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Open Access Research article

The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns

Hanane Moummou12, Yvonne Kallberg3, Libert Brice Tonfack14, Bengt Persson56 and Benoît van der Rest17*

Author affiliations

1 Université de Toulouse, INPT-ENSAT, UMR990 Génomique et Biotechnologie des Fruits, Avenue de l’Agrobiopole, BP 32607, Castanet-Tolosan, F-31326, France

2 Laboratory of Food Science, Faculty of Science Semlalia, University CADI AYYAD, Marrakech, Morocco

3 Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Centre for Molecular Medicine, Karolinska Institutet, SE-171 77, Stockholm, Sweden

4 Laboratory of Biotechnology and Environment, Unit of Plant Physiology and Improvement, Department of Plant Biology, Faculty of Science, University of Yaounde 1, PO BOX 812, Yaounde, Cameroon

5 Science for Life Laboratory, Department of Cell and Molecular Biology (CMB), Karolinska Institutet, SE-17177, Stockholm, Sweden

6 IFM Bioinformatics and Swedish e-Science Research Centre (SeRC), Linköping University, SE-58183, Linköping, Sweden

7 INRA, UMR990 Génomique et Biotechnologie des Fruits, 24 Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France

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Citation and License

BMC Plant Biology 2012, 12:219  doi:10.1186/1471-2229-12-219

Published: 20 November 2012

Abstract

Background

Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved ‘Rossmann-fold’ structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce.

Results

Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types — ‘classical’, ‘extended’ and ‘divergent’ — but a minority (10% of the predicted SDRs) could not be classified into these general types (‘unknown’ or ‘atypical’ types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families — tropinone reductase-like proteins (SDR65C), ‘ABA2-like’-NAD dehydrogenase (SDR110C), ‘salutaridine/menthone-reductase-like’ proteins (SDR114C), ‘dihydroflavonol 4-reductase’-like proteins (SDR108E) and ‘isoflavone-reductase-like’ (SDR460A) proteins — have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified.

Conclusion

The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms (‘higher plants’) SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution.

Keywords:
Short-chain dehydrogenase/reductase (SDRs); SDR nomenclature initiative; Hidden markov model; Multigenic family; Plant