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Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Huang, Cui-Qin and Gasser, Robin B. and Cantacessi, Cinzia and Nisbet, Alasdair J. and Zhong, Weiwei and Sternberg, Paul W. and Loukas, Alex and Mulvenna, Jason and Lin, Rui-Qing and Chen, Ning and Zhu, Xing-Quan (2008) Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum. PLoS Neglected Tropical Diseases, 2 (6). e246. ISSN 1935-2735. http://resolver.caltech.edu/CaltechAUTHORS:HUAplosntd08

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Abstract

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism.


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http://dx.doi.org/10.1371/journal.pntd.0000246DOIUNSPECIFIED
Additional Information:© 2008 Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: January 8, 2008; Accepted: May 13, 2008; Published: June 18, 2008. Editor: Michael Cappello, Yale Child Health Research Center, United States of America. This work was supported by the National Natural Science Foundation of China (grant no. 36071578), International Foundation for Science (grant no. B/4018-1), the Scientific and Technological Programme of Guangdong Province (grant no. 2004B50201020) (XQZ), the Australian Research Council (RBG and AL), the Howard Hughes Medical Institute (PWS), and the National Health and Medical Research Council of Australia (AL and JM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. XQZ, RBG, and CC conceived and planned the research, and participated in data collection and analysis. CQH, RBG, CC, AJN, WZ, PWS, AL, JM, RQL, NC, and XQZ analysed the data, and RBG, CC, AJN, WZ, PWS, AL, and JM interpreted the data. All authors contributed to the analyses and to the manuscript. All authors read and approved the final version of the manuscript. Competing Interests: The authors have declared that no competing interests exist.
Funders:
Funding AgencyGrant Number
National Natural Science Foundation of China36071578
International Foundation for ScienceB/4018-1
Scientific and Technological Programme, Guangdong Province2004B50201020
Australian Research CouncilUNSPECIFIED
Howard Hughes Medicial InstituteUNSPECIFIED
National Health and Medical Research Council of AustraliaUNSPECIFIED
Record Number:CaltechAUTHORS:HUAplosntd08
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:HUAplosntd08
Official Citation:Huang C-Q, Gasser RB, Cantacessi C, Nisbet AJ, Zhong W, et al. (2008) Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum. PLoS Negl Trop Dis 2(6): e246. doi:10.1371/journal.pntd.0000246
Usage Policy:This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
ID Code:12907
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:16 Jan 2009 00:00
Last Modified:09 Jan 2013 18:06

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