Marine Biotechnology

, Volume 16, Issue 4, pp 423–435

Transcriptional Assessment by Microarray Analysis and Large-Scale Meta-analysis of the Metabolic Capacity of Cardiac and Skeletal Muscle Tissues to Cope With Reduced Nutrient Availability in Gilthead Sea Bream (Sparus aurata L.)

  • Josep A. Calduch-Giner
  • Yann Echasseriau
  • Diego Crespo
  • Daniel Baron
  • Josep V. Planas
  • Patrick Prunet
  • Jaume Pérez-Sánchez
Original Article

DOI: 10.1007/s10126-014-9562-3

Cite this article as:
Calduch-Giner, J.A., Echasseriau, Y., Crespo, D. et al. Mar Biotechnol (2014) 16: 423. doi:10.1007/s10126-014-9562-3

Abstract

The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart > red skeletal muscle > white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips (http://fishandchips.genouest.org/index.php) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species.

Keywords

Feeding level Skeletal muscle Heart Microarray Meta-analysis Mitochondria 

Supplementary material

10126_2014_9562_MOESM1_ESM.docx (53 kb)
Supplemental Table A1Datasets included in the bioinformatic meta-analysis tool Fish and Chips. (DOCX 53 kb)
10126_2014_9562_MOESM2_ESM.docx (28 kb)
Supplemental Table A2Genes differentially expressed by restricted ration size in white skeletal muscle. Genes sharing the enriched GO terms “protein ubiquitination”, “proteolysis”, or “ubiquitin-dependent protein catabolic process” are highlighted in bold. (DOCX 28 kb)
10126_2014_9562_MOESM3_ESM.docx (20 kb)
Supplemental Table A3Genes differentially expressed by restricted ration size in red skeletal muscle. (DOCX 19 kb)
10126_2014_9562_MOESM4_ESM.docx (47 kb)
Supplemental Table A4Genes differentially expressed by restricted ration size in cardiac muscle. Genes sharing the enriched GO terms “regulation of transcription”, “signal transduction”, or “signaling pathway” are highlighted in bold. (DOCX 46 kb)
10126_2014_9562_MOESM5_ESM.docx (39 kb)
Supplemental Table A5Overlapping annotated genes between clusters in the first and second round of cluster comparison. (DOCX 38 kb)

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Josep A. Calduch-Giner
    • 1
  • Yann Echasseriau
    • 2
  • Diego Crespo
    • 3
  • Daniel Baron
    • 4
  • Josep V. Planas
    • 3
  • Patrick Prunet
    • 2
  • Jaume Pérez-Sánchez
    • 1
  1. 1.Nutrigenomics and Fish Growth Endocrinology GroupInstituto de Acuicultura Torre de la Sal (IATS–CSIC)CastellónSpain
  2. 2.INRA, UR1037 LPGP Fish Physiology and GenomicsRennesFrance
  3. 3.Departament de Fisiologia i Immunologia, Facultat de BiologiaUniversitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB)BarcelonaSpain
  4. 4.INSERM, UMR 1064NantesFrance

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