title: Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species.
abstract: OBJECTIVE
  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.
  
  
  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.
authors: Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613. mohanty@i2r.a-star.edu.sg
authors: Bijayalaxmi
authors: B
authors: Mohanty
authors: S P T
authors: SP
authors: Krishnan
authors: Sanjay
authors: S
authors: Swarup
authors: Vladimir B
authors: VB
authors: Bajic
mesh_terms: D000693:Anaerobiosis; D000818:Animals; D017360:Arabidopsis / Q000145:classification / Q000235:genetics; D001483:Base Sequence; D016384:Consensus Sequence; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D004798:Enzymes / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000145:classification / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D010944:Plants / Q000145:classification / Q000235:genetics*; D011401:Promoter Regions, Genetic
chemical_list: D018744:DNA, Plant; D004798:Enzymes; D010940:Plant Proteins