Journal de biochimie et de physiologie végétales
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Medicago sativa L. β-Amylase Core Promoter has Motifs in Common with Arabidopsis Key Starch Degradation Genes

Brett Fugate, Denise Medrano, Joyce Ache Gana, Aida Abraha and Suzanne M Cunningham

β-amylase is an enzyme involved in the degradation of transitory starch in photosynthetic tissues of plants and
is expressed in high levels in the roots of Medicago sativa L. How the β -amylase gene MsBAM1 is regulated in
the roots is not clear. The aims of this study were to: isolate the core promoter of MsBAM1, decipher motifs in silico
that are associated with the elevated root specific response, and to find common motifs among core promoters
of important starch degradation genes in Medicago sativa MsBAM1 and Arabidopsis (AtGWD, AtPWD, AtMEX1,
AtBAM 1 & 3, and AtISA3). Primers were designed from homologous β-amylase genes and used in PCR with
M. sativa gDNA. Gel purified PCR band(s) were sequenced, verified and annotated. The starch genes and equal
numbers of Arabidopsis non-starch genes promoters were analyzed by the transcription factor binding site database
(PLACE). Motif frequencies between starch and non-starch genes were statistically analyzed. A TATA-box motif
was identified in the MsBAM1 core promoter. Chi-square and Fisher’s exact test analyses revealed significance of
the frequency of the motifs ROOTMOTIFTAPOX1 (RMP1) and GATABOX (GATA) between starch and non-starch
genes, but not the DOF motif. The RMP1 and GATA motifs were detected in MsBAM1 and in all the Arabidopsis
starch degradation genes but only in a few of the non-starch genes. However, the DOF motif was found in all starch
and non-starch degradation genes in similar frequencies. These motifs may work in combination with other known
cis-regulatory elements to confer root-enhanced expression in alfalfa roots and co-transcriptional regulation in the
starch degradation pathway