Genome-wide analysis of gene expression profiles associated with cell cycle transitions in growing organs of Arabidopsis

Control of division and differentiation of plant stem cells and their derivatives

The core mechanism of the plant cell cycle is conserved with all other eukaryotes but several aspects are unique to plant cells. Key characteristics of plant development include indeterminate growth and repetitive organogenesis derived from stem cell pools and they may explain the existence of the high number of cell cycle regulators in plants. In this review, we give an overview of the plant cell cycle and its regulatory components. Furthermore, we discuss the cell cycle aspects of plant stem cell maintenance and how the cell cycle relates to cellular differentiation during development. We exemplify this transition by focusing on organ initiation in the shoot.

Multi-scale phenotyping of leaf expansion in response to environmental changes: the whole is more than the sum of parts

The leaf is a multi-scale dynamic unit that is determined by mechanisms at different organizational scales (cell, tissue, whole leaf and whole plant) and affected by both internal (genotype) and external (environmental) determinisms. The recent development of phenotyping platforms and imaging techniques provides new insights into the temporal and spatial patterns of leaf growth as affected by those determinisms. Conclusions about the overriding mechanisms often depend on the considered organizational scale and of time resolution which varies from minutes to several weeks. Analyses of leaf growth responses to environmental conditions have revealed robust emerging properties at whole plant or whole leaf scales. They have highlighted that the control of individual leaf expansion is more complex than merely the sum of cellular processes, and the control at the whole plant level is more complex than the sum of individual leaf expansions. However, in many cases, the integrated leaf-growth variable can be simplified to a limited set of underlying variables to be measured for comparative analyses of leaf growth or modelling purposes.

Effects of phenylcarboxylic acids on mitosis, endoreduplication and expression of cell cycle-related genes in roots of cucumber (Cucumis sativus L.)

Several benzoic and cinnamic acid derivatives were identified from cucumber root exudates. The effects of these phenylcarboxylic acids on root growth and cell cycle progression were examined in germinated seeds of cucumber. All 12 phenylcarboxylic acids (0.25 mM) tested significantly inhibited cucumber radicle growth, and cinnamic acid exerted a dose-dependent inhibitory effect. At 6 h after exposure to the acids, transcript levels of the cell cycle-related genes, including two cyclin-dependent kinases (CDKs) and four cyclins were reduced. Among them, transcript of CycB, a marker gene for mitosis showed a remarkable reduction. The temporal analysis showed that expression of mitotic genes (CDKB, CycA, and CycB) were reduced throughout the experiment, while the reduction of the other genes (CDKA, CycD3;1, and CycD3;2) were observed only at earlier time points. At 48 h after treatment with benzoic and cinnamic acids, an enhancement of endoreduplication was observed. Further time course analysis indicated that endoreduplication started as early as 6 h after exposure to cinnamic acid. These results provide evidence that exposure to benzoic and cinnamic acids can induce rapid and dramatic down-regulation of cell cycle-related genes, thus leading to root growth inhibition. Meanwhile, the block of mitosis caused by phenylcarboxylic acids also induced an increased level of endoreduplication.

Differential expression of the CBF pathway and cell cycle-related genes in Arabidopsis accessions in response to chronic low-temperature exposure

Low, non-freezing temperatures are a major factor limiting growth and development of vegetation in cold climates. Activation of the C-repeat binding factor (CBF) regulatory pathway by acute cold treatment is important for cold acclimation and freezing tolerance in Arabidopsis thaliana; however, the potential role of this pathway in response to chronic cold treatment has been less well characterised. We studied long-term (chronic) effects of low, non-freezing temperatures on the expression of CBF pathway genes (CBF2/3, COR15a, RD29A) and cell cycle-related genes (CDKA;1, CYCD2;1, CYCB1;1) in roots of accessions from habitats differing in growing season temperatures. Elongation rates of primary roots at 21 and 10 degrees C were not significantly correlated with average growing season temperatures, indicating that there is no ecotypic differentiation for these traits. Measurements of mRNA accumulation in roots of seven accessions showed that expression of CBF2/3, COR15a and RD29A is induced by both acute cold treatment (2-24 h at 4 degrees C) and chronic cold treatment (5-6 weeks at 10 degrees C), while CYCB1;1 is only induced by chronic cold treatment. RD29A and COR15a mRNA levels were correlated (P < 0.05) with the rate of root elongation in the cold for three high-altitude accessions relative to the common laboratory stain, Col-0. Our results are consistent with the hypothesis that induction of CBF2/3, COR15a, RD29A and CYCB1;1 is a physiological response to cold that, in the case of RD29A and COR15a, may be important for root growth at low temperatures.

The Arabidopsis cell division cycle

Plant cells have evolved a complex circuitry to regulate cell division. In many aspects, the plant cell cycle follows a basic strategy similar to other eukaryotes. However, several key issues are unique to plant cells. In this chapter, both the conserved and unique cellular and molecular properties of the plant cell cycle are reviewed. In addition to division of individual cells, the specific characteristic of plant organogenesis and development make that cell proliferation control is of primary importance during development. Therefore, special attention should be given to consider plant cell division control in a developmental context. Proper organogenesis depends on the formation of different cell types. In plants, many of the processes leading to cell differentiation rely on the occurrence of a different cycle, termed the endoreplication cycle, whereby cells undergo repeated full genome duplication events in the absence of mitosis and increase their ploidy. Recent findings are focusing on the relevance of changes in chromatin organization for a correct cell cycle progression and, conversely, in the relevance of a correct functioning of chromatin remodelling complexes to prevent alterations in both the cell cycle and the endocycle.

DNA stress checkpoint control and plant development

Plants are sedentary, and so have unavoidably close contact with agents that target their genome integrity. To sense and react to these threats, plants have evolved DNA stress checkpoint mechanisms that arrest the cell cycle and activate the DNA repair machinery to preserve the genome content. Although the pathways that maintain DNA integrity are largely conserved among eukaryotic organisms, plants put different accents on cell cycle control under DNA stress and might have their own way to cope with it.

FZR2/CCS52A1 expression is a determinant of endoreduplication and cell expansion in Arabidopsis

Endoreduplication, a modified cell cycle that allows cells to increase ploidy without subsequent cell division, is a key component of plant growth and development. In this work, we show that some, but not all, of the endoreduplication of Arabidopsis (Arabidopsis thaliana) is mediated by the expression of a WD40 gene, FIZZY-RELATED2 (FZR2). Loss-of-function alleles show reduced endoreduplication and reduced expansion in trichomes and other leaf cells. Misexpression of FZR2 is sufficient to drive ectopic or extra endoreduplication in leaves, roots, and flowers, leading to alteration of cell sizes and, sometimes, organ size and shape. Our data, which suggest that reduced cell size can be compensated by increased cell proliferation to allow normal leaf morphology, are discussed with respect to the so-called compensation mechanism of plant development.

Environmental effects on spatial and temporal patterns of leaf and root growth

Leaves and roots live in dramatically different habitats, but are parts of the same organism. Automated image processing of time-lapse records of these organs has led to understanding of spatial and temporal patterns of growth on time scales from minutes to weeks. Growth zones in roots and leaves show distinct patterns during a diel cycle (24 h period). In dicot leaves under nonstressful conditions these patterns are characterized by endogenous rhythms, sometimes superimposed upon morphogenesis driven by environmental variation. In roots and monocot leaves the growth patterns depend more strongly on environmental fluctuations. Because the impact of spatial variations and temporal fluctuations of above- and belowground environmental parameters must be processed by the plant body as an entire system whose individual modules interact on different levels, growth reactions of individual modules are often highly nonlinear. A mechanistic understanding of plant resource use efficiency and performance in a dynamically fluctuating environment therefore requires an accurate analysis of leaf and root growth patterns in conjunction with knowledge of major intraplant communication systems and metabolic pathways.

The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana

In contrast to animal growth, plant growth is largely post-embryonic. Therefore plants have developed new mechanisms to precisely regulate cell proliferation by means of internal and external stimuli whilst the general core cell cycle machinery is conserved between eukaryotes. In this work we demonstrate a role for the Arabidopsis thaliana DNA-binding-with-one-finger (DOF) transcription factor OBP1 in the control of cell division upon developmental signalling. Inducible overexpression of OBP1 resulted in a significant overrepresentation of cell cycle genes among the upregulated transcripts. Direct targets of OBP1, as verified by chromatin immunoprecipitation, include at least the core cell cycle gene CYCD3;3 and the replication-specific transcription factor gene AtDOF2;3. Consistent with our molecular data, short-term activation of OBP1 in cell cultures affected cell cycle re-entry, shortening the duration of the G(1) phase and the overall length of the cell cycle, whilst constitutive overexpression of OBP1 in plants influenced cell size and cell number, leading to a dwarfish phenotype. Expression during embryogenesis, germination and lateral root initiation suggests an important role for OBP1 in cell cycle re-entry, operating as a transcriptional regulator of key cell cycle genes. Our findings provide significant input into our understanding of how cell cycle activity is incorporated into plant growth and development.

New clues to organ size control in plants

A review of the mechanisms that control organ size in plants.

Plant growth has unparalleled importance for human civilization, yet we are only starting to gain an understanding of its mechanisms. The growth rate and final size of plant organs is determined by both genetic constraints and environmental factors. Regulatory inputs act at two control points: on proliferation; and on the transition between proliferation and differentiation. Cell-autonomous and short-range growth signals act within meristematic domains, whereas diffusible signals from differentiated parts to proliferating cells provide measures of geometry and size and channel environmental inputs.

ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription

In multicellular organisms, organogenesis requires a tight control of the balance between cell division and cell differentiation. Distinct signalling pathways that connect both cellular processes with developmental cues might have evolved to suit different developmental plans. Here, we identified and characterized a novel protein that interacts with pre-replication complex (pre-RC) subunits, designated Armadillo BTB Arabidopsis protein 1 (ABAP1). Overexpression of ABAP1 in plants limited mitotic DNA replication and decreased cell proliferation in leaves, whereas ABAP1 downregulation increased cell division rates. Activity of ABAP1 in transcription was supported by its association with the transcription factor AtTCP24. The ABAP1-AtTCP24 complex bound specifically to the promoters of AtCDT1a and AtCDT1b in vitro and in vivo. Moreover, expression levels of AtCDT1a and AtCDT1b were reduced in ABAP1-overexpressing plants and they were increased in plants with reduced levels of ABAP1. We propose that ABAP1 participates in a negative feedback loop regulating mitotic DNA replication during leaf development, either by repressing transcription of pre-RC genes and possibly by regulating pre-RC utilization through direct association with pre-RC components.

Atypical E2F activity restrains APC/CCCS52A2 function obligatory for endocycle onset

The endocycle represents an alternative cell cycle that is activated in various developmental processes, including placental formation, Drosophila oogenesis, and leaf development. In endocycling cells, mitotic cell cycle exit is followed by successive doublings of the DNA content, resulting in polyploidy. The timing of endocycle onset is crucial for correct development, because polyploidization is linked with cessation of cell division and initiation of terminal differentiation. The anaphase-promoting complex/cyclosome (APC/C) activator genes CDH1, FZR, and CCS52 are known to promote endocycle onset in human, Drosophila, and Medicago species cells, respectively; however, the genetic pathways governing development-dependent APC/C(CDH1/FZR/CCS52) activity remain unknown. We report that the atypical E2F transcription factor E2Fe/DEL1 controls the expression of the CDH1/FZR orthologous CCS52A2 gene from Arabidopsis thaliana. E2Fe/DEL1 misregulation resulted in untimely CCS52A2 transcription, affecting the timing of endocycle onset. Correspondingly, ectopic CCS52A2 expression drove cells into the endocycle prematurely. Dynamic simulation illustrated that E2Fe/DEL1 accounted for the onset of the endocycle by regulating the temporal expression of CCS52A2 during the cell cycle in a development-dependent manner. Analogously, the atypical mammalian E2F7 protein was associated with the promoter of the APC/C-activating CDH1 gene, indicating that the transcriptional control of APC/C activator genes by atypical E2Fs might be evolutionarily conserved.

Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection

Geminiviruses are small DNA viruses that use plant replication machinery to amplify their genomes. Microarray analysis of the Arabidopsis (Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection uncovered 5,365 genes (false discovery rate <0.005) differentially expressed in infected rosette leaves at 12 d postinoculation. Data mining revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and induces expression of genes involved in programmed cell death, genotoxic stress, and DNA repair. CaLCuV also altered expression of cell cycle-associated genes, preferentially activating genes expressed during S and G2 and inhibiting genes active in G1 and M. A limited set of core cell cycle genes associated with cell cycle reentry, late G1, S, and early G2 had increased RNA levels, while core cell cycle genes linked to early G1 and late G2 had reduced transcripts. Fluorescence-activated cell sorting of nuclei from infected leaves revealed a depletion of the 4C population and an increase in 8C, 16C, and 32C nuclei. Infectivity studies of transgenic Arabidopsis showed that overexpression of CYCD3;1 or E2FB, both of which promote the mitotic cell cycle, strongly impaired CaLCuV infection. In contrast, overexpression of E2FA or E2FC, which can facilitate the endocycle, had no apparent effect. These results showed that geminiviruses and RNA viruses interface with the host pathogen response via a common mechanism, and that geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastoma-related protein/E2F regulatory network and facilitating progression into the endocycle.

The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1

Complete and accurate chromosomal DNA replication is essential for the maintenance of the genetic integrity of all organisms. Errors in replication are buffered by the activation of DNA stress checkpoints; however, in plants, the relative importance of a coordinated induction of DNA repair and cell cycle-arresting genes in the survival of replication mutants is unknown. In a systematic screen for Arabidopsis thaliana E2F target genes, the E2F TARGET GENE 1 (ETG1) was identified as a novel evolutionarily conserved replisome factor. ETG1 was associated with the minichromosome maintenance complex and was crucial for efficient DNA replication. Plants lacking the ETG1 gene had serrated leaves due to cell cycle inhibition triggered by the DNA replication checkpoints, as shown by the transcriptional induction of DNA stress checkpoint genes. The importance of checkpoint activation was highlighted by double mutant analysis: whereas etg1 mutant plants developed relatively normally, a synthetically lethal interaction was observed between etg1 and the checkpoint mutants wee1 and atr, demonstrating that activation of a G2 cell cycle checkpoint accounts for survival of ETG1-deficient plants.

Global expression profiling in leaves of free-growing aspen

BACKGROUND

Genomic studies are routinely performed on young plants in controlled environments which is very different from natural conditions. In reality plants in temperate countries are exposed to large fluctuations in environmental conditions, in the case of perennials over several years. We have studied gene expression in leaves of a free-growing aspen (Populus tremula) throughout multiple growing seasons

RESULTS

We show that gene expression during the first month of leaf development was largely determined by a developmental program although leaf expansion, chlorophyll accumulation and the speed of progression through this program was regulated by the temperature. We were also able to define "transcriptional signatures" for four different substages of leaf development. In mature leaves, weather factors were important for gene regulation.

CONCLUSION

This study shows that multivariate methods together with high throughput transcriptional methods in the field can provide additional, novel information as to plant status under changing environmental conditions that is impossible to mimic in laboratory conditions. We have generated a dataset that could be used to e.g. identify marker genes for certain developmental stages or treatments, as well as to assess natural variation in gene expression.

Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis

In darkness, shoot apex growth is repressed, but it becomes rapidly activated by light. We show that phytochromes and cryptochromes play largely redundant roles in this derepression in Arabidopsis thaliana. We examined the light activation of transcriptional changes in a finely resolved time course, comparing the shoot apex (meristem and leaf primordia) and the cotyledon and found >5700 differentially expressed genes. Early events specific to the shoot apices included the repression of genes for Really Interesting New Gene finger proteins and basic domain/leucine zipper and basic helix-loop-helix transcription factors. The downregulation of auxin and ethylene and the upregulation of cytokinin and gibberellin hormonal responses were also characteristic of shoot apices. In the apex, genes involved in ribosome biogenesis and protein translation were rapidly and synchronously induced, simultaneously with cell proliferation genes, preceding visible organ growth. Subsequently, the activation of signaling genes and transcriptional signatures of cell wall expansion, turgor generation, and plastid biogenesis were apparent. Furthermore, light regulates the forms and protein levels of two transcription factors with opposing functions in cell proliferation, E2FB and E2FC, through the Constitutively Photomorphogenic1 (COP1), COP9-Signalosome5, and Deetiolated1 light signaling molecules. These data provide the basis for reconstruction of the regulatory networks for light-regulated meristem, leaf, and cotyledon development.

Farnesylation directs AtIPT3 subcellular localization and modulates cytokinin biosynthesis in Arabidopsis

Cytokinins regulate cell division and differentiation as well as a number of other processes implicated in plant development. The first step of cytokinin biosynthesis in Arabidopsis (Arabidopsis thaliana) is catalyzed by adenosine phosphate-isopentenyltransferases (AtIPT). The enzymes are localized in plastids or the cytoplasm where they utilize the intermediate dimethylallyl-diphosphate from the methylerythritolphosphate or mevalonic acid pathways. However, the regulatory mechanisms linking AtIPT activity and cytokinin biosynthesis with cytokinin homeostasis and isoprenoid synthesis are not well understood. Here, we demonstrate that expression of AtIPT3, one member of the adenosine AtIPT protein family in Arabidopsis, increased the production of specific isopentenyl-type cytokinins. Moreover, AtIPT3 is a substrate of the protein farnesyl transferase, and AtIPT3 farnesylation directed the localization of the protein in the nucleus/cytoplasm, whereas the nonfarnesylated protein was located in the plastids. AtIPT3 gain-of-function mutant analysis indicated that the different subcellular localization of the farnesylated protein and the nonfarnesylated protein was closely correlated with either isopentenyl-type or zeatin-type cytokinin biosynthesis. In addition, mutation of the farnesyl acceptor cysteine-333 of AtIPT3 abolishes cytokinin production, suggesting that cysteine-333 has a dual and essential role for AtIPT3 farnesylation and catalytic activity.

Mitochondrial type-I prohibitins of Arabidopsis thaliana are required for supporting proficient meristem development

The Arabidopsis thaliana genome expresses five evolutionarily conserved prohibitin (PHB) genes that are divided into type-I (AtPHB3 and AtPHB4) and type-II (AtPHB1, AtPHB2 and AtPHB6) classes, based on their phylogenetic relationships with yeast PHB1 and PHB2, respectively. Yeast and animal PHBs are reported to have diverse roles in the cell cycle, mitochondrial electron transport, aging and apoptosis. All transcribed Arabidopsis PHB genes are primarily expressed in both shoot and root proliferative tissues, where they are present in mitochondrial multimeric complexes. Loss of function of the type-I AtPHB4 had no phenotypic effects, while loss of function of the homologous AtPHB3 caused mitochondrial swelling, decreased meristematic cell production, increased cell division time and reduced cell expansion rates, leading to severe growth retardation. Double knockout atphb3 atphb4 plants were not viable, but transgenic lines overexpressing AtPHB3 or AtPHB4 showed leaf shape aberrations and an increased shoot branching phenotype. Genome-wide microarray analysis revealed that both knockout and overexpression perturbations of AtPHB3 and AtPHB4 provoked an altered abundance of mitochondrial and stress-related transcripts. We propose that plant type-I PHBs take part in protein complexes that are necessary for proficient mitochondrial function or biogenesis, thereby supporting cell division and differentiation in apical tissues.

The ins and outs of the plant cell cycle

Plant growth and development are driven by the continuous generation of new cells. Whereas much has been learned at a molecular level about the mechanisms that orchestrate progression through the different cell-cycle phases, little is known about how the cell-cycle machinery operates in the context of an entire plant and contributes to growth, cell differentiation and the formation of new tissues and organs. Here, we discuss how intrinsic developmental signals and environmental cues affect cell-cycle entry and exit.

Coordination of carbon supply and plant growth

Plants must achieve a balance between carbon assimilation, storage and growth, but little is known about how this is achieved. We describe evidence for the existence of regulatory mechanisms that coordinate carbon supply and use, and the likely central role of sugar signalling. We propose the existence of both 'acute' and 'acclimatory' responses to alterations in carbon supply, the latter tuning the balance between carbon supply and demand to optimise the capacity for sustained growth. A full understanding of these responses requires new, systems-level approaches that integrate information from transcriptomic, enzyme activity, metabolomic and growth analyses. We illustrate the complexity of acute and acclimatory responses by consideration of the control of starch synthesis and degradation in leaves. Finally, we consider how carbon balance may be linked to growth, and the importance of these linkages for sustained plant growth in a changing environment.

A molecular timetable for apical bud formation and dormancy induction in poplar

The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula x Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs.

Cytological investigations of the Arabidopsis thaliana elo1 mutant give new insights into leaf lateral growth and Elongator function

BACKGROUND AND AIMS

Leaf growth is a complex developmental process controlled by genetic and environmental factors and is determined by a proliferation, expansion and maturation phase. Mutational analysis in Arabidopsis thaliana showed that leaf size and shape is dependent on cell division and cell expansion activity. An investigation was made at the cytophysiological and ultrastructural level of the elo1 mutant of Arabidopsis thaliana, which is defective in one of the components of the histone acetyl transferase Elongator complex and displays a distinct 'narrow leaves' phenotype, owing to a reduced cell number and no transition between petiole and lamina. Relative expression levels of three sucrose metabolism/transport-related genes were also investigated. The aim was to determine the physiological basis of leaf morphology in this mutant, by investigating the modulatory role of sucrose.

METHODS

The elo1 mutant was taken as representative of all the elo mutations and investigated at cytophysiological level. A germination test and growth assays were performed on seedlings grown for 21 d at different sucrose concentrations. Leaf morphometric and ultrastructural features were also investigated by image analysis and electron microscopy, respectively. Finally, a quantitative PCR (qPCR) analysis was performed with three sucrose metabolism/transport-related genes that were investigated under different sucrose concentrations.

KEY RESULTS

elo1 plants at high sucrose concentrations exhibited an enhancement of germination and inhibition of leaf growth as compared with wild-type plants. qPCR experiments with three sucrose metabolism/transport-related genes showed an interaction between sucrose availability and the elo1 mutation. Furthermore, electron microscopy analysis provided the first ultrastructural description of an elo mutant, which showed a hypotonic vacuole, alterations in the size of grana and starch grains in the chloroplasts, and the massive presence of Golgi vesicles in the cytoplasm.

CONCLUSIONS

Based on the results obtained it is proposed that mechanisms producing carbon assimilates or importing sucrose could be affected in elo1 plants and could account for the observed differences, implying a role for Elongator in the regulation of these processes.

Actin-related proteins in chromatin-level control of the cell cycle and developmental transitions

Regulating developmental transitions, cell proliferation and cell death through differential gene expression is essential to the ontogeny of all multicellular organisms. Chromatin remodeling is an active process that is necessary for managing the genome-wide suppression of gene activities resulting from DNA compaction. Recent data in plants suggest a general theme, whereby chromatin remodeling complexes containing nuclear actin-related proteins (ARPs) potentiate the activities of crucial regulatory genes involved in plant growth and development, in addition to their basal activities on a much larger set of genes.

Genome-wide identification and expression analysis of rice cell cycle genes

Cyclins, cyclin-dependent kinases, and a number of other proteins control the progression of plant cell cycle. Although extensive studies have revealed the roles of some cell cycle regulators and the underlying mechanisms in Arabidopsis, relatively a small number of cell cycle regulators were functionally analyzed in rice. In this study, we describe 41 regulators in the rice genome. Our results indicate that the rice genome contains a less number of the core cell cycle regulators than the Arabidopsis one does, although the rice genome is much larger than the Arabidopsis one. Eight groups of CDKs similar to those in Arabidopsis were identified in the rice genome through phylogenetic analysis, and the corresponding members in the different groups include E2F, CKI, Rb, CKS and Wee. The structures of the core cell regulators were relatively conserved between the rice and Arabidopsis genomes. Furthermore, the expression of the majority of the core cell cycle genes was spatially regulated, and the most closely related ones showed very similar patterns of expression, suggesting functional redundancy and conservation between the highly similar core cell cycle genes in rice and Arabidopsis. Following auxin or cytokinin treatment, the expression of the core cell cycle genes was either upregulated or downregulated, suggesting that auxin and/or cytokinin may directly regulate the expression of the core cell cycle genes. Our results provide basic information to understand the mechanism of cell cycle regulation and the functions of the rice cell cycle genes.

Analysis of leaf development in fugu mutants of Arabidopsis reveals three compensation modes that modulate cell expansion in determinate organs

In multicellular organisms, the coordination of cell proliferation and expansion is fundamental for proper organogenesis, yet the molecular mechanisms involved in this coordination are largely unexplored. In plant leaves, the existence of this coordination is suggested by compensation, in which a decrease in cell number triggers an increase in mature cell size. To elucidate the mechanisms of compensation, we isolated five new Arabidopsis (Arabidopsis thaliana) mutants (fugu1-fugu5) that exhibit compensation. These mutants were characterized together with angustifolia3 (an3), erecta (er), and a KIP-RELATED PROTEIN2 (KRP2) overexpressor, which were previously reported to exhibit compensation. Time-course analyses of leaf development revealed that enhanced cell expansion in fugu2-1, fugu5-1, an3-4, and er-102 mutants is induced postmitotically, indicating that cell enlargement is not caused by the uncoupling of cell division from cell growth. In each of the mutants, either the rate or duration of cell expansion was selectively enhanced. In contrast, we found that enhanced cell expansion in KRP2 overexpressor occurs during cell proliferation. We further demonstrated that enhanced cell expansion occurs in cotyledons with dynamics similar to that in leaves. In contrast, cell expansion was not enhanced in roots even though they exhibit decreased cell numbers. Thus, compensation was confirmed to occur preferentially in determinate organs. Flow cytometric analyses revealed that increases in ploidy level are not always required to trigger compensation, suggesting that compensation is only partially mediated by ploidy-dependent processes. Our results suggest that compensation reflects an organ-wide coordination of cell proliferation and expansion in determinate organs, and involves at least three different expansion pathways.

E2F regulates FASCIATA1, a chromatin assembly gene whose loss switches on the endocycle and activates gene expression by changing the epigenetic status

Maintenance of genome integrity depends on histone chaperone-mediated chromatin reorganization. DNA replication-associated nucleosome deposition relies on chromatin assembly factor-1 (CAF-1). Depletion of CAF-1 in human cells leads to cell death, whereas in Arabidopsis (Arabidopsis thaliana), where it is involved in heterochromatin compaction and homologous recombination, plants are viable. The mechanism that makes the lack of CAF-1 activity compatible with development is not known. Here, we show that the FASCIATA1 (FAS1) gene, which encodes the CAF-1 large subunit, is a target of E2F transcription factors. Mutational studies demonstrate that one of the two E2F binding sites in its promoter has an activator role, whereas the other has a repressor function. Loss of FAS1 results in reduced type A cyclin-dependent kinase activity, inhibits mitotic progression, and promotes a precocious and systemic switch to the endocycle program. Selective up-regulation of the expression of a subset of genes, including those involved in activation of the G2 DNA damage checkpoint, also occurs upon FAS1 loss. This activation is not the result of a global change in chromatin structure, but depends on selective epigenetic changes in histone acetylation and methylation within a small region in their promoters. This suggests that correct chromatin assembly during the S-phase is required to prevent unscheduled changes in the epigenetic marks of target genes. Interestingly, activation of the endocycle switch as well as introduction of activating histone marks in the same set of G2 checkpoint genes are detected upon treatment of wild-type plants with DNA-damaging treatments. Our results are consistent with a model in which defects in chromatin assembly during the S-phase and DNA damage signaling share part of a pathway, which ultimately leads to mitotic arrest and triggers the endocycle program. Together, this might be a bypass mechanism that makes development compatible with cell division arrest induced by DNA damage stress.

Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes

Low temperature inhibits the growth of maize (Zea mays) seedlings and limits yield under field conditions. To study the mechanism of cold-induced growth retardation, we exposed maize B73 seedlings to low night temperature (25 degrees C /4 degrees C, day/night) from germination until the completion of leaf 4 expansion. This treatment resulted in a 20% reduction in final leaf size compared to control conditions (25 degrees C/18 degrees C, day/night). A kinematic analysis of leaf growth rates in control and cold-treated leaves during daytime showed that cold nights affected both cell cycle time (+65%) and cell production (-22%). In contrast, the size of mature epidermal cells was unaffected. To analyze the effect on cell cycle progression at the molecular level, we identified through a bioinformatics approach a set of 43 cell cycle genes and analyzed their expression in proliferating, expanding, and mature cells of leaves exposed to either control or cold nights. This analysis showed that: (1) the majority of cell cycle genes had a consistent proliferation-specific expression pattern; and (2) the increased cell cycle time in the basal meristem of leaves exposed to cold nights was associated with differential expression of cell cycle inhibitors and with the concomitant down-regulation of positive regulators of cell division.

Transcriptional profiling of the Arabidopsis embryo

We have used laser-capture microdissection to isolate RNA from discrete tissues of globular, heart, and torpedo stage embryos of Arabidopsis (Arabidopsis thaliana). This was amplified and analyzed by DNA microarray using the Affymetrix ATH1 GeneChip, representing approximately 22,800 Arabidopsis genes. Cluster analysis showed that spatial differences in gene expression were less significant than temporal differences. Time course analysis reveals the dynamics and complexity of gene expression in both apical and basal domains of the developing embryo, with several classes of synexpressed genes identifiable. The transition from globular to heart stage is associated in particular with an up-regulation of genes involved in cell cycle control, transcriptional regulation, and energetics and metabolism. The transition from heart to torpedo stage is associated with a repression of cell cycle genes and an up-regulation of genes encoding storage proteins, and pathways of cell growth, energy, and metabolism. The torpedo stage embryo shows strong functional differentiation in the root and cotyledon, as inferred from the classes of genes expressed in these tissues. The time course of expression of the essential EMBRYO-DEFECTIVE genes shows that most are expressed at unchanging levels across all stages of embryogenesis. We show how identified genes can be used to generate cell type-specific markers and promoter activities for future application in cell biology.

The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth

Chromatin modification and transcriptional activation are novel roles for E3 ubiquitin ligase proteins that have been mainly associated with ubiquitin-dependent proteolysis. We identified HISTONE MONOUBIQUITINATION1 (HUB1) (and its homolog HUB2) in Arabidopsis thaliana as RING E3 ligase proteins with a function in organ growth. We show that HUB1 is a functional homolog of the human and yeast BRE1 proteins because it monoubiquitinated histone H2B in an in vitro assay. Hub knockdown mutants had pale leaf coloration, modified leaf shape, reduced rosette biomass, and inhibited primary root growth. One of the alleles had been designated previously as ang4-1. Kinematic analysis of leaf and root growth together with flow cytometry revealed defects in cell cycle activities. The hub1-1 (ang4-1) mutation increased cell cycle duration in young leaves and caused an early entry into the endocycles. Transcript profiling of shoot apical tissues of hub1-1 (ang4-1) indicated that key regulators of the G2-to-M transition were misexpressed. Based on the mutant characterization, we postulate that HUB1 mediates gene activation and cell cycle regulation probably through chromatin modifications.

The plant cell cycle--15 years on

The basic components of the plant cell cycle are G1 (postmitotic interphase), S-phase (DNA synthesis phase), G2 (premitotic interphase) and mitosis/cytokinesis. Proliferating cells are phosphoregulated by cyclin-dependent protein kinases (CDKs). Plant D-type cyclins are sensors of the G0 to G1 transition, and are also important for G2/M. At G1/S, the S-phase transcription factor, E2F, is released from inhibitory retinoblastoma protein. Negative regulation of G1 events is through KRPs (Kip-related proteins). Plant S-phase genes are similar to animal ones, but timing of expression can be different (e.g. CDC6 at the start of S-phase) and functional evidence is limited. At G2/M, A-type and the unique B-type CDKs when bound to A, B and D cyclins, drive cells into division; they are negatively regulated by ICK1/2 and perhaps also by WEE1 kinase. In Arabidopsis, a putative CDC25 lacks a regulatory domain. Mitosis depends on correct temporal activity of CDKs, Aurora kinases and anaphase promotion complex; CDK-cyclin B activity beyond metaphase is catastrophic. Endoreduplication (re-replication of DNA in the absence of mitosis) is characterized by E2F expression and down-regulation of mitotic cyclins. Some cell size data support, whilst others negate, the idea of cell size having an impact on development.

Spatio-temporal leaf growth patterns of Arabidopsis thaliana and evidence for sugar control of the diel leaf growth cycle

Leaf growth dynamics are driven by diel rhythms. The analysis of spatio-temporal leaf growth patterns in Arabidopsis thaliana wild type and mutants of interest is a promising approach to elucidate molecular mechanisms controlling growth. The diel availability of carbohydrates is thought to affect diel growth. A digital image sequence processing (DISP)-based noninvasive technique for visualizing and quantifying highly resolved spatio-temporal leaf growth was adapted for the model plant A. thaliana. Diel growth patterns were analysed for the wild type and for a mutant with altered diel carbohydrate metabolism. A. thaliana leaves showed highest relative growth rates (RGRs) at dawn and lowest RGRs at the beginning of the night. Along the lamina, a clear basipetal gradient of growth rate distribution was found, similar to that in many other dicotyledonous species. The starch-free 1 (stf1) mutant revealed changed temporal growth patterns with reduced nocturnal, and increased afternoon, growth activity. The established DISP technique is presented as a valuable tool to detect altered temporal growth patterns in A. thaliana mutants. Endogenous changes in the diel carbohydrate availability of the starch-free mutant clearly affected its diel growth rhythms.

Developmentally controlled farnesylation modulates AtNAP1;1 function in cell proliferation and cell expansion during Arabidopsis leaf development

In multicellular organisms, organogenesis requires tight control and coordination of cell proliferation, cell expansion, and cell differentiation. We have identified Arabidopsis (Arabidopsis thaliana) nucleosome assembly protein 1 (AtNAP1;1) as a component of a regulatory mechanism that connects cell proliferation to cell growth and expansion during Arabidopsis leaf development. Molecular, biochemical, and kinetic studies of AtNAP1;1 gain- or loss-of-function mutants indicate that AtNAP1;1 promotes cell proliferation or cell expansion in a developmental context and as a function of the farnesylation status of the protein. AtNAP1;1 was farnesylated and localized to the nucleus during the cell proliferation phase of leaf development when it promotes cell division. Later in leaf development, nonfarnesylated AtNAP1;1 accumulates in the cytoplasm when it promotes cell expansion. Ectopic expression of nonfarnesylated AtNAP1;1, which localized to the cytoplasm, disrupts this developmental program by promoting unscheduled cell expansion during the proliferation phase.

Plant endoplasmin supports the protein secretory pathway and has a role in proliferating tissues

Endoplasmin is a molecular chaperone of the heat-shock protein 90 class located in the endoplasmic reticulum and its activity is poorly characterized in plants. We assessed the ability of endoplasmin to alleviate stress via its transient overexpression in tobacco protoplasts treated with tunicamycin, an inhibitor of glycosylation and inducer of the unfolded protein response (UPR). Endoplasmin supported the secretion of a model secretory protein but was less effective than BiP, the endoplasmic reticulum member of the heat-shock protein 70 family. Consistently, immunoprecipitation experiments with in vivo radioactively labelled proteins using an antiserum prepared against Arabidopsis endoplasmin showed that a much smaller number of newly synthesized polypeptides associated with endoplasmin than with BiP. Synthesis of endoplasmin was enhanced by UPR inducers in tobacco seedlings but not protoplasts. As BiP synthesis was induced in both systems, we conclude that the UPR acts differently, at least in part, on the expression of the two chaperones. Endoplasmin was not detectable in extracts of leaves and stems of the Arabidopsis endoplasmin T-DNA insertion mutant shepherd. However, the chaperone is present, albeit at low levels, in shepherd mutant callus, mature roots and tunicamycin-treated seedlings, demonstrating that the mutation is leaky. Reduced endoplasmin in the shepherd mutant has no effect on BiP protein levels in callus or mature roots, leaves and stems, but is compensated by increased BiP in seedlings. This increase occurs in proliferating rather than expanding leaf cells, indicating an important role for endoplasmin in proliferating plant tissues.

BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways

The BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leaves.

Cell Cycle Regulation in Plant Development

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.

The cyclin-dependent kinase inhibitor Orysa;KRP1 plays an important role in seed development of rice

Kip-related proteins (KRPs) play a major role in the regulation of the plant cell cycle. We report the identification of five putative rice (Oryza sativa) proteins that share characteristic motifs with previously described plant KRPs. To investigate the function of KRPs in rice development, we generated transgenic plants overexpressing the Orysa;KRP1 gene. Phenotypic analysis revealed that overexpressed KRP1 reduced cell production during leaf development. The reduced cell production in the leaf meristem was partly compensated by an increased cell size, demonstrating the existence of a compensatory mechanism in monocot species by which growth rate is less reduced than cell production, through cell expansion. Furthermore, Orysa;KRP1 overexpression dramatically reduced seed filling. Sectioning through the overexpressed KRP1 seeds showed that KRP overproduction disturbed the production of endosperm cells. The decrease in the number of fully formed seeds was accompanied by a drop in the endoreduplication of endosperm cells, pointing toward a role of KRP1 in connecting endocycle with endosperm development. Also, spatial and temporal transcript detection in developing seeds suggests that Orysa;KRP1 plays an important role in the exit from the mitotic cell cycle during rice grain formation.

Cyclin-dependent kinase inhibitors in yeast, animals, and plants: a functional comparison

The cell cycle is remarkably conserved in yeast, animals, and plants and is controlled by cyclin-dependent kinases (CDKs). CDK activity can be inhibited by binding of CDK inhibitory proteins, designated CKIs. Numerous studies show that CKIs are essential in orchestrating eukaryotic cell proliferation and differentiation. In yeast, animals, and plants, CKIs act as regulators of the G1 checkpoint in response to environmental and developmental cues and assist during mitotic cell cycles by inhibiting CDK activity required to arrest mitosis. Furthermore, CKIs play an important role in regulating cell cycle exit that precedes differentiation and in promoting differentiation in cooperation with transcription factors. Moreover, CKIs are essential to control CDK activity in endocycling cells. So, in yeast, animals, and plants, CKIs share many functional similarities, but their functions are adapted toward the specific needs of the eukaryote.

Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development

Chromatin assembly factor CAF-1 facilitates the formation of nucleosomes on newly replicated DNA in vitro. However, the role of CAF-1 in development is poorly understood because mutants are not available in most multicellular model organisms. Biochemical evidence suggests that FASCIATA1, FASCIATA2 and MSI1 form CAF-1 in Arabidopsis thaliana. Because fasciata mutants are viable, CAF-1 is not essential for cell division in plants. Arabidopsis CAF-1 mutants have defects in shoot apical meristems; in addition, CAF-1 is required to establish seedling architecture, leaf size and trichome differentiation. CAF-1 is needed to restrict branching of trichomes on rosette leaves. Increased trichome branching in CAF-1 mutants is not strictly correlated with increased nuclear DNA content. In addition, fas2 glabra3 double mutants show an additive genetic interaction, demonstrating that CAF-1 acts genetically parallel to the GLABRA3-containing, endoreduplication-coupled trichome branching pathway. However, CAF-1 is often needed to restrict endoreduplication, because seedlings of most CAF-1 mutants have increased ploidy. Notably, in the Landsberg erecta background, loss of CAF-1 does not affect ploidy, demonstrating that loss of CAF-1 can be compensated in some Arabidopsis accessions. These results reveal that the functions of FAS1, FAS2 and MSI1 are not restricted to meristems, but are also needed to control genome replication at multiple steps of development.

Cell and leaf size plasticity in Arabidopsis: what is the role of endoreduplication?

Leaf area expansion is affected by environmental conditions because of differences in cell number and/or cell size. Increases in the DNA content (ploidy) of a cell by endoreduplication are related to its size. The aim of this work was to determine how cell ploidy interacts with the regulation of cell size and with leaf area expansion. The approach used was to grow Arabidopsis thaliana plants performing increased or decreased rounds of endoreduplication under shading and water deficit. The shading and water deficit treatments reduced final leaf area and cell number; however, cell area was increased and decreased, respectively. These differences in cell size were unrelated to alterations of the endocycle, which was reduced by these treatments. The genetic modification of the extent of endoreduplication altered leaf growth responses to shading and water deficit. An increase in the extent of endoreduplication in a leaf rendered it more sensitive to the shade treatment but less sensitive to water deficit conditions. The link between the control of whole organ and individual cell expansion under different environmental conditions was demonstrated by the correlation between the plasticity of cell size and the changes in the duration of leaf expansion.

Microarray analysis of transcript accumulation during perithecium development in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum)

Gibberella zeae (anamorph Fusarium graminearum) is the causal agent of Fusarium head blight (FHB) of wheat and barley in the United States. Ascospores forcibly discharged from mature fruiting bodies, the perithecia, serve as the primary inoculum for FHB epidemics. To identify genes important for perithecium development and function, a cDNA microarray that covered 11% of the G. zeae genome was constructed. The microarray was used to measure changes in transcription levels of genes expressed during three successive stages of perithecium development. When compared with vegetative mycelia, 651 (31%) cDNA clones showed changes in transcript levels in at least one of the three developmental stages. During perithecium development, 263 (13%) cDNA clones showed temporal changes in transcript profiles. Transcripts that showed the greatest changes in levels in maturing perithecia belonged to genes in the FunCat main functional categories of cell rescue, metabolism, cell type differentiation, energy, and cellular transport. For genes related to metabolism and cell type differentiation, transcripts showed the highest levels in immature perithecia, whereas for cellular transport-related genes, transcripts showed the highest levels in mature perithecia. This study represents the first large-scale investigation of both spatial and temporal changes in transcript levels during perithecium development. It provides clear evidence that the sexual development in fungi is a complex, multigenic process and identifies genes involved in sexual development of this agriculturally important fungus.

Nocturnal changes in leaf growth of Populus deltoides are controlled by cytoplasmic growth

Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.

The TORNADO1 and TORNADO2 genes function in several patterning processes during early leaf development in Arabidopsis thaliana

In multicellular organisms, patterning is a process that generates axes in the primary body plan, creates domains upon organ formation, and finally leads to differentiation into tissues and cell types. We identified the Arabidopsis thaliana TORNADO1 (TRN1) and TRN2 genes and their role in leaf patterning processes such as lamina venation, symmetry, and lateral growth. In trn mutants, the leaf venation network had a severely reduced complexity: incomplete loops, no tertiary or quaternary veins, and vascular islands. The leaf laminas were asymmetric and narrow because of a severely reduced cell number. We postulate that the imbalance between cell proliferation and cell differentiation and the altered auxin distribution in both trn mutants cause asymmetric leaf growth and aberrant venation patterning. TRN1 and TRN2 were epistatic to ASYMMETRIC LEAVES1 with respect to leaf asymmetry, consistent with their expression in the shoot apical meristem and leaf primordia. TRN1 codes for a large plant-specific protein with conserved domains also found in a variety of signaling proteins, whereas TRN2 encodes a transmembrane protein of the tetraspanin family whose phylogenetic tree is presented. Double mutant analysis showed that TRN1 and TRN2 act in the same pathway.

Quantitative analyses of cell division in plants

At the molecular level regulatory interactions between cell cycle genes are being uncovered rapidly, but less progress is made in unravelling how these molecular events regulate growth processes at the level of cells and of the whole organism. The main obstacle is the absence of a set of analytical tools that are powerful enough to determine pertinent parameters and, at the same time, relatively easy to use by non-specialized laboratories. Appropriate methodology to obtain this type of data has been pioneered in the first half of the last century and is now commonly defined as 'kinematic analysis'. Unfortunately, the laborious nature of these analyses and the relatively complex numerical methods used, have limited their use to only a handful of specialized research groups. In this article we attempt to present an accessible entry to this methodology, particularly in terms of the mathematical framework. We start describing the simplest possible system, i.e., a virtually homogenous cell suspension culture. Then, we outline the analysis of dicotyledonous leaves, root tips, monocotyledonous leaves, and finally shoot apical meristems. For each of these systems we discuss the details of the calculation of cell division parameters such as cell cycle duration, size of the meristem and number of cells contained in it, which enables answering fundamental questions about the relative contribution of differences in cell production and cell size to variation in growth. In addition, we discuss the assumptions and limitations of these and alternative methodologies with the aim to facilitate the choice of appropriate analyses depending on the specific research question.

Functional dynamics of plant growth and photosynthesis--from steady-state to dynamics--from homogeneity to heterogeneity

Plants are much more dynamic than we usually expect them to be. This dynamic behaviour is of paramount importance for their performance under natural conditions, when resources are distributed heterogeneously in space and time. However, plants are not only the cue ball of their physical and chemical environment. Endogenous rhythms and networks controlling photosynthesis and growth buffer plant processes from external fluctuations. This review highlights recent evidence of the importance of dynamic temporal and spatial organization of photosynthesis and of growth in leaves and roots. These central processes for plant performance differ strongly in their dependence on environmental impact and endogenous properties, respectively. Growth involves a wealth of processes ranging from the supply of resources from external and internal sources to the growth processes themselves. In contrast, photosynthesis can only take place when light and CO2 are present and thus clearly requires 'input from the environment'. Nevertheless, growth and photosynthesis are connected to each other via mechanisms that are still not fully understood. Recent advances in imaging technology have provided new insights into the dynamics of plant-environment interactions. Such processes do not only play a crucial role in understanding stress response of plants under extreme environmental conditions. Dynamics of plants under modest growth conditions rise from endogenous mechanisms as well as exogenous impact too. It is thus an important task for future research to identify how dynamic external conditions interact with plant-internal signalling networks to optimize plant behaviour in real time and to understand how plants have adapted to characteristic spatial and temporal properties of the resources from their environment, on which they depend on.

The Arabidopsis leaf as a model system for investigating the role of cell cycle regulation in organ growth

The role of cell cycle regulation and cell division in plant growth and organ development is controversial. Some experimental data are most easily interpreted from the 'cellular perspective' that cell division drives growth, whereas other observations are more consistent with the 'organismal perspective' that cell division is merely a consequence of growth, and to a large extent facultative. Here we develop a model of cell cycle regulation in the context of leaf development based on literature, published kinematic analysis, flow-cytometric and transcriptomic data obtained from growing Arabidopsis leaves. We tested this model by comparing the in silico inhibition of the cell cycle progression with the experimental observations of transgenic plants overexpressing the cell cycle inhibitor Arath;KRP2. The model simulates the behaviour of proliferating cells quite well, but is inadequate in describing the effects on expanding cells. This may point to a difference in the nature of the expansion process during the proliferating and non-dividing phase of leaf development.

Moving with the flow: what transport laws reveal about cell division and expansion

This material was presented as a keynote talk for the symposium, "Crosstalk between cell division and expansion," organized by G.T.S. Beemster and H. Tsukaya at the International Botanical Congress, Vienna in July, 2005. The review focuses on the utility of continuity equations to understand relationships among cell size, division and expansion; insights from Lagrangian or cell-specific descriptions of developmental variables; and a growth-diffusion equation to show effects of root growth zones on the surrounding soil.

RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth

How cells achieve their final sizes is a pervasive biological question. One strategy to increase cell size is for the cell to amplify its chromosomal DNA content through endoreduplication cycles. Although endoreduplication is widespread in eukaryotes, we know very little about its molecular mechanisms. Successful progression of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understand how DNA is endoreduplicated and how this process is regulated, we isolated a dwarf Arabidopsis mutant, hyp7 (hypocotyl 7), in which various large cell types that in the wild type normally endoreduplicate multiple times complete only the first two rounds of endoreduplication and stall at 8C. HYP7 encodes the RHL1 (ROOT HAIRLESS 1) protein, and sequence analysis reveals that RHL1 has similarity to the C-terminal domain of mammalian DNA topo IIalpha, another type II topo that shares little sequence homology with topo VI. RHL1 shows DNA binding activity in vitro, and we present both genetic and in vivo evidence that RHL1 forms a multiprotein complex with plant topo VI. We propose that RHL1 plays an essential role in the topo VI complex to modulate its function and that the two distantly related topos, topo II and topo VI, have evolved a common domain that extends their function. Our data suggest that plant topo II and topo VI play distinct but overlapping roles during the mitotic cell cycle and endoreduplication cycle.

The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes

Exit from the mitotic cell cycle and initiation of cell differentiation frequently coincides with the onset of endoreduplication, a modified cell cycle during which DNA continues to be duplicated in the absence of mitosis. Although the mitotic cell cycle and the endoreduplication cycle share much of the same machinery, the regulatory mechanisms controlling the transition between both cycles remain poorly understood. We show that the A-type cyclin-dependent kinase CDKA;1 and its specific inhibitor, the Kip-related protein, KRP2 regulate the mitosis-to-endocycle transition during Arabidopsis thaliana leaf development. Constitutive overexpression of KRP2 slightly above its endogenous level only inhibited the mitotic cell cycle-specific CDKA;1 kinase complexes, whereas the endoreduplication cycle-specific CDKA;1 complexes were unaffected, resulting in an increase in the DNA ploidy level. An identical effect on the endoreduplication cycle could be observed by overexpressing KRP2 exclusively in mitotically dividing cells. In agreement with a role for KRP2 as activator of the mitosis-to-endocycle transition, KRP2 protein levels were more abundant in endoreduplicating than in mitotically dividing tissues. We illustrate that KRP2 protein abundance is regulated posttranscriptionally through CDK phosphorylation and proteasomal degradation. KRP2 phosphorylation by the mitotic cell cycle-specific CDKB1;1 kinase suggests a mechanism in which CDKB1;1 controls the level of CDKA;1 activity through regulating KRP2 protein abundance. In accordance with this model, KRP2 protein levels increased in plants with reduced CDKB1;1 activity. Moreover, the proposed model allowed a dynamical simulation of the in vivo observations, validating the sufficiency of the regulatory interactions between CDKA;1, KRP2, and CDKB1;1 in fine-tuning the mitosis-to-endocycle transition.