From raw materials to validated system: the construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite

Physiological Genomics - Tập 42 Số 2 - Trang 219-235 - 2010
Arun Rawat1, Kurt A. Gust2, Youping Deng3, Natàlia García‐Reyero4, Michael J. Quinn5, Mark S. Johnson5, Karl J. Indest2, Mohamed O. Elasri6, Edward J. Perkins2
1[Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA]
2U.S. Army Engineer Research and Development Center, Environmental Laboratory, EP-P;
3SpecPro Incorporated, Environmental Laboratory, EP-P, Vicksburg;
4Jackson State University, Department of Chemistry, Jackson, Mississippi;
5U.S. Army Center for Health Promotion and Preventative Medicine, Aberdeen Proving Ground, Maryland
6Department of Biological Sciences, University of Southern Mississippi, Hattiesburg.

Tóm tắt

The limited availability of genomic tools and data for nonmodel species impedes computational and systems biology approaches in nonmodel organisms. Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite ( Colinus virginianus ) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field contaminant of military concern. Massively parallel pyrosequencing of a normalized multitissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts that were annotated with gene ontology (GO), pathway information, and protein domain analysis. Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60 days (d) to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including: prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia, and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcript expression analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT exposure case study. Furthermore, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.

Từ khóa


Tài liệu tham khảo

10.1016/S0022-2836(05)80360-2

10.1038/75556

10.1093/bioinformatics/17.6.509

10.1006/jmbi.1998.2144

10.1152/physiolgenomics.00207.2005

10.1186/1471-2164-9-183

10.1186/1471-2164-10-S2-S3

10.1038/ng0502-19

Darling A, 2003, 4th International Conference on Linux Clusters: the HPC Revolution 2003, in conjunction with ClusterWorld Conference & Expo

10.1186/gb-2003-4-5-p3

10.1104/pp.103.028019

10.1016/S0738-081X(97)00202-2

10.1111/j.1365-294X.2008.03699.x

10.1371/journal.pcbi.0010045

10.1111/j.1095-8649.2008.01904.x

10.2337/db07-1087

Gouault-Helimann M, 1979, Nouv Presse Med, 8, 3249

10.1016/B978-044452771-4/50010-9

10.1152/jn.1998.80.6.3120

10.1093/toxsci/kfp091

10.1093/nar/gkj021

10.1186/gb-2008-9-2-r40

10.1038/ng1236

10.1038/nprot.2008.211

10.1101/gr.9.9.868

Iseli C, 1999, Proc Int Conf Intell Syst Mol Biol, 138

10.1080/10915810591007247

10.1897/06-525.1

10.1006/eesa.1999.1893

10.1093/nar/gkj102

10.1093/toxsci/kfm297

10.1126/science.1132939

10.1210/endo.139.3.5836

10.1152/advan.00052.2006

10.1096/fj.08-119420

10.1093/bioinformatics/bti430

10.1038/nature03959

10.1186/1471-2164-10-219

10.1093/bioinformatics/btm585

Morteau O, 2004, Oral Tolerance: the Response of the Intestinal Mucosa to Dietary Antigens., 70

10.1093/nar/gkm378

10.1080/03601230802598995

10.1093/nar/gki442

10.1897/07-123R.1

10.1897/08-418.1

10.1186/1471-2105-9-S9-S7

10.1080/10915810050074937

10.1016/j.tibtech.2007.08.005

10.1186/1471-2105-8-217

10.2193/0022-541X(2005)69[1321:UTNABB]2.0.CO;2

10.2174/156652407779940413

10.1016/j.ecoenv.2007.08.019

10.1093/nar/gkg124

Talmage SC, 1999, Rev Environ Contam Toxicol, 161, 1

10.1016/j.cbpa.2006.11.039

10.1186/1471-2164-8-341

Turk E, 1994, J Biol Chem, 269, 15204, 10.1016/S0021-9258(17)36592-4

10.1101/gr.4602906

10.1111/j.1365-294X.2008.03666.x

10.1186/gb-2007-8-1-r9

10.1016/j.copbio.2007.11.005

10.1093/toxsci/kfl080

10.1093/nar/gkl167

10.1093/nar/gkl031

10.1093/bioinformatics/17.9.847

Thông tin
Thông tin xuất bản

Physiological Genomics

Tập 42 Số 2

219-235

Thông tin tác giả