Genome-Wide Analysis of Gene Expression Profiles Associated with Cell Cycle Transitions in Growing Organs of Arabidopsis

Abstract

Organ growth results from the progression of component cells through subsequent phases of proliferation and expansion before reaching maturity. We combined kinematic analysis, flowcytometry, and microarray analysis to characterize cell cycle regulation during the growth process of leaves 1 and 2 of Arabidopsis (Arabidopsis thaliana). Kinematic analysis showed that the epidermis proliferates until day 12; thereafter, cells expand until day 19 when leaves reach maturity. Flowcytometry revealed that endoreduplication occurs from the time cell division rates decline until the end of cell expansion. Analysis of 10 time points with a 6k-cDNA microarray showed that transitions between the growth stages were closely reflected in the mRNA expression data. Subsequent genome-wide microarray analysis on the three main stages allowed us to categorize known cell cycle genes into three major classes: constitutively expressed, proliferative, and inhibitory. Comparison with published expression data obtained from root zones corresponding to similar developmental stages and from synchronized cell cultures supported this categorization and enabled us to identify a high confidence set of 131 proliferation genes. Most of those had an M phase-dependent expression pattern and, in addition to many known cell cycle-related genes, there were at least 90 that were unknown or previously not associated with proliferation.

TheArabidopsis thalianaHomolog of YeastBRE1Has a Function in Cell Cycle Regulation during Early Leaf and Root Growth

“…A search in Gene Atlas and Gene Chronologer of GENEVESTI-GATOR also showed expression of HUB1 (266817_at and 266818_at probe sets) and HUB2 (259652_at and 259662_at probe sets) in all tissues and developmental stages (Zimmermann et al, 2004). According to a microarray analysis of leaf development (Beemster et al, 2005), the HUB1 and HUB2 genes were constitutively expressed during proliferation, expansion, and mature-stage phases of leaf and root development. Moreover, the expression level of both genes remained constant throughout the cell cycle (Menges et al, 2005).…”

“…In hub1-1, a proportion of cells exited the mitotic cycle very early; however, at the end of leaf development, 50% of the cells still remained with a 2C/4C content, suggesting that not all cells were stimulated to endoreduplicate. In wild-type leaves, the endoreduplication process starts after cessation of the mitotic cycle and when cells enter into the differentiation phase (Beemster et al, 2005). During development, a block of the G2-to-M transition may also result in an increased endoreduplication.…”

“…To examine the changes in cell division and expansion underlying the growth phenotype, we performed a kinematic analysis (Beemster et al, 2005) on epidermal cells of leaves 1 and 2 of in vitro-grown mutant and wild-type plants. Five days after sowing (DAS), leaf blade area and epidermal cell number were similar in Ler and hub1-1 ( Figures 3B and 3C), but both parameters increased more slowly in hub1-1 than in Ler between 5 to 10 DAS, ultimately resulting in a reduced leaf size (47%) and number of epidermal cells (48%) in hub1-1 leaves by day 18, when the growth phase ended in both lines.…”

“…The flow cytometry and the kinematic analyses of leaf growth were performed on plants grown in vitro as described by Beemster et al (2005). Two biological and three technical replicates were used at each time point for flow cytometry measurement on first leaves, hypocotyls, and roots.…”

DELLA Signaling Mediates Stress-Induced Cell Differentiation in Arabidopsis Leaves through Modulation of Anaphase-Promoting Complex/Cyclosome Activity

“…Initially, all cells in the leaf primordium are dividing, but later in development, cell division ceases from the tip to the base of the leaf, resulting in a cell cycle arrest front moving across the leaf (Donnelly et al, 1999;Kazama et al, 2010;Andriankaja et al, 2012). This transition from cell proliferation to cell expansion is accompanied by a switch from the mitotic cell cycle to endoreduplication, during which the genome is replicated, but mitosis does not occur, leading to cells with higher ploidy levels (Beemster et al, 2005). The current view is that this developmental transition from mitosis to endocycle, or mitotic exit, is triggered by a decrease in mitotic (B-type) cyclindependent kinase (CDK) activity (De Veylder et al, 2007;Breuer et al, 2010).…”