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The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns
University of Toulouse, France .
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics.
University of Toulouse, France .
Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics.
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2012 (English)In: BMC Plant Biology, ISSN 1471-2229, Vol. 12, no 219Article in journal (Refereed) Published
Abstract [en]

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. less thanbrgreater than less thanbrgreater thanResults: 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. less thanbrgreater than less thanbrgreater thanConclusion: 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.

Place, publisher, year, edition, pages
BioMed Central , 2012. Vol. 12, no 219
Keyword [en]
Short-chain dehydrogenase/reductase (SDRs), SDR nomenclature initiative, Hidden markov model, Multigenic family, Plant
National Category
Medical and Health Sciences
URN: urn:nbn:se:liu:diva-88672DOI: 10.1186/1471-2229-12-219ISI: 000313689900001OAI: diva2:605476

Funding Agencies|EGIDE|MA-06-155|Libert Brice Tonfack from "Service de Cooperation et dAction Culturelle" of the French Embassy (Cameroon)||

Available from: 2013-02-14 Created: 2013-02-14 Last updated: 2013-02-19

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