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AOBPreview published online on July 18, 2005
Annals of Botany, doi:10.1093/aob/mci219
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© The Author 2005. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 29, 2004
Revised December 16, 2004
Accepted January 31, 2005

Special Issue: Article

Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species

BIJAYALAXMI MOHANTY 1*, S. P. T. KRISHNAN 1, SANJAY SWARUP 2, and VLADIMIR B. BAJIC 1

1 Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
2 Department of Biological Sciences, National University of Singapore, Singapore

* To whom correspondence should be addressed.
BIJAYALAXMI MOHANTY, E-mail: mohanty{at}i2r.a-star.edu.sg


  Abstract

• Background and Aims Plants can suffer from oxygen limitation during flooding or more complete submergence and may therefore switch from Kreb's cycle respiration to fermentation in association with the expression of anaerobically inducible genes coding for enzymes involved in glycolysis and fermentation. The aim of this study was to clarify mechanisms of transcriptional regulation of these anaerobic genes by identifying motifs shared by their promoter regions.

• Methods Statistically significant motifs were detected by an in silico method from 13 promoters of anaerobic genes. The selected motifs were common for the majority of analysed promoters. Their significance was evaluated by searching for their presence in transcription factor-binding site databases (TRANSFAC, PlantCARE and PLACE). Using several negative control data sets, it was tested whether the motifs found were specific to the anaerobic group.

• Key Results Previously, anaerobic response elements have been identified in maize (Zea mays) and arabidopsis (Arabidopsis thaliana) genes. Known functional motifs were detected, such as GT and GC motifs, but also other motifs shared by most of the genes examined. Five motifs detected have not been found in plants hitherto but are present in the promoters of animal genes with various functions. The consensus sequences of these novel motifs are 5'-AAACAAA-3', 5'-AGCAGC-3', 5'-TCATCAC-3', 5'-GTTT(A/C/T)GCAA-3' and 5'-TTCCCTGTT-3'.

• Conclusions It is believed that the promoter motifs identified could be functional by conferring anaerobic sensitivity to the genes that possess them. This proposal now requires experimental verification.

Keywords: Anaerobic genes, promoters, motifs, anaerobic response elements, ab initio motif detection, transcription factors, transcription factor-binding sites, Arabidopsis thaliana, ethanolic fermentative pathway.
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