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The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis, 3D modelling and expression profiling

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Abstract

As precursors of wax compounds, very long chain fatty acids participate in the limitation of non-stomatal water loss and the prevention of pathogen attacks. They also serve as energy storage in seeds and as membrane building blocks. Their biosynthesis is catalyzed by the acyl-CoA elongase, a membrane-bound enzymatic complex containing four distinct enzymes (KCS, KCR, HCD and ECR). Twenty-one 3-ketoacyl-CoA synthase (KCS) genes have been identified in Arabidopsis thaliana genome. In this paper we present an overview of the acyl-CoA elongase genes in Arabidopsis focusing on the entire KCS family. We show that the KCS family is made up of 8 distinct subclasses, according to their phylogeny, duplication history, genomic organization, protein topology and 3D modelling. The analysis of the subcellular localization in tobacco cells of the different subunits of the acyl-CoA elongase shows that all these proteins are localized in the endoplasmic reticulum demonstrating that VLCFA production occurs in this compartment. The expression patterns in Arabidopsis of the acyl-CoA elongase genes suggest several levels of regulations at the tissular or organ level but also under stress conditions suggesting a complex organization of this multigenic family.

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Abbreviations

ECR:

Trans-2,3-enoyl-CoA reductase

ER:

Endoplasmic reticulum

EST:

Expressed sequence tag

GUS:

β-Glucuronidase

HCD:

3-Hydroxacyl-CoA dehydratase

KCR:

3-Ketoacyl-CoA reductase

KCS:

3-Ketoacyl-CoA synthase

TAG:

Triacylglycerols

VLCFA:

Long chain fatty acid

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Acknowledgements

We thank Dr. Ljerka Kunst (Department of Botany; University of British Columbia; Canada) and Dr. Donghui Li (TAIR curator; Carnegie Institution; Stanford; USA) for help in preparing the KCS nomenclature. We thank the confocal microscope facilities of the IFR 103 (IBVM, Institut National de la Recherche Agronomique-Bordeaux) and Dr. V. Coulon for help in preparing the manuscript. This work was funded by the Ministère de l’Enseignement Supérieur et de la Recherche (France) (doctoral fellowship to B.B.) and the Conseil Régional d’Aquitaine (France) (doctoral fellowship to C.G.). This work was supported by the French Agence Nationale de la Recherche (contract ANR-JC05-45555; S.R.). This work received support from the Centre National de la Recherche Scientifique and the University Victor Segalen Bordeaux 2.

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  1. Laboratoire de Biogenèse Membranaire, Université Victor Ségalen Bordeaux 2, CNRS, UMR5200, 146 rue Léo Saignat, Case 92, 33076, Bordeaux Cedex, France

    Jérôme Joubès, Sylvain Raffaele, Brice Bourdenx, Christel Garcia, Jeanny Laroche-Traineau, Patrick Moreau, Frédéric Domergue & René Lessire

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  1. Jérôme Joubès
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  2. Sylvain Raffaele
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Correspondence to Jérôme Joubès.

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Supplemental Figure S1

Details on homology modeling used to build KCS1 3D model (PPT 62 kb)

Supplemental Table S1

Identity percentages between the different KCS proteins (XLS 21 kb)

Supplemental Table S2

Promoter motifs in ELONGASE genes (XLS 51 kb)

Supplemental Table S3

A subset of expression data of Arabidopsis KCS genes (XLS 359 kb)

Supplemental Table S4

Primers used for PCR cloning and QPCR analysis (XLS 28 kb)

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Joubès, J., Raffaele, S., Bourdenx, B. et al. The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis, 3D modelling and expression profiling. Plant Mol Biol 67, 547–566 (2008). https://doi.org/10.1007/s11103-008-9339-z

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