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Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf

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Abstract

Rice (Oryza sativa L.) as a model and crop plant with a sequenced genome offers an outstanding experimental system for discovering and functionally analyzing the major cell cycle control elements in a cereal species. In this study, we identified the core cell cycle genes in the rice genome through a hidden Markov model search and multiple alignments supported with the use of short protein sequence probes. In total we present 55 rice putative cell cycle genes with locus identity, chromosomal location, approximate chromosome position and EST accession number. These cell cycle genes include nine cyclin dependent-kinase (CDK) genes, 27 cyclin genes, one CKS gene, two RBR genes, nine E2F/DP/DEL genes, six KRP genes, and one WEE gene. We also provide characteristic protein sequence signatures encoded by CDK and cyclin gene variants. Promoter analysis by the FootPrinter program discovered several motifs in the regulatory region of the core cell cycle genes. As a first step towards functional characterization we performed transcript analysis by RT-PCR to determine gene specific variation in transcript levels along the rice leaves. The meristematic zone of the leaves where cells are actively dividing was identified based on kinematic analysis and flow cytometry. As expected, expression of the majority of cell cycle genes was exclusively associated with the meristematic region. However genes such as different D-type cyclins, DEL1, KRP1/3, and RBR2 were also expressed in leaf segments representing the transition zone in which cells start differentiation.

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Acknowledgments

The authors would like to thank Wim Van Caeneghem for skillful advice with real-time PCR analysis, Klaas Vandepoele for assistance in the annotation process of the rice cell cycle genes, Yves van de Peer and the members of the Bioinformatics group for providing appropriate infrastructure for the annotation process. This work was partly supported by a grant from the Institute for the Promotion of Innovation by Science and Technology in Flanders (postdoctoral fellowship to R.M.B.), A.P-Sz was supported by OTKA-68896 and the János Bolyai Research Scholarship of the Hungarian Academy of Sciences.

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    1. Biological Research Center, HAS, Temesvári krt 62, Szeged, 6726, Hungary

      A. Pettkó-Szandtner, M. Cserháti & D. Dudits

    2. Nebraska Medical Center, Omaha, NE, 68198-5145, USA

      M. Cserháti

    3. Plant Systems Biology, VIB, Technologiepark 927, 9052, Zwijnaarde, Belgium

      A. Pettkó-Szandtner, M. Cserháti, R. M. Barrôco, S. Hariharan & G. T. S. Beemster

    4. Department of Biology, University of Antwerp, Antwerp, Belgium

      G. T. S. Beemster

    5. CropDesign N.V./BASF, Technologiepark 921C, 9052, Ghent, Zwijnaarde, Belgium

      R. M. Barrôco

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    Pettkó-Szandtner, A., Cserháti, M., Barrôco, R.M. et al. Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf. J Plant Res 128, 953–974 (2015). https://doi.org/10.1007/s10265-015-0754-3

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    • DOI: https://doi.org/10.1007/s10265-015-0754-3

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