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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
The Plant Short-Chain Dehydrogenase (SDR) superfamily: Genome-wide inventory and diversification patterns
BMC Plant Biology, Volume 12, Article 219, Year 2012
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Description
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. © 2012 Moummou et al.; licensee BioMed Central Ltd.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3541173/bin/1471-2229-12-219-S1.xls
https://efashare.b-cdn.net/share/pmc/articles/PMC3541173/bin/1471-2229-12-219-S2.xls
https://efashare.b-cdn.net/share/pmc/articles/PMC3541173/bin/1471-2229-12-219-S3.ppt
Authors & Co-Authors
Moummou, Hanane
France, Toulouse
Institut National Polytechnique de Toulouse
Morocco, Marakech
Faculté Des Sciences Semlalia
Kallberg, Yvonne
Sweden, Stockholm
Karolinska Institutet
Tonfack, Libert Brice
France, Toulouse
Institut National Polytechnique de Toulouse
Cameroon, Yaounde
Université de Yaoundé I
Persson, Bengt L.
Sweden, Stockholm
Karolinska Institutet
Sweden, Linkoping
Linköpings Universitet
van der Rest, Benoît
France, Toulouse
Institut National Polytechnique de Toulouse
France, Castanet-tolosan
Génomique et Biotechnologie Des Fruits - Gbf
Statistics
Citations: 106
Authors: 5
Affiliations: 6
Identifiers
Doi:
10.1186/1471-2229-12-219
e-ISSN:
14712229