Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus.
BACKGROUND
Brown algae are plant multi-cellular organisms occupying most of the world coasts and are essential actors in the constitution of ecological niches at the shoreline. Ectocarpus siliculosus is an emerging model for brown algal research. Its genome has been sequenced, and several tools are being developed to perform analyses at different levels of cell organization, including transcriptomic expression analyses. Several topics, including physiological responses to osmotic stress and to exposure to contaminants and solvents are being studied in order to better understand the adaptive capacity of brown algae to pollution and environmental changes. A series of genes that can be used to normalise expression analyses is required for these studies.


RESULTS
We monitored the expression of 13 genes under 21 different culture conditions. These included genes encoding proteins and factors involved in protein translation (ribosomal protein 26S, EF1alpha, IF2A, IF4E) and protein degradation (ubiquitin, ubiquitin conjugating enzyme) or folding (cyclophilin), and proteins involved in both the structure of the cytoskeleton (tubulin alpha, actin, actin-related proteins) and its trafficking function (dynein), as well as a protein implicated in carbon metabolism (glucose 6-phosphate dehydrogenase). The stability of their expression level was assessed using the Ct range, and by applying both the geNorm and the Normfinder principles of calculation.


CONCLUSIONS
Comparisons of the data obtained with the three methods of calculation indicated that EF1alpha (EF1a) was the best reference gene for normalisation. The normalisation factor should be calculated with at least two genes, alpha tubulin, ubiquitin-conjugating enzyme or actin-related proteins being good partners of EF1a. Our results exclude actin as a good normalisation gene, and, in this, are in agreement with previous studies in other organisms.
Le Bail
Aude
A
UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, F 29682, Roscoff, France. lebail@sb-roscoff.fr
Dittami
Simon M
SM
de Franco
Pierre-Olivier
PO
Rousvoal
Sylvie
S
Cock
Mark J
MJ
Tonon
Thierry
T
Charrier
Bénédicte
B
D020418:Algal Proteins / Q000235:genetics*; D003470:Culture Media; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D000459:Phaeophyceae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*
D020418:Algal Proteins; D003470:Culture Media