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Published on June 7, 2007; 10.1104/pp.107.101105

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Received April 16, 2007
Accepted May 29, 2007

Genome-wide Analysis of the Core DNA Replication Machinery in the Higher Plants Arabidopsis and Oryza sativa

Randall W. Shultz , Vinaya M. Tatineni , Linda Hanley-Bowdoin *, and William F. Thompson

Department of Plant Biology; Department of Statistical Genetics and Bioinformatics; Department of Molecular and Structural Biochemistry; North Carolina State University, Raleigh, NC, USA

Core DNA replication proteins mediate the initiation, elongation and Okazaki fragment maturation functions of DNA replication. Although this process is generally conserved in eukaryotes, important differences in the molecular architecture of the DNA replication machine and the function of individual subunits have been reported in various model systems. We have combined genome-wide bioinformatic analyses of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) with published experimental data to provide a comprehensive view of the core DNA replication machinery in plants. Many components identified in this analysis have not been studied previously in plant systems, including the GINS complex (PSF1, PSF2, PSF3 and SLD5), MCM8, MCM9, MCM10, NOC3, POLA2, POLA3, POLA4, POLD3, POLD4, and RNASEH2. Our results indicate that the core DNA replication machinery from plants is more similar to vertebrates than single-celled yeasts, suggesting that animal models may be more relevant to plant systems. However, we also uncovered some important differences between plants and vertebrate machinery. For example, we did not identify geminin or RNASEH1 genes in plants. Our analyses also indicate that plants may be unique among eukaryotes in that they have multiple copies of numerous core DNA replication genes. This finding raises the question of whether specialized functions have evolved in some cases. This analysis establishes that the core DNA replication machinery is highly conserved across plant species and displays many features in common with other eukaryotes and some characteristics that are unique to plants.




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