A family of cyclin D homologs from plants differentially controlled by growth regulators and containing the conserved retinoblastoma protein interaction motif

Unraveling Morphological, Physiological, and Transcriptomic Alterations Underlying the Formation of Little Leaves in Phytoplasma-Infected Sweet Cherry Trees

Phytoplasmas are minute phytopathogenic bacteria that induce excessive vegetative growth, known as witches' broom (WB), in many infected plant species during the later stages of infection. The WB structure is characterized by densely clustered little (small) leaves, which are frequently accompanied by chlorosis (yellowing). The mechanisms behind the formation of little leaves within WB structures (LL-WB) are poorly understood. To address this gap, the LL-WB formation was extensively studied using sweet cherry virescence (SCV) phytoplasma-infected sweet cherry plants. Based on morphological examinations, signs of premature leaf senescence were observed in LL-WB samples, including reduced leaf size, chlorosis, and alterations in shape. Subsequent physiological analyses indicated decreased sucrose and glucose levels and changes in hormone concentrations in LL-WB samples. Additionally, the transcriptomic analysis revealed impaired ribosome biogenesis and DNA replication. As an essential process in protein production, the compromised ribosome biogenesis and the inhibited DNA replication led to cell cycle arrest, thus affecting leaf morphogenesis and further plant development. Moreover, the expression of marker genes involved in premature leaf senescence was significantly altered. These results indicate a complicated interplay between the development of leaves, premature leaf senescence, and pathogen-induced stress responses in SCV phytoplasma-infected sweet cherry trees. The results of this study provide insight into understanding the underlying molecular mechanisms driving the formation of little leaves and interactions between plants and pathogens. The findings might help control phytoplasma diseases in sweet cherry cultivation.

Regulation of cell cycle in plant gametes: when is the right time to divide?

Cell division is a fundamental process shared across diverse life forms, from yeast to humans and plants. Multicellular organisms reproduce through the formation of specialized types of cells, the gametes, which at maturity enter a quiescent state that can last decades. At the point of fertilization, signalling lifts the quiescent state and triggers cell cycle reactivation. Studying how the cell cycle is regulated during plant gamete development and fertilization is challenging, and decades of research have provided valuable, yet sometimes contradictory, insights. This Review summarizes the current understanding of plant cell cycle regulation, gamete development, quiescence, and fertilization-triggered reactivation.

The role of D3-type cyclins is related to cytokinin and the bHLH transcription factor SPATULA in Arabidopsis gynoecium development

MAIN CONCLUSION

We studied the D3-type cyclin function during gynoecium development in Arabidopsis and how they are related to the hormone cytokinin and the transcription factor SPATULA. Growth throughout the life of plants is sustained by cell division and differentiation processes in meristematic tissues. In Arabidopsis, gynoecium development implies a multiphasic process where the tissues required for pollination, fertilization, and seed development form. The Carpel Margin Meristem (CMM) is a mass of undifferentiated cells that gives rise to the gynoecium internal tissues, such as septum, ovules, placenta, funiculus, transmitting tract, style, and stigma. Different genetic and hormonal factors, including cytokinin, control the CMM function. Cytokinin regulates the cell cycle transitions through the activation of cell cycle regulators as cyclin genes. D3-type cyclins are expressed in proliferative tissues, favoring the mitotic cell cycle over the endoreduplication. Though the role of cytokinin in CMM and gynoecium development is highly studied, its specific role in regulating the cell cycle in this tissue remains unclear. Additionally, despite extensive research on the relationship between CYCD3 genes and cytokinin, the regulatory mechanism that connects them remains elusive. Here, we found that D3-type cyclins are expressed in proliferative medial and lateral tissues. Conversely, the depletion of the three CYCD3 genes showed that they are not essential for gynoecium development. However, the addition of exogenous cytokinin showed that they could control the division/differentiation balance in gynoecium internal tissues and outgrowths. Finally, we found that SPATULA can be a mechanistic link between cytokinin and the D3-type cyclins. The data suggest that the role of D3-type cyclins in gynoecium development is related to the cytokinin response, and they might be activated by the transcription factor SPATULA.

Sugar signals pedal the cell cycle!

Cell cycle involves the sequential and reiterative progression of important events leading to cell division. Progression through a specific phase of the cell cycle is under the control of various factors. Since the cell cycle in multicellular eukaryotes responds to multiple extracellular mitogenic cues, its study in higher forms of life becomes all the more important. One such factor regulating cell cycle progression in plants is sugar signalling. Because the growth of organs depends on both cell growth and proliferation, sugars sensing and signalling are key control points linking sugar perception to regulation of downstream factors which facilitate these key developmental transitions. However, the basis of cell cycle control via sugars is intricate and demands exploration. This review deals with the information on sugar and TOR-SnRK1 signalling and how they manoeuvre various events of the cell cycle to ensure proper growth and development.

Functional characterization of D-type cyclins involved in cell division in rice

BACKGROUND

D-type cyclins (CYCD) regulate the cell cycle G1/S transition and are thus closely involved in cell cycle progression. However, little is known about their functions in rice.

RESULTS

We identified 14 CYCD genes in the rice genome and confirmed the presence of characteristic cyclin domains in each. The expression of the OsCYCD genes in different tissues was investigated. Most OsCYCD genes were expressed at least in one of the analyzed tissues, with varying degrees of expression. Ten OsCYCD proteins could interact with both retinoblastoma-related protein (RBR) and A-type cyclin-dependent kinases (CDKA) forming holistic complexes, while OsCYCD3;1, OsCYCD6;1, and OsCYCD7;1 bound only one component, and OsCYCD4;2 bound to neither protein. Interestingly, all OsCYCD genes except OsCYCD7;1, were able to induce tobacco pavement cells to re-enter mitosis with different efficiencies. Transgenic rice plants overexpressing OsCYCD2;2, OsCYCD6;1, and OsCYCD7;1 (which induced cell division in tobacco with high-, low-, and zero-efficiency, respectively) were created. Higher levels of cell division were observed in both the stomatal lineage and epidermal cells of the OsCYCD2;2- and OsCYCD6;1-overexpressing plants, with lower levels seen in OsCYCD7;1-overexpressing plants.

CONCLUSIONS

The distinct expression patterns and varying effects on the cell cycle suggest different functions for the various OsCYCD proteins. Our findings will enhance understanding of the CYCD family in rice and provide a preliminary foundation for the future functional verification of these genes.

Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level

Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1-D7) and 7 (CDKA-CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.

Ectopic Expression of Poplar PsnCYCD1;1 Reduces Cell Size and Regulates Flower Organ Development in Nicotiana tabacum

The D-type cyclin (CYCD) gene, as the rate-limiting enzyme in the G1 phase of cell cycle, plays a vital role in the process of plant growth and development. Early studies on plant cyclin mostly focused on herbs, such as Arabidopsis thaliana. The sustainable growth ability of woody plants is a unique characteristic in the study of plant cyclin. Here, the promoter of PsnCYCD1;1 was cloned from poplar by PCR and genetically transformed into tobacco. A strong GUS activity was observed in the areas with vigorous cell division, such as stem tips, lateral buds, and young leaves. The PsnCYCD1;1-GFP fusion expression vector was transformed into tobacco, and the green fluorescence signal was observed in the nucleus. Compared with the control plant, the transgenic tobacco showed significant changes in the flower organs, such as enlargement of sepals, petals, and fruits. Furthermore, the stems of transgenic plants were slightly curved at each stem node, the leaves were curled on the adaxial side, and the fruits were seriously aborted after artificial pollination. Microscopic observation showed that the epidermal cells of petals, leaves, and seed coats of transgenic plants became smaller. The transcriptional levels of endogenous genes, such as NtCYCDs, NtSTM, NtKNAT1, and NtASs, were upregulated by PsnCYCD1;1. Therefore, PsnCYCD1;1 gene played an important role in the regulation of flower organ and stem development, providing new understanding for the functional characterization of CYCD gene and new resources for improving the ornamental value of horticultural plants.

Overexpression Populus d-Type Cyclin Gene PsnCYCD1;1 Influences Cell Division and Produces Curved Leaf in Arabidopsis thaliana

d-type cyclins (CYCDs) are a special class of cyclins and play extremely important roles in plant growth and development. In the plant kingdom, most of the existing studies on CYCDs have been done on herbaceous plants, with few on perennial woody plants. Here, we identified a Populus d-type cyclin gene, PsnCYCD1;1, which is mainly transcribed in leaf buds and stems. The promoter of PsnCYCD1;1 activated GUS gene expression and transgenic Arabidopsis lines were strongly GUS stained in whole seedlings and mature anthers. Moreover, subcellular localization analysis showed the fluorescence signal of PsnCYCD1;1-GFP fusion protein is present in the nucleus. Furthermore, overexpression of the PsnCYCD1;1 gene in Arabidopsis can promote cell division and lead to small cell generation and cytokinin response, resulting in curved leaves and twisted inflorescence stems. Moreover, the transcriptional levels of endogenous genes, such as ASs, KNATs, EXP10, and PHB, were upregulated by PsnCYCD1;1. Together, our results indicated that PsnCYCD1;1 participates in cell division by cytokinin response, providing new information on controlling plant architecture in woody plants.

Overexpression of PtoCYCD3;3 Promotes Growth and Causes Leaf Wrinkle and Branch Appearance in Populus

D-type cyclin (cyclin D, CYCD), combined with cyclin-dependent kinases (CDKs), participates in the regulation of cell cycle G1/S transition and plays an important role in cell division and proliferation. CYCD could affect the growth and development of herbaceous plants, such as Arabidopsis thaliana, by regulating the cell cycle process. However, its research in wood plants (e.g., poplar) is poor. Phylogenetic analysis showed that in Populus trichocarpa, CYCD3 genes expanded to six members, namely PtCYCD3;1–6. P. tomentosa CYCD3 genes were amplified based on the CDS region of P. trichocarpa CYCD3 genes. PtoCYCD3;3 showed the highest expression in the shoot tip, and the higher expression in young leaves among all members. Therefore, this gene was selected for further study. The overexpression of PtoCYCD3;3 in plants demonstrated obvious morphological changes during the observation period. The leaves became enlarged and wrinkled, the stems thickened and elongated, and multiple branches were formed by the plants. Anatomical study showed that in addition to promoting the differentiation of cambium tissues and the expansion of stem vessel cells, PtoCYCD3;3 facilitated the division of leaf adaxial epidermal cells and palisade tissue cells. Yeast two-hybrid experiment exhibited that 12 PtoCDK proteins could interact with PtoCYCD3;3, of which the strongest interaction strength was PtoCDKE;2, whereas the weakest was PtoCDKG;3. Molecular docking experiments further verified the force strength of PtoCDKE;2 and PtoCDKG;3 with PtoCYCD3;3. In summary, these results indicated that the overexpression of PtoCYCD3;3 significantly promoted the vegetative growth of Populus, and PtoCYCD3;3 may interact with different types of CDK proteins to regulate cell cycle processes.

At-CycD2 Enhances Accumulation of Above-Ground Biomass and Recombinant Proteins in Transgenic Nicotiana benthamiana Plants

Transient expression in Nicotiana benthamiana holds great potential for recombinant protein manufacturing due to its advantages in terms of speed and yield compared to stably transformed plants. To continue improving the quantity of recombinant proteins the plant host will need to be modified at both plant and cellular levels. In attempt to increase leaf mass fraction, we transformed N. benthamiana with the At-CycD2 gene, a positive regulator of the cell cycle. Phenotypic characterization of the T₁ progeny plants revealed their accelerated above-ground biomass accumulation and enhanced rate of leaf initiation. In comparison to non-transgenic control the best performing line At-CycD2-15 provided 143 and 140% higher leaf and stem biomass fractions, respectively. The leaf area enlargement of the At-CycD2-15 genotype was associated with the increase of epidermal cell number compensated by slightly reduced cell size. The production capacity of the At-CycD2-15 transgenic line was superior to that of the non-transgenic N. benthamiana. The accumulation of transiently expressed GFP and scFv-TM43-E10 proteins per unit biomass was increased by 138.5 and 156.7%, respectively, compared to the wild type. With these results we demonstrate the potential of cell cycle regulator gene At-CycD2 to modulate both plant phenotype and intracellular environment of N. benthamiana for enhanced recombinant protein yield.

Roles of plant retinoblastoma protein: cell cycle and beyond

The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.

Temporal and Spatial Expression Analysis of Shoot-Regeneration Regulatory Genes during the Adventitious Shoot Formation in Hypocotyl and Cotyledon Explants of Tomato (CV. Micro-Tom)

Enhancing the competence for plant regeneration in tissue culture studies is an important issue not only for efficient genetic transformation of commercial crops but also for the reproducibility of scientific reports. In this study, we investigated optimization of several tissue culture conditions including plant growth regulators, types and ages of explants, culture densities, and plant position in order to improve the competence of adventitious shoot formation of the tomato (Solanum lycopersicum cv. Micro-Tom). In addition, we examined the differential expression of D-type cyclin (CYCD3-1) and several shoot regeneration regulatory genes from hypocotyl and cotyledon explants of tomato during shoot organogenesis. A treatment of 1 mg L-1 Zeatin and 0.1 mg L-1 Indole-3-acetic acid (IAA) in Murashige and Skoog (MS) medium containing 3% sucrose was optimal for adventitious shoot formation from hypocotyl and cotyledon explants. The younger explants exhibited more shoot formation regardless of explant types. Additionally, those closest to the shoot apical meristem produced more shoots compared to the other regions in the hypocotyl and the cotyledon explants. Gene expression of CYCD3-1, SHOOT MERISTEMLESS (STM), and cytokinin dependent WUSCHEL (WUS) was significantly higher in younger explants than in older ones. Furthermore, an increase in CYCD3-1, STM, and WUS expression was evident at the distal part of hypocotyls and the proximal part of cotyledons compared to other regions. These differential gene expression profiles exhibited good agreement with the results of shoot formation obtained from diverse explants of tomato. These results suggest that temporal and spatial gene expression of shoot regeneration regulatory genes plays an important role in enhancing the competence and the reproducibility of adventitious shoot formation from tomato explants.

Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation

The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.

Synergistic effect of cytokinin and gibberellins stimulates release of dormancy in tea (Camellia sinensis (L.) O. Kuntze) bud

Reactivation of dormant meristem in banjhi (dormant) shoots is important to enhance the quality and quantity of tea production. The field grown tea bushes were subjected to treatment with dormancy breaking agents such as potassium nitrate (KNO₃), thiourea, sodium nitro prusside (SNP), the phytohormones kinetin (Kn) and gibberellins (GA). The efficacy of Kn and GA were comparatively lesser than KNO₃ while the combination of Kn and GA (50 and100 ppm respectively) resulted in better dormancy reduction in tea buds. This observation was supported by our results from gene expression study where accumulation patterns of mRNAs corresponding to histones (H2A, H2B, H3 and H4), cyclins (B2, D1 and D3), cyclin-dependent kinase (CDKA), ubiquitination enzymes (FUS, EXT CE2), cyclophilin, E2F, and tubulin were analyzed during growth-dormancy cycles in tea apical buds under the influence of Kn, GA and their combinations. The level of these mRNAs was low in dormant buds, which was significantly increased by foliar application of GA and Kn combination. The present study indicated that the foliar application of GA in combination with Kn will help to improve quality and quantity of tea production by breaking dormancy and stimulating the bud growth.

Enhanced foreign protein accumulation in Nicotiana benthamiana leaves co-infiltrated with a TMV vector and plant cell cycle regulator genes

In this short communication, we report that the cell cycle checkpoint genes At-CycD2 and At-CDC27a from Arabidopsis thaliana enhance the transient heterologous protein expression in Nicotiana benthamiana. We selected a well-studied and widely used virus expression vector based on TMV for the delivery of recombinant proteins into the host plant. Co-infiltration of TMV-gfp and binary expression vectors carrying the At-CycD2 and At-CDC27a genes, respectively, resulted in enhanced GFP fluorescence in agroinoculated leaves. These findings corresponded with the observation of (1) higher mRNA levels for TMV and gfp and (2) increased GFP protein accumulation. Furthermore, by co-delivery of the TMV-scFv-TM43-E10 and At-CycD2/At-CDC27a expressing constructs we observed an enhanced amount of the scFv-TM43-E10 antibody fragment compared to the delivery of the TMV-scFv-TM43-E10 alone. We anticipate that this finding might be adapted for enhancing foreign protein production in N. benthamiana as the host plant.

Multifaceted activity of cytokinin in leaf development shapes its size and structure in Arabidopsis

The phytohormone cytokinin has been shown to affect many aspects of plant development ranging from the regulation of the shoot apical meristem to leaf senescence. However, some studies have reported contradictory effects of cytokinin on leaf physiology. Therefore cytokinin treatments cause both chlorosis and increased greening and both lead to decrease or increase in cell size. To elucidate this multifaceted role of cytokinin in leaf development, we have employed a system of temporal controls over the cytokinin pool and investigated the consequences of modulated cytokinin levels in the third leaf of Arabidopsis. We show that, at the cell proliferation phase, cytokinin is needed to maintain cell proliferation by blocking the transition to cell expansion and the onset of photosynthesis. Transcriptome profiling revealed regulation by cytokinin of a gene suite previously shown to affect cell proliferation and expansion and thereby a molecular mechanism by which cytokinin modulates a molecular network underlying the cellular responses. During the cell expansion phase, cytokinin stimulates cell expansion and differentiation. Consequently, a cytokinin excess at the cell expansion phase results in an increased leaf and rosette size fueled by higher cell expansion rate, yielding higher shoot biomass. Proteome profiling revealed the stimulation of primary metabolism by cytokinin, in line with an increased sugar content that is expected to increase turgor pressure, representing the driving force of cell expansion. Therefore, the developmental timing of cytokinin content fluctuations, together with a tight control of primary metabolism, is a key factor mediating transitions from cell proliferation to cell expansion in leaves.

Genome-Wide Analysis of the D-type Cyclin Gene Family Reveals Differential Expression Patterns and Stem Development in the Woody Plant Prunus mume

Cyclins, a prominent class of cell division regulators, play an extremely important role in plant growth and development. D-type cyclins (CYCDs) are the rate-limiting components of the G1 phase. In plants, studies of CYCDs are mainly concerned with herbaceous plants, yet little information is available about these genes in perennial woody plants, especially ornamental plants. Here, twelve Prunus mume CYCD (PmCYCDs) genes are identified and characterized. The PmCYCDs were named on the basis of orthologues in Arabidopsis thaliana and Oryza sativa. Gene structure and conserved domains of each subgroup CYCDs was similar to that of their orthologues in A. thaliana and O. sativa. However, PmCYCDs exhibited different tissue-specific expression patterns in root, stem, leaf, bud, and fruit organs. The results of qRT-PCR showed that all PmCYCDs, except PmCYCD5;2 and PmCYCD7;1, were primarily highly expressed in leaf buds, shoots, and stems. In addition, the transcript levels of PmCYCD genes were analyzed in roots under different treatments, including exogenous applications of NAA, 6-BA, GA3, ABA, and sucrose. Interestingly, although PmCYCDs were induced by sucrose, the extent of gene induction among PmCYCD subgroups varied. The induction of PmCYCD1;2 by hormones depended on the presence of sucrose. PmCYCD3;1 was stimulated by NAA, and induction was strengthened when sugar and hormones were applied together. Taken together, our study demonstrates that PmCYCDs are functional in plant stem development and provides a basis for selecting members of the cyclin gene family as candidate genes for ornamental plant breeding.

Modulation of CycD3;1-CDK complexes by phytohormones and sucrose during maize germination

Maize CycD3;1 associates to CDKA or CDKB1;1 proteins during germination and the complexes formed develop kinase activity. These complexes appear to vary in size as germination proceeds, suggesting association to different sets of proteins. CycD3;1 and associated CDK proteins respond to phytohormones and sucrose. Results revealed a reduction in the CycD3;1 protein amount along germination in the presence of indoleacetic acid (IAA) or abscisic acid (ABA), although in the latter protein levels recover at the end of germination. While the levels of CDKA increase with IAA, they decrease with ABA. Both phytohormones, IAA and ABA, increase levels of CDKB1;1 only during the early germination times. CycD3;1 associated kinase activity is only reduced by both phytohormones towards the end of the germination period. On the other hand, lack of sucrose in the imbibition medium strongly reduces CycD3;1 protein levels without affecting the levels of neither CDKA nor CDKB1;1. The corresponding CycD3;1 associated kinase activity is also severely decreased. The presence of sucrose in the medium appears to stabilize the CycD3;1 protein levels.

25 Years of Cell Cycle Research: What's Ahead?

We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.

Phytochrome-mediated regulation of cell division and growth during regeneration and sporeling development in the liverwort Marchantia polymorpha

Light regulates various aspects of development throughout the life cycle of sessile land plants. Photoreceptors, such as the red (R) and far-red (FR) light receptors phytochromes, play pivotal roles in modulating developmental programs. Reflecting high developmental plasticity, plants can regenerate tissues, organs, and whole bodies from varieties of cells. Among land plants, bryophytes exhibit extraordinary competency of regeneration under hormone-free conditions. As an environmental factor, light plays critical roles in regeneration of bryophytes. However, how light regulates regeneration remains unknown. Here we show that using the liverwort Marchantia polymorpha, which contains a single phytochrome gene, the phytochrome regulates re-entry into the cell cycle and cell shape in newly regenerating tissues. Our morphological and cytological observations revealed that S-phase entry of G1-arrested epidermal cells around the midrib on the ventral surface of thallus explants was greatly retarded in the dark or under phytochrome-inactive R/FR cycle irradiation conditions, where, nevertheless, small, laterally narrow regenerants were eventually formed. Thus, consistent with earlier descriptions published over a century ago, light is not essential for, but exerts profound effects on regeneration in M. polymorpha. Ventral cells in regenerants grown under R/FR cycle conditions were longer and narrower than those under R cycle. Expression of a constitutively active mutant of M. polymorpha phytochrome allowed regeneration of well grown, widely expanded thalli even in the dark when sugar was supplied, further demonstrating that the phytochrome signal promotes cell proliferation, which is rate-limited by sucrose availability. Similar effects of R and FR irradiation on cell division and elongation were observed in sporelings as well. Thus, besides activation of photosynthesis, major roles of R in regeneration of M. polymorpha are to facilitate proliferation of rounder cells through the phytochrome by mechanisms that are likely to operate in the sporeling.

Historical review of research on plant cell dedifferentiation

Plant cell dedifferentiation has long attracted interest as a key process for understanding the plasticity of plant development. In early studies, typical examples of plant cell dedifferentiation were described as physiological and cytological changes associated with wound healing or regenerative development. Subsequently, plant tissue and cell culture techniques, in which exciting progress was achieved after discovery of the hormonal control of cell proliferation and organogenesis in vitro in the 1950s, have been used extensively to study dedifferentiation. The pioneer studies of plant tissue/cell culture led to the hypothesis that many mature plant cells retain totipotency and related dedifferentiation to the initial step of the expression of totipotency. Plant tissue/cell cultures have provided experimental systems not only for physiological analysis, but also for genetic and molecular biological analysis, of dedifferentiation. More recently, proteomic, transcriptomic, and epigenetic analyses have been applied to the study of plant cell dedifferentiation. All of these works have expanded our knowledge of plant cell dedifferentiation, and current research is contributing to unraveling the molecular mechanisms. The present article provides a brief overview of the history of research on plant cell dedifferentiation.

Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division

The retinoblastoma (Rb) protein was identified as a human tumour suppressor protein that controls various stages of cell proliferation through the interaction with members of the E2F family of transcription factors. It was originally thought to be specific to animals but plants contain homologues of Rb, called RETINOBLASTOMA-RELATED (RBR). In fact, the Rb-E2F module seems to be a very early acquisition of eukaryotes. The activity of RBR depends on phosphorylation of certain amino acid residues, which in most cases are well conserved between plant and animal proteins. In addition to its role in cell-cycle progression, RBR has been shown to participate in various cellular processes such as endoreplication, transcriptional regulation, chromatin remodelling, cell growth, stem cell biology, and differentiation. Here, we discuss the most recent advances to define the role of RBR in cell proliferation and asymmetric cell division. These and other reports clearly support the idea that RBR is used as a landing platform of a plethora of cellular proteins and complexes to control various aspects of cell physiology and plant development.

Systemic control of cell division and endoreduplication by NAA and BAP by modulating CDKs in root tip cells of Allium cepa

Molecular mechanism regulated by auxin and cytokinin during endoreduplication, cell division, and elongation process is studied by using Allium cepa roots as a model system. The activity of CDK genes modulated by auxin and cytokinin during cell division, elongation, and endoreduplication process is explained in this research work. To study the significance of auxin and cytokinin in the management of cell division and endoreduplication process in plant meristematic cells at molecular level endoreduplication was developed in root tips of Allium cepa by giving colchicine treatment. There were inhibition of vegetative growth, formation of c-tumor at root tip, and development of endoreduplicated cells after colchicine treatment. This c-tumor was further treated with NAA and BAP to reinitiate vegetative growth in roots. BAP gave positive response in reinitiation of vegetative growth of roots from center of c-tumor. However, NAA gave negative response in reinitiation of vegetative growth of roots from c-tumor. Further, CDKs gene expression analysis from normal, endoreduplicated, and phytohormone (NAA or BAP) treated root tip was done and remarkable changes in transcription level of CDK genes in normal, endoreduplicated, and phytohormones treated cells were observed.

Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

Background

The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this study, we conducted a comprehensive evolutionary analysis of CDK and cyclin proteins in metazoans and their unicellular relatives.

Results

Our analysis divided the CDK family into eight subfamilies. Seven subfamilies (CDK1/2/3, CDK5, CDK7, CDK 20, CDK8/19, CDK9, and CDK10/11) are conserved in metazoans and fungi, with the remaining subfamily, CDK4/6, found only in eumetazoans. With respect to cyclins, cyclin C, H, L, Y subfamilies, and cyclin K and T as a whole subfamily, are generally conserved in animal, fungi, and amoeba Dictyostelium discoideum. In contrast, cyclin subfamilies B, A, E, and D, which are cell cycle-related, have distinct evolutionary histories. The cyclin B subfamily is generally conserved in D. discoideum, fungi, and animals, whereas cyclin A and E subfamilies are both present in animals and their unicellular relatives such as choanoflagellate Monosiga brevicollis and filasterean Capsaspora owczarzaki, but are absent in fungi and D. discoideum. Although absent in fungi and D. discoideum, cyclin D subfamily orthologs can be found in the early-emerging, non-opisthokont apusozoan Thecamonas trahens. Within opisthokonta, the cyclin D subfamily is conserved only in eumetazoans, and is absent in fungi, choanoflagellates, and the basal metazoan Amphimedon queenslandica.

Conclusions

Our data indicate that the CDK4/6 subfamily and eumetazoans emerged simultaneously, with the evolutionary conservation of the cyclin D subfamily also tightly linked with eumetazoan appearance. Establishment of the CDK4/6-cyclin D complex may have been the key step in the evolution of cell cycle control during eumetazoan emergence.

Cytokinins

Cytokinins are N (6) substituted adenine derivatives that affect many aspects of plant growth and development, including cell division, shoot initiation and growth, leaf senescence, apical dominance, sink/source relationships, nutrient uptake, phyllotaxis, and vascular, gametophyte, and embryonic development, as well as the response to biotic and abiotic factors. Molecular genetic studies in Arabidopsis have helped elucidate the mechanisms underlying the function of this phytohormone in plants. Here, we review our current understanding of cytokinin biosynthesis and signaling in Arabidopsis, the latter of which is similar to bacterial two-component phosphorelays. We discuss the perception of cytokinin by the ER-localized histidine kinase receptors, the role of the AHPs in mediating the transfer of the phosphoryl group from the receptors to the response regulators (ARRs), and finally the role of the large ARR family in cytokinin function. The identification and genetic manipulation of the genes involved in cytokinin metabolism and signaling have helped illuminate the roles of cytokinins in Arabidopsis. We discuss these diverse roles, and how other signaling pathways influence cytokinin levels and sensitivity though modulation of the expression of cytokinin signaling and metabolic genes.

The Arabidopsis homeobox gene SHOOT MERISTEMLESS has cellular and meristem-organisational roles with differential requirements for cytokinin and CYCD3 activity

The Arabidopsis class-1 KNOX gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor essential for shoot apical meristem (SAM) formation and sustained activity. STM activates cytokinin (CK) biosynthesis in the SAM, but the extent to which STM function is mediated through CK is unclear. Here we show that STM inhibits cellular differentiation and endoreduplication, acting through CK and the CK-inducible CYCD3 cell cycle regulators, establishing a mechanistic link to cell cycle control which provides sustained mitotic activity to maintain a pool of undifferentiated cells in the SAM. Equivalent functions are revealed for the related KNOX genes KNAT1/BP and KNAT2 through ectopic expression. STM is also required for proper meristem organisation and can induce de novo meristem formation when expressed ectopically, even when CK levels are reduced or CK signaling is impaired. This function in meristem establishment and organisation can be replaced by KNAT1/BP, but not KNAT2, despite its activation of CK responses, suggesting that promotion of CK responses alone is insufficient for SAM organisation. We propose that STM has dual cellular and meristem-organisational functions that are differentially represented in the class-1 KNOX gene family and have differing requirements for CK and CYCD3.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Getting to the roots of it: Genetic and hormonal control of root architecture

Root system architecture (RSA) - the spatial configuration of a root system - is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants.

Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling

The shoot apical meristem (SAM) is a small population of stem cells that continuously generates organs and tissues. This review covers our current understanding of organ initiation by the SAM in Arabidopsis thaliana. Meristem function and maintenance involves two major hormones, cytokinins and auxins. Cytokinins appear to play a major role in meristem maintenance and in controlling meristematic properties, such as cell proliferation. Self-organizing transport processes, which are still only partially understood, lead to the patterned accumulation of auxin at particular positions, where organs will grow out. A major downstream target of auxin-mediated growth regulation is the cell wall, which is a determinant for both growth rates and growth distribution, but feedbacks with metabolism and the synthetic capacity of the cytoplasm are crucial as well. Recent work has also pointed at a potential role of mechanical signals in growth coordination, but the precise mechanisms at work remain to be elucidated.

Enhancement of secondary xylem cell proliferation by Arabidopsis cyclin D overexpression in tobacco plants

Secondary xylem is composed of daughter cells produced by the vascular cambium in the stem. Cell proliferation of the secondary xylem is the result of long-range cell division in the vascular cambium. Most xylem cells have a thickened secondary cell wall, representing a large amount of biomass storage. Therefore, regulation of cell division in the vascular cambium and differentiation into secondary xylem is important for biomass production. Cell division is regulated by cell cycle regulators. In this study, we confirm that cell cycle regulators influence cell division in the vascular cambium in tobacco. We produced transgenic tobacco that expresses Arabidopsis thaliana cyclin D2;1 (AtcycD2;1) and AtE2Fa-DPa under the control of the CaMV35S promoter. Each gene is a positive regulator of the cell cycle, and is known to influence the transition from G1 phase to S phase. AtcycD2;1-overexpressing tobacco had more secondary xylem cells when compared with control plants. In order to evaluate cell division activity in the vascular cambium, we prepared a Populus trichocarpa cycB1;1 (PtcycB1;1) promoter containing a destruction box motif for ubiquitination and a β-glucuronidase-encoding gene (PtcycB1;1pro:GUS). In transgenic tobacco containing PtcycB1;1pro:GUS, GUS staining was specifically observed in meristem tissues, such as the root apical meristem and vascular cambium. In addition, mitosis-monitoring plants containing AtcycD2;1 had stronger GUS staining in the cambium when compared with control plants. Our results indicated that overexpression of AtcycD enhances cell division in the vascular cambium and increases secondary xylem differentiation in tobacco.

KEY MESSAGE

We succeeded in inducing cell proliferation of cambium and enlargement of secondary xylem region by AtcycD overexpression. We also evaluated mitotic activity in cambium using cyclin-GUS fusion protein from poplar.

Leaf size control: complex coordination of cell division and expansion

Size control of multicellular organisms poses a longstanding biological question that has always fascinated scientists. Currently the question is far from being resolved because of the complexity of and interconnection between cell division and cell expansion, two different events necessary to form a mature organ. Because of the importance of plants for food and renewable energy sources, dissecting the genetic networks underlying plant growth and organ size is becoming a high priority in plant science worldwide. Here, we review the current understanding of the cellular and molecular mechanisms that govern leaf organ size and discuss future prospects on research aiming at understanding organ size regulation.

Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production

Sucrose synthase (Sus) is a key enzyme in the breakdown of sucrose and is considered a biochemical marker for sink strength, especially in crop species, based on mutational and gene suppression studies. It remains elusive, however, whether, or to what extent, increase in Sus activity may enhance sink development. We aimed to address this question by expressing a potato Sus gene in cotton where Sus expression has been previously shown to be critical for normal seed and fiber development. Segregation analyses at T1 generation followed by studies in homozygous progeny lines revealed that increased Sus activity in cotton (1) enhanced leaf expansion with the effect evident from young leaves emerging from shoot apex; (2) improved early seed development, which reduced seed abortion, hence enhanced seed set, and (3) promoted fiber elongation. In young leaves of Sus overexpressing lines, fructose concentrations were significantly increased whereas, in elongating fibers, both fructose and glucose levels were increased. Since hexoses contribute little to osmolality in leaves, in contrast to developing fibers, it is concluded that high Sus activity promotes leaf development independently of osmotic regulation, probably through sugar signaling. The analyses also showed that doubling the Sus activity in 0-d cotton seeds increased their fresh weight by about 30%. However, further increase in Sus activity did not lead to any further increase in seed weight, indicating an upper limit for the Sus overexpression effect. Finally, based on the observed additive effect on fiber yield from increased fiber length and seed number, a new strategy is proposed to increase cotton fiber yield by improving seed development as a whole, rather than solely focusing on manipulating fiber growth.

Elongator complex is critical for cell cycle progression and leaf patterning in Arabidopsis

The mitotic cell cycle in higher eukaryotes is of pivotal importance for organ growth and development. Here, we report that Elongator, an evolutionarily conserved histone acetyltransferase complex, acts as an important regulator of mitotic cell cycle to promote leaf patterning in Arabidopsis. Mutations in genes encoding Elongator subunits resulted in aberrant cell cycle progression, and the altered cell division affects leaf polarity formation. The defective cell cycle progression is caused by aberrant DNA replication and increased DNA damage, which activate the DNA replication checkpoint to arrest the cell cycle. Elongator interacts with proliferating cell nuclear antigen (PCNA) and is required for efficient histone 3 (H3) and H4 acetylation coupled with DNA replication. Levels of chromatin-bound H3K56Ac and H4K5Ac known to associate with replicons during DNA replication were reduced in the mutants of both Elongator and chromatin assembly factor 1 (CAF-1), another protein complex that physically interacts with PCNA for DNA replication-coupled chromatin assembly. Disruptions of CAF-1 also led to severe leaf polarity defects, which indicated that Elongator and CAF-1 act, at least partially, in the same pathway to promote cell cycle progression. Collectively, our results demonstrate that Elongator is an important regulator of mitotic cell cycle, and the Elongator pathway plays critical roles in promoting leaf polarity formation.

Cell cycle-dependent phosphorylation of pRb-like protein in root meristem cells of Vicia faba

The retinoblastoma tumor suppressor protein (pRb) regulates cell cycle progression by controlling the G1-to-S phase transition. As evidenced in mammals, pRb has three functionally distinct binding domains and interacts with a number of proteins including the E2F family of transcription factors, proteins with a conserved LxCxE motif (D-type cyclin), and c-Abl tyrosine kinase. CDK-mediated phosphorylation of pRb inhibits its ability to bind target proteins, thus enabling further progression of the cell cycle. As yet, the roles of pRb and pRb-binding factors have not been well characterized in plants. By using antibody which specifically recognizes phosphorylated serines (S807/811) in the c-Abl tyrosine kinase binding C-domain of human pRb, we provide evidence for the cell cycle-dependent changes in pRb-like proteins in root meristems cells of Vicia faba. An increased phosphorylation of this protein has been found correlated with the G1-to-S phase transition.

The family of maize D-type cyclins: genomic organization, phylogeny and expression patterns

Cyclin proteins, associated to cyclin-dependent kinases (CDKs), play fundamental roles in cell cycle control as they constitute a very important driving force to allow cell cycle progression. D-type cyclins (CycDs) are important both for interpreting external mitogenic signals and in the control of the G1 phase. The maize (Zea mays) genome appears to contain at least 17 different CycD genes, and they fall into the subgroups previously described for other plants. Maize CycDs have been named according to identity percentages of the corresponding orthologs in rice and Arabidopsis. In silico analysis confirmed the presence of characteristic cyclin domains in each maize CycD gene and showed that their genomic organization is similar to their orthologs in rice and Arabidopsis. The expression of maize CycD genes was followed in seeds, during germination in the presence/absence of exogenously added hormones, and also in different plantlet tissues (mesocotyl, root tips and first leaf). Most cyclins were expressed in germinating seeds and at least in one of the plantlet tissues tested; almost all of the detected cyclins show an accumulating pattern of mRNA along germination (0-24 h) and higher levels in root tissue. Interestingly, some cyclins show high levels in non-proliferating tissues as leaf. Addition of auxins or cytokinins does not seem to importantly modify transcript levels; on the other hand, addition of abscisic acid repressed the expression of several cyclins. The role of each CycD during germination and plant growth and its interaction with other cell cycle proteins becomes a topic of the highest interest.

Cell-cycle control as a target for calcium, hormonal and developmental signals: the role of phosphorylation in the retinoblastoma-centred pathway

BACKGROUND

During the life cycle of plants, both embryogenic and post-embryogenic growth are essentially based on cell division and cell expansion that are under the control of inherited developmental programmes modified by hormonal and environmental stimuli. Considering either stimulation or inhibition of plant growth, the key role of plant hormones in the modification of cell division activities or in the initiation of differentiation is well supported by experimental data. At the same time there is only limited insight into the molecular events that provide linkage between the regulation of cell-cycle progression and hormonal and developmental control. Studies indicate that there are several alternative ways by which hormonal signalling networks can influence cell division parameters and establish functional links between regulatory pathways of cell-cycle progression and genes and protein complexes involved in organ development.

SCOPE

An overview is given here of key components in plant cell division control as acceptors of hormonal and developmental signals during organ formation and growth. Selected examples are presented to highlight the potential role of Ca(2+)-signalling, the complex actions of auxin and cytokinins, regulation by transcription factors and alteration of retinoblastoma-related proteins by phosphorylation.

CONCLUSIONS

Auxins and abscisic acid can directly influence expression of cyclin, cyclin-dependent kinase (CDK) genes and activities of CDK complexes. D-type cyclins are primary targets for cytokinins and over-expression of CyclinD3;1 can enhance auxin responses in roots. A set of auxin-activated genes (AXR1-ARGOS-ANT) controls cell number and organ size through modification of CyclinD3;1 gene expression. The SHORT ROOT (SHR) and SCARECROW (SCR) transcriptional factors determine root patterning by activation of the CYCD6;1 gene. Over-expression of the EBP1 gene (plant homologue of the ErbB-3 epidermal growth factor receptor-binding protein) increased biomass by auxin-dependent activation of both D- and B-type cyclins. The direct involvement of auxin-binding protein (ABP1) in the entry into the cell cycle and the regulation of leaf size and morphology is based on the transcriptional control of D-cyclins and retinoblastoma-related protein (RBR) interacting with inhibitory E2FC transcriptional factor. The central role of RBRs in cell-cycle progression is well documented by a variety of experimental approaches. Their function is phosphorylation-dependent and both RBR and phospho-RBR proteins are present in interphase and mitotic phase cells. Immunolocalization studies showed the presence of phospho-RBR protein in spots of interphase nuclei or granules in mitotic prophase cells. The Ca(2+)-dependent phosphorylation events can be accomplished by the calcium-dependent, calmodulin-independent or calmodulin-like domain protein kinases (CDPKs/CPKs) phosphorylating the CDK inhibitor protein (KRP). Dephosphorylation of the phospho-RBR protein by PP2A phosphatase is regulated by a Ca(2+)-binding subunit.

Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells

Plant retinoblastoma-related (RBR) proteins are primarily considered as key regulators of G(1)/S phase transition, with functional roles in a variety of cellular events during plant growth and organ development. Polyclonal antibody against the C-terminal region of the Arabidopsis RBR1 protein also specifically recognizes the alfalfa 115 kDa MsRBR protein, as shown by the antigen competition assay. The MsRBR protein was detected in all cell cycle phases, with a moderate increase in samples representing G(2)/M cells. Antibody against the human phospho-pRb peptide (Ser807/811) cross-reacted with the same 115 kDa MsRBR protein and with the in vitro phosphorylated MsRBR protein C-terminal fragment. Phospho-MsRBR protein was low in G(1) cells. Its amount increased upon entry into the S phase and remained high during the G(2)/M phases. Roscovitine treatment abolished the activity of alfalfa MsCDKA1;1 and MsCDKB2;1, and the phospho-MsRBR protein level was significantly decreased in the treated cells. Colchicine block increased the detected levels of both forms of MsRBR protein. Reduced levels of the MsRBR protein in cells at stationary phase or grown in hormone-free medium can be a sign of the division-dependent presence of plant RBR proteins. Immunolocalization of the phospho-MsRBR protein indicated spots of variable number and size in the labelled interphase nuclei and high signal intensity of nuclear granules in prophase. Structures similar to phospho-MsRBR proteins cannot be recognized in later mitotic phases. Based on the presented western blot and immunolocalization data, the possible involvement of RBR proteins in G(2)/M phase regulation in plant cells is discussed.

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks

Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5' half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.

Reactivation of meristem activity and sprout growth in potato tubers require both cytokinin and gibberellin

Reactivation of dormant meristems is of central importance for plant fitness and survival. Due to their large meristem size, potato (Solanum tuberosum) tubers serve as a model system to study the underlying molecular processes. The phytohormones cytokinins (CK) and gibberellins (GA) play important roles in releasing potato tuber dormancy and promoting sprouting, but their mode of action in these processes is still obscure. Here, we established an in vitro assay using excised tuber buds to study the dormancy-releasing capacity of GA and CK and show that application of gibberellic acid (GA(3)) is sufficient to induce sprouting. In contrast, treatment with 6-benzylaminopurine induced bud break but did not support further sprout growth unless GA(3) was administered additionally. Transgenic potato plants expressing Arabidopsis (Arabidopsis thaliana) GA 20-oxidase or GA 2-oxidase to modify endogenous GA levels showed the expected phenotypical changes as well as slight effects on tuber sprouting. The isopentenyltransferase (IPT) from Agrobacterium tumefaciens and the Arabidopsis cytokinin oxidase/dehydrogenase1 (CKX) were exploited to modify the amounts of CK in transgenic potato plants. IPT expression promoted earlier sprouting in vitro. Strikingly, CKX-expressing tubers exhibited a prolonged dormancy period and did not respond to GA(3). This supports an essential role of CK in terminating tuber dormancy and indicates that GA is not sufficient to break dormancy in the absence of CK. GA(3)-treated wild-type and CKX-expressing tuber buds were subjected to a transcriptome analysis that revealed transcriptional changes in several functional groups, including cell wall metabolism, cell cycle, and auxin and ethylene signaling, denoting events associated with the reactivation of dormant meristems.

The D-type cyclin gene (Nicta;CycD3;4) controls cell cycle progression in response to sugar availability in tobacco

D-type cyclins play key roles in the G1-to-S phase transition that occurs in response to nutrient and hormonal signals. In higher plants, sucrose is the major transported carbon source, and is likely to be a major determinant of cell division. To elucidate how sugar affects on the regulation of cell cycle machinery and plant development, we examined the role of carbon sources on the expression of cell-cycle-related genes in transgenic tobacco plants overexpressing Nicta;CycD3;4. The Nicta;CycD3;4 overexpressed transgenic plants showed accelerated growth and remarkable increase in the number of cells in the S and G2 phases in response to sucrose concentrations. Increased expressions level of Nicta;CycD3;4 gene was observed in transgenic tobacco plants grown on 1/2 strength MS medium supplemented with a high concentration of sugar. Moreover, the expression of sugar-sensing-related gene, invertase, was also maintained at a high level in transgenic tobacco plants with elevated sugar availability. These findings indicate that sugar availability plays a role during the G1 phase and the transition of the G1-to-S phase of cell cycle by controlling the expression of Nicta;CycD3;4.

Expression of Kip-related protein 4 gene (KRP4) in response to auxin and cytokinin during growth of Arabidopsis thaliana

The cell cycle is regulated by cyclin-dependent kinase (CDK)- cyclin complexes as well as other regulators. We isolated Kip-related protein 4 (KRP4) cDNA that encodes 289 amino acids including six conserved domains. To investigate the expression pattern of KRP4 as well as of other cell cycle-related genes associated with plant hormones, Arabidopsis seedlings were cultured on MS medium containing auxin or cytokinin. All seedlings treated with phytohormones displayed an increased proportion of cells in S phase. A higher proportion of cells in G2 phase was observed in seedlings treated with NAA. RT-PCR confirmed that the expression of KRP4 was decreased after treatment with phytohormones, and that CDKA and D-type cyclin transcription was increased. Additionally, mitotic cyclins were up-regulated by NAA treatment. These results suggest that KRP4 as well as other cell cycle-related genes might contribute to the control of plant growth in response to exogenous hormones.

Integration of light signals by the retinoblastoma pathway in the control of S phase entry in the picophytoplanktonic cell Ostreococcus

Although the decision to proceed through cell division depends largely on the metabolic status or the size of the cell, the timing of cell division is often set by internal clocks such as the circadian clock. Light is a major cue for circadian clock entrainment, and for photosynthetic organisms it is also the main source of energy supporting cell growth prior to cell division. Little is known about how light signals are integrated in the control of S phase entry. Here, we present an integrated study of light-dependent regulation of cell division in the marine green alga Ostreococcus. During early G1, the main genes of cell division were transcribed independently of the amount of light, and the timing of S phase did not occur prior to 6 hours after dawn. In contrast S phase commitment and the translation of a G1 A-type cyclin were dependent on the amount of light in a cAMP–dependent manner. CyclinA was shown to interact with the Retinoblastoma (Rb) protein during S phase. Down-regulating Rb bypassed the requirement for CyclinA and cAMP without altering the timing of S phase. Overexpression of CyclinA overrode the cAMP–dependent control of S phase entry and led to early cell division. Therefore, the Rb pathway appears to integrate light signals in the control of S phase entry in Ostreococcus, though differential transcriptional and posttranscriptional regulations of a G1 A-type cyclin. Furthermore, commitment to S phase depends on a cAMP pathway, which regulates the synthesis of CyclinA. We discuss the relative involvements of the metabolic and time/clock signals in the photoperiodic control of cell division.

Microalgae from phytoplankton play an essential role in the biogeochemical cycles through carbon dioxide assimilation in the oceans where they account for more than half of organic carbon production. Photosynthetic cells use light energy for cell growth, but light can also reset the circadian clock, which is involved in the timing of cell division. How light signals are integrated in the control of cell division remains largely unknown in photosynthetic cells. We have used the marine picoeukaryotic alga Ostreococcus to dissect the molecular mechanisms of light-dependent control of cell division. We found that the Retinoblastoma pathway integrates light signals which regulate the synthesis of CyclinA in response to cAMP. Alteration of CyclinA or Rb levels triggers cell division in limiting light conditions and bypasses the need for cAMP. In addition, CyclinA overexpression affects the timing of S phase entry. This first integrated study of light-dependent regulation of cell division in photosynthetic cells provides insight into the underlying molecular mechanisms.

Expressions of ECE-CYC2 clade genes relating to abortion of both dorsal and ventral stamens in Opithandra (Gesneriaceae)

BACKGROUND

ECE-CYC2 clade genes known in patterning floral dorsoventral asymmetry (zygomorphy) in Antirrhinum majus are conserved in the dorsal identity function including arresting the dorsal stamen. However, it remains uncertain whether the same mechanism underlies abortion of the ventral stamens, an important morphological trait related to evolution and diversification of zygomorphy in Lamiales sensu lato, a major clade of predominantly zygomorphically flowered angiosperms. Opithandra (Gesneriaceae) is of particular interests in addressing this question as it is in the base of Lamiales s.l., an early representative of this type zygomorphy.

RESULTS

We investigated the expression patterns of four ECE-CYC2 clade genes and two putative target cyclinD3 genes in Opithandra using RNA in situ hybridization and RT-PCR. OpdCYC gene expressions were correlated with abortion of both dorsal and ventral stamens in Opithandra, strengthened by the negatively correlated expression of their putative target OpdcyclinD3 genes. The complement of OpdcyclinD3 to OpdCYC expressions further indicated that OpdCYC expressions were related to the dorsal and ventral stamen abortion through negative effects on OpdcyclinD3 genes.

CONCLUSION

These results suggest that ECE-CYC2 clade TCP genes are not only functionally conserved in the dorsal stamen repression, but also involved in arresting ventral stamens, a genetic mechanism underlying the establishment of zygomorphy with abortion of both the dorsal and ventral stamens evolved in angiosperms, especially within Lamiales s.l.

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.

Eternal youth, the fate of developing Arabidopsis leaves upon Rhodococcus fascians infection

The phytopathogenic actinomycete Rhodococcus fascians induces neoplastic shooty outgrowths on infected hosts. Upon R. fascians infection of Arabidopsis (Arabidopsis thaliana), leaves are formed with small narrow lamina and serrated margins. These symptomatic leaves exhibit reduced tissue differentiation, display more but smaller cells that do not endoreduplicate, and accumulate in the G1 phase of the cell cycle. Together, these features imply that leaf growth occurs primarily through mitotic cell division and not via cell expansion. Molecular analysis revealed that cell cycle gene expression is activated continuously throughout symptomatic leaf development, ensuring persistent mitotic cycling and inhibition of cell cycle exit. The transition at the two major cell cycle checkpoints is stimulated as a direct consequence of the R. fascians signals. The extremely reduced phenotypical response of a cyclind3;1-3 triple knockout mutant indicates that the D-type cyclin/retinoblastoma/E2F transcription factor pathway, as a major mediator of cell growth and cell cycle progression, plays a key role in symptom development and is instrumental for the sustained G1-to-S and G2-to-M transitions during symptomatic leaf growth.