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Multiple promoters are a common feature of mitochondrial genes in Arabidopsis

Oxford University Press
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gki179 337..346 Multiple promoters are a common feature of mitochondrial genes in Arabidopsis Kristina K€uuhn, Andreas Weihe and Thomas Bo¨rner* Institut f€uur Biologie/Genetik, Humboldt-Universita¨t zu Berlin, Chausseestr. 117, D-10115 Berlin, Germany Received November 15, 2004; Revised and Accepted December 20, 2004 ABSTRACT Mitochondrial genes in the plant Arabidopsis thaliana are transcribed by two phage-type RNA polymerases encoded in the nucleus. Little is known about cis- elements that are recognized by these enzymes and mediate the transcription of the Arabidopsis mito- chondrial genome. Here, 30 transcription initiation sites of 12 mitochondrial genes and gene clusters have been determined using 50-RACE and ribo- nuclease protection analysis of primary transcripts labelled in vitro by guanylyltransferase. A total of 9 out of 12 genes were found to possess multiple pro- moters, revealing for the first time that multiple pro- moters are a common feature of mitochondrial genes in a dicotyledonous plant. No differences in promoter utilization were observed between leaves and flowers, suggesting that promoter multiplicity reflects a relaxed promoter specificity rather than a regulatory role of promoter selection. Nearly half the identified transcription initiation sites displayed immediately upstream a CRTA core sequence, which was mostly seen within the previously described CRTAAGAGA promoter motif or a novel CGTATATAA promoter ele- ment. About as many promoters possessed an ATTA or RGTA core. Our data indicate that the majority of mitochondrial promoters in Arabidopsis deviate significantly from the nonanucleotide consensus derived earlier for dicot mitochondrial promoters. INTRODUCTION Plant mitochondrial genomes considerably vary in size but contain a fairly stable number of 50–60 genes (1–4). These may be dispersed or organized in gene clusters and pre- dominantly encode components of the respiratory chain and of the translational apparatus. The machinery that transcribes t

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