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Short dispersed repeats in the Chlamydomonas chloroplast genome are collocated with sites for mRNA 3′ end formation

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Abstract

The Chlamydomonas reinhardtii chloroplast genome possesses thousands of small dispersed repeats (SDRs), which are of unknown function. Here, we used the petA gene as a model to investigate the role of SDRs in mRNA 3′ end formation. In wild-type cells, petA mRNA accumulated as a major 1.3-kb transcript, whose 3′ end was mapped to the distal end of a predicted stem-loop structure. To determine whether this stem-loop was required for petA mRNA stability, a series of deletions was constructed. These deletion strains accumulated a variety of petA mRNAs, for which approximate 3′ ends were deduced. These 3′ ends were found to flank stem-loop structures, many of which were formed partially or completely from inverted copies of SDRs. All strains accumulated wild-type levels of cytochrome f, demonstrating that alternative 3′ termini are compatible with efficient translation. The ability to form alternative mRNA termini using SDRs lends additional flexibility to the chloroplast gene expression apparatus and thus could confer an evolutionary advantage.

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Acknowledgements

We thank Linda Rymarquis and Katia Wostrikoff for their assistance in RNA and protein analysis, Elise Kikis in preparing PCR probes for S1 protection, and Jude Maul for SDR analysis. This work was supported by National Science Foundation award MCB 0091020 to D.B.S., with early experiments supported by a Georges Morel Prize and Guggenheim Fellowship awarded to D.B.S. That phase of the work was carried out in the laboratory of Francis-André Wollman, Institut de Biochimie Physico-Chimique, Paris, where D.B.S. was a sabbatical visitor. We thank all members of that laboratory for their interest and support. C.L.S. was supported by an Olin Graduate Fellowship.

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  1. Amanda Hicks

    Present address: National College of Naturopathic Medicine, Portland, Oregon, USA

  2. Clare Simpson

    Present address: Carnegie Institute Washington, Stanford University, Stanford, CA 94305, USA

Authors and Affiliations

  1. Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY 14853, USA

    Henry S. Jiao, Amanda Hicks, Clare Simpson & David B. Stern

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  1. Henry S. Jiao
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Correspondence to David B. Stern.

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Communicated by F.-A. Wollman

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Jiao, H.S., Hicks, A., Simpson, C. et al. Short dispersed repeats in the Chlamydomonas chloroplast genome are collocated with sites for mRNA 3′ end formation. Curr Genet 45, 311–322 (2004). https://doi.org/10.1007/s00294-004-0487-7

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