Cell cycle regulation is of pivotal importance for plant growth and development. Although plant cell division shares basic mechanisms with all eukaryotes, plants have evolved novel molecules orchestrating the cell cycle. Some regulatory proteins, such as cyclins and inhibitors of cyclin-dependent kinases, are particularly numerous in plants, possibly reflecting the remarkable ability of plants to modulate their postembryonic development. Many plant cells also can continue DNA replication in the absence of mitosis, a process known as endoreduplication, causing polyploidy. Here, we review the molecular mechanisms that regulate cell division and endoreduplication and we discuss our understanding, albeit very limited, on how the cell cycle is integrated with plant development.

We provide a comprehensive expression map of the different genes (TIR1/AFBs, ARFs and Aux/IAAs) involved in the signalling pathway regulating gene transcription in response to auxin in the shoot apical meristem (SAM).We demonstrate a relatively simple structure of this pathway using a high-throughput yeast two-hybrid approach to obtain the Aux/IAA-ARF full interactome.The topology of the signalling network was used to construct a model for auxin signalling and to predict a role for the spatial regulation of auxin signalling in patterning of the SAM.We used a new sensor to monitor the input in the auxin signalling pathway and to confirm the model prediction, thus demonstrating that auxin signalling is essential to create robust patterns at the SAM.

Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was applied to determine the core cell cycle genes in the recently completed Arabidopsis genome sequence. In total, 61 genes were identified belonging to seven selected families of cell cycle regulators, for which 30 are new or corrections of the existing annotation. A new class of putative cell cycle regulators was found that probably are competitors of E2F/DP transcription factors, which mediate the G1-to-S progression. In addition, the existing nomenclature for cell cycle genes of Arabidopsis was updated, and the physical positions of all genes were compared with segmentally duplicated blocks in the genome, showing that 22 core cell cycle genes emerged through block duplications. This genome-wide analysis illustrates the complexity of the plant cell cycle machinery and provides a tool for elucidating the function of new family members in the future. INTRODUCTIONCell proliferation is controlled by a universally conserved molecular machinery in which the core key players are Ser/ Thr kinases, known as cyclin-dependent kinases (CDKs). CDK activity is regulated in a complex manner, including phosphorylation/dephosphorylation by specific kinases/phosphatases and association with regulatory proteins. Although many cell cycle genes of plants have been identified in the last decade (for review, see Stals and Inzé, 2001), the correct number of CDKs, cyclins, and interacting proteins with a role in cell cycle control is unknown. Now that the complete sequence of the nuclear genome of Arabidopsis is available (Arabidopsis Genome Initiative, 2000), it is possible to scan an entire plant genome for all of these core cell cycle genes and determine their numbers, positions on the chromosomes, and phylogenetic relationships. From an evolutionary point of view, this core cell cycle gene catalog would be extremely interesting because it allows us to determine which processes are specific to plants and which are conserved among all eukaryotes. Furthermore, there is a unique opportunity to unravel in future experiments the functions and interactions of newly found family members of primary cell cycle regulators, thus expanding our knowledge of how the cell cycle is regulated in plants.Nevertheless, a genome-wide inventory of all core cell cycle genes is possible only when the available raw sequence data are annotated correctly. Although genome-wide annotations of organisms sequenced by large consortia have produced huge amounts of information that benefits the scientific community, this automated high-throughput annotation is far from optimal (Devos and Valencia, 2001). For this reason, it is not easy to extract clear biological information from these public databases. When high-quality annotation is needed, a supervised semiautomatic annotation may be a good compromise between quality and speed.Generally, annotation is performed in two...