of an infected tick. Discover the latest research on babesiosis here.

© 2021 Meta ULC. All rights reserved