Abstract
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 (go ichi ni san) 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 (Saccharomyces cerevisiae), 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.
Highlights
Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication
To identify the core DNA replication genes in Arabidopsis and rice, we developed an approach that incorporated experimental data from the literature with homology-based computational gene annotation
The BLAST algorithm was used to search against the translated Arabidopsis genome database at The Arabidopsis Information Resource (TAIR), and sequences with significant similarity were assigned putative annotations based on their functions in yeast and animal systems
Summary
Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication. 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. Our analyses 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. A detailed understanding of the core DNA replication machinery in plants will provide researchers with an important tool for understanding what makes plants unique with respect to replicative and developmental capacity and for investigating how plant strategies compare to the mechanisms employed by animals
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