Cell cycle controls: genome-wide analysis in Arabidopsis

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.

Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean

Seed size and weight are important factors that influence soybean yield. Combining the weighted gene co-expression network analysis (WGCNA) of 45 soybean accessions and gene dynamic changes in seeds at seven developmental stages, we identified candidate genes that may control the seed size/weight. Among these, a PLATZ-type regulator overlapping with 10 seed weight QTLs was further investigated. This zinc-finger transcriptional regulator, named as GmPLATZ, is required for the promotion of seed size and weight in soybean. The GmPLATZ may exert its functions through direct binding to the promoters and activation of the expression of cyclin genes and GmGA20OX for cell proliferation. Overexpression of the GmGA20OX enhanced seed size/weight in soybean. We further found that the GmPLATZ binds to a 32-bp sequence containing a core palindromic element AATGCGCATT. Spacing of the flanking sequences beyond the core element facilitated GmPLATZ binding. An elite haplotype Hap3 was also identified to have higher promoter activity and correlated with higher gene expression and higher seed weight. Orthologues of the GmPLATZ from rice and Arabidopsis play similar roles in seeds. Our study reveals a novel module of GmPLATZ-GmGA20OX/cyclins in regulating seed size and weight and provides valuable targets for breeding of crops with desirable agronomic traits.

Cytokinin regulates female gametophyte development by cell cycle modulation in Arabidopsis thaliana

Male and female gametophyte development, double fertilization, and embryogenesis are key to alternating generations in angiosperms. The female gametophyte of Arabidopsis is an eight-nucleate haploid structure developed from functional megaspores (FMs) through three flawless mitoses regulated by a series of cell cycle genes. Cytokinin, an important phytohormone, plays a critical role in the regulation of plant growth and development. However, the mechanisms by which cytokinins regulate female gametophyte development remain largely unknown. In this study, we constructed transgenic plants (pES1::CKX1) with low cytokinin levels in the embryo sac. Phenotypic analysis showed that pES1::CKX1 inhibits female gametophyte development. Microscopic observation revealed that female gametophyte development of pES1::CKX1 was delayed. The promoters of all cell cycle genes were cloned and transformed into wild-type (WT). We crossed these transgenic plants of cell cycle genes expressed in ovules with pES1::CKX1 and compared the expression level of β-glucuronidase (GUS) in pES1::CKX1 and WT. Many cell cycle-regulated genes were up or downregulated in pES1::CKX1 compared with WT, and the embryo sac development cell cycle in cycd2;1/+ cycd3;3 was defective. Our results demonstrated that cytokinin affects cell division in the female gametophyte by affecting the expression of cell cycle genes.

A Journey to the Core of the Plant Cell Cycle

Production of new cells as a result of progression through the cell division cycle is a fundamental biological process for the perpetuation of both unicellular and multicellular organisms. In the case of plants, their developmental strategies and their largely sessile nature has imposed a series of evolutionary trends. Studies of the plant cell division cycle began with cytological and physiological approaches in the 1950s and 1960s. The decade of 1990 marked a turn point with the increasing development of novel cellular and molecular protocols combined with advances in genetics and, later, genomics, leading to an exponential growth of the field. In this article, I review the current status of plant cell cycle studies but also discuss early studies and the relevance of a multidisciplinary background as a source of innovative questions and answers. In addition to advances in a deeper understanding of the plant cell cycle machinery, current studies focus on the intimate interaction of cell cycle components with almost every aspect of plant biology.

A YABBY gene CRABS CLAW a (CRCa) negatively regulates flower and fruit sizes in tomato

CRABS CLAW (CRC) is a YABBY transcription factor that plays a pivotal role in carpel development and flower meristem determinacy. Here, we characterized a CRC homolog SlCRCa and elucidated its specific roles in tomato (Solanum lycopersicum). SlCRCa is highly expressed in the petals and stamens, and is responsive to gibberellin (GA) treatment. Overexpression of SlCRCa in tomato reduces the sizes of petals, stamens, and fruits, while the inverse phenotypes are induced by knockdown of SlCRCa. Furthermore, histological investigation suggests that the smaller or larger fruits in SlCRCa-overexpressing or SlCRCa-RNAi plants are mainly determined by the decreases or increases in cell layers and cell sizes in pericarp, respectively. Through transcriptome and qRT-PCR analyses, we speculate that SlCRCa inhibits cell division by regulating the transcription of cell division-related genes, and also suppresses cell expansion by modulating the expansin genes and GA pathway in tomato fruits. Besides, SlCRCa is involved in the feedback regulation of GA biosynthesis. Our findings reveal that SlCRCa negatively regulates fruit size by affecting cell division and cell expansion, and it is also an inhibitor of floral organ sizes in tomato.

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus.

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.

OsCYCP4s coordinate phosphate starvation signaling with cell cycle progression in rice

Phosphate starvation leads to a strong reduction in shoot growth and yield in crops. The reduced shoot growth is caused by extensive gene expression reprogramming triggered by phosphate deficiency, which is not itself a direct consequence of low levels of shoot phosphorus. However, how phosphate starvation inhibits shoot growth in rice is still unclear. In this study, we determined the role of OsCYCP4s in the regulation of shoot growth in response to phosphate starvation in rice. We demonstrate that the expression levels of OsCYCP4s, except OsCYCP4;3, were induced by phosphate starvation. Overexpression of the phosphate starvation induced OsCYCP4s could compete with the other cyclins for the binding with cyclin-dependent kinases, therefore suppressing growth by reducing cell proliferation. The phosphate starvation induced growth inhibition in the loss-of-function mutants cycp4;1, cycp4;2, and cycp4;4 is partially compromised. Furthermore, the expression of some phosphate starvation inducible genes is negatively modulated by these cyclins, which indicates that these OsCYCP4s may also be involved in phosphate starvation signaling. We conclude that phosphate starvation induced OsCYCP4s might coordinate phosphate starvation signaling and cell cycle progression under phosphate starvation stress.

Generation of High Yielding and Fragrant Rice (Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations

The significant increase in grain yield and quality are often antagonistic but a constant demand for breeders and consumers. Some genes related to cytochrome P450 family are known for rice organ growth but their role in controlling grain yield is still unknown. Here, we generated new rice mutants with high yield and improved aroma by simultaneously editing three cytochrome P450 homoeologs (Os03g0603100, Os03g0568400, and GL3.2) and OsBADH2 with the CRISPR/Cas9 system, and RNA-sequencing and proteomic analysis were performed to unveil the subsequent changes. High mutation efficiency was achieved in both target sites of each gene and the mutations were predominantly only deletions, while insertions were rare, and no mutations were detected in the five most likely off-target sites against each sgRNA. Mutants exhibited increased grain size, 2-acetyl-1-pyrroline (2AP) content, and grain cell numbers while there was no change in other agronomic traits. Transgene-DNA-free mutant lines appeared with a frequency of 44.44% and homozygous mutations were stably transmitted, and bi-allelic and heterozygous mutations followed Mendelian inheritance, while the inheritance of chimeric mutations was unpredictable. Deep RNA sequencing and proteomic results revealed the regulation of genes and proteins related to cytochrome P450 family, grain size and development, and cell cycle. The KEGG and hub-gene and protein network analysis showed that the gene and proteins related to ribosomal and photosynthesis pathways were mainly enriched, respectively. Our findings provide a broad and detailed basis to understand the role of CRISPR/Cas9 in rice yield and quality improvement.

Transcriptome profiling reveals genes involved in spine development during CsTTG1-regulated pathway in cucumber (Cucumis sativus L.)

The cucumber (Cucumis sativus L.), a type of fleshy fruit, is covered with spines (multicellular trichomes), which have a crucial impact on the economic value of the crop. Previous studies have found that CsTTG1 plays important roles in the initiation and further differentiation of cucumber spines, but how spine formation is regulated at the molecular level by CsTTG1 remains poorly understood. In this study, we characterized a cucumber 35S:CsTTG1 transgenic T2 line, OE-2, which bears relatively large and long spines compared with the small and short spines of the wild type (WT). Phenotypic measurements and histological analyses revealed that this phenotypic change was attributed to significant increases in cell number and size. Comparison of ovary epidermis transcriptomes between OE-2 and WT by DGE (Digital Gene Expression) analysis identified 1241 differentially expressed genes, among which 712 genes were dramatically upregulated and 529 downregulated in the ovary epidermis of OE-2. XTH23 and Cyclin family genes were significantly activated in OE-2, and transcription factors (TFs) were found to participate in spine size regulation in OE-2. Further analyses confirmed that GA was implicated in the regulation of fruit spine development in cucumber. Thus, our study provides a foundation for dissecting the molecular regulatory networks of fruit spine control in cucumber.

Advances Towards How Meiotic Recombination Is Initiated: A Comparative View and Perspectives for Plant Meiosis Research

Meiosis is an essential cell-division process for ensuring genetic diversity across generations. Meiotic recombination ensures the accuracy of genetic interchange between homolous chromosomes and segregation of parental alleles. Programmed DNA double-strand breaks (DSBs), catalyzed by the evolutionarily conserved topoisomerase VIA (a subunit of the archaeal type II DNA topoisomerase)-like enzyme Spo11 and several other factors, is a distinctive feature of meiotic recombination initiation. The meiotic DSB formation and its regulatory mechanisms are similar among species, but certain aspects are distinct. In this review, we introduced the cumulative knowledge of the plant proteins crucial for meiotic DSB formation and technical advances in DSB detection. We also summarized the genome-wide DSB hotspot profiles for different model organisms. Moreover, we highlighted the classical views and recent advances in our knowledge of the regulatory mechanisms that ensure the fidelity of DSB formation, such as multifaceted kinase-mediated phosphorylation and the consequent high-dimensional changes in chromosome structure. We provided an overview of recent findings concerning DSB formation, distribution and regulation, all of which will help us to determine whether meiotic DSB formation is evolutionarily conserved or varies between plants and other organisms.

Poly(ADP-ribose) polymerases regulate cell division and development in Arabidopsis roots

Root organogenesis involves cell division, differentiation and expansion. The molecular mechanisms regulating root development are not fully understood. In this study, we identified poly(adenosine diphosphate (ADP)-ribose) polymerases (PARPs) as new players in root development. PARP catalyzes poly(ADP-ribosyl)ation of proteins by repeatedly adding ADP-ribose units onto proteins using nicotinamide adenine dinucleotide (NAD⁺ ) as the donor. We found that inhibition of PARP activities by 3-aminobenzomide (3-AB) increased the growth rates of both primary and lateral roots, leading to a more developed root system. The double mutant of Arabidopsis PARPs, parp1parp2, showed more rapid primary and lateral root growth. Cyclin genes regulating G1-to-S and G2-to-M transition were up-regulated upon treatment by 3-AB. The proportion of 2C cells increased while cells with higher DNA ploidy declined in the roots of treated plants, resulting in an enlarged root meristematic zone. The expression level of PARP2 was very low in the meristematic zone but high in the maturation zone, consistent with a role of PARP in inhibiting mitosis and promoting cell differentiation. Our results suggest that PARPs play an important role in root development by negatively regulating root cell division.

Nitric oxide-cytokinin interplay influences selenite sensitivity in Arabidopsis

Selenite oppositely modifies cytokinin and nitric oxide metabolism in Arabidopsis organs. A mutually negative interplay between the molecules exists in selenite-exposed roots; and their overproduction causes selenite insensitivity. Selenium-induced phytotoxicity is accompanied by developmental alterations such as primary root (PR) shortening. Growth changes are provoked by the modulation of hormone status and signalling. Cytokinin (CK) cooperates with the nitric oxide (NO) in many aspects of plant development; however, their interaction under abiotic stress has not been examined. Selenite inhibited the growth of Arabidopsis seedlings and reduced root meristem size through cell division arrest. The CK-dependent pARR5::GUS activity revealed the intensification of CK signalling in the PR tip, which may be partly responsible for the root meristem shortening. The selenite-induced alterations in the in situ expressions of cytokinin oxidases (AtCKX4::GUS, AtCKX5::GUS) are associated with selenite-triggered changes of CK signalling. In wild-type (WT) and NO-deficient nia1nia2 root, selenite led to the diminution of NO content, but CK overproducer ipt-161 and -deficient 35S:CKX2 roots did not show NO decrease. Exogenous NO (S-nitroso-N-acetyl-DL-penicillamine, SNAP) reduced the pARR5::GFP and pTCS::GFP expressions. Roots of the 35S:CKX and cyr1 plants suffered more severe selenite-triggered viability loss than the WT, while in ipt-161 and gsnor1-3 no obvious viability decrease was observed. Exogenous NO ameliorated viability loss, but benzyladenine intensified it. Based on the results, selenite impacts development by oppositely modifying CK signalling and NO level. In the root system, CK signalling intensifies which possibly contributes to the nitrate reductase-independent NO diminution. A mutually negative CK-NO interplay exists in selenite-exposed roots; however, overproduction of both molecules worsens selenite sensing. Hereby, we suggest novel regulatory interplay and role for NO and CK in abiotic stress signalling.

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation for dissecting the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.

Wuschel-related homeobox 8/9 is important for proper embryo patterning in the gymnosperm Norway spruce

Proper embryo development is crucial as that is when the primary body axes are established. In Arabidopsis, AtWOX8 and AtWOX9, members of the Wuschel-related homeobox (WOX) gene family, are critical for embryo development. In Norway spruce, PaWOX8/9, which is expressed in embryos, is the homologue of AtWOX8 and AtWOX9. In this work, it is shown that the transcript abundance of PaWOX8/9 is high during early and late embryogeny and that it decreases when the maturation phase starts. To address the function of PaWOX8/9 during embryo development, RNAi lines were established to down-regulate the transcript level of PaWOX8/9, using both constitutive and inducible promoters. Embryos in the PaWOX8/9 RNAi lines show an aberrant morphology caused by disturbed orientation of the cell division plane at the basal part of the embryonal mass during early and late embryogeny. In addition, the transcript level of several key cell-cycle-regulating genes, for example, PaE2FAB-like and PaCYCLIN B-like, are affected in the PaWOX8/9 RNAi lines. Taken together, our results suggest that PaWOX8/9 may perform an evolutionarily conserved function as a regulator of the establishment of the apical-basal embryo pattern.

GhH2A12, a replication-dependent histone H2A gene from Gossypium hirsutum, is negatively involved in the development of cotton fiber cells

GhH2A12 was preferentially expressed at the initiation and early elongation stage of cotton fiber development, and overexpression of GhH2A12 caused retardation of fiber initiation and produced shorter fibers. Histone H2A is a component of eukaryotic chromatin whose function has not been studied in cotton. We have isolated an H2A gene encoding 156 amino acids, named GhH2A12. Like other plant histone H2As, GhH2A12 contains a typical SPKK motif in the carboxy-terminal and a plant-unique peptide-binding A/T-rich DNA region, and it was localized to the nucleus. GhH2A12 was preferentially expressed at the initiation and early elongation stage of cotton fiber, from 0 to 5 days post anthesis and the transcript level declined rapidly when the fiber entered the fast elongation stage, suggesting that GhH2A12 was involved in fiber differentiation. Therefore, GhH2A12 overexpression and RNAi transgenic cotton lines were developed via Agrobacterium tumefaciens-mediated transformation. Overexpression of GhH2A12 caused retardation of fiber initiation and produced shorter fibers and lower lint percentages. Moreover, the overexpressors showed negative effects on seedling growth, and the leaf emergence was delayed compared to wild type. However, no significant change in the GhH2A12 suppression line was observed. Coupled with retardation of fiber initiation, upregulation of GhH2A12 downregulated the expression of genes involved in cell-cycle performance. These results suggest that GhH2A12 might regulate fiber differentiation via regulating the cell cycle-related genes.

Over-expression of SlCycA3 gene in Arabidopsis accelerated the cell cycle transition

We characterised an A-type cyclin SlCycA3 (AJ243453) from tomato (Solanum lycopersicum L.). Phylogenetic analysis based on the deduced amino acid sequence revealed that SlCycA3 was 71% identical to A3-type cyclin in Nicotiana tabacum L. (CAA63540), 48% identical to its homologue found in Arabidopsis thaliana (NP_199122), and 48% identical to its homologue in Pisum sativum L. (CAB77269). SlCycA3 gene was transformed into Arabidopsis plants in order to study its function. The hypocotyl length of transgenic plants was approximately half the length of wild-type plants, and the cell size in the transgenic lines was also smaller. The transgenic plants had longer roots than the wild type. Overexpression of SlCycA3 gene accelerated the cell cycle from G1/S transition to early M-phase, thereby accelerating the cell division. When the plants were treated with IAA and 3-indolebutyric acid (IBA) for 2 days, the transgenic plants produced more lateral roots than wild type. Treatment with IBA significantly increased the cell number in the G2-phase in transgenic plants compared with wild type after treatment for 10 days, whereas the proportion of cells in the S-phase was strongly increased by IAA treatment both in wild-type and transgenic plants. These results suggest a possible key role for cyclin in regulating root growth and development and provide some evidence of cell division underlying hormone treatment in plants.

Dissimilar effects of β-lapachone- and hydroxyurea-induced DNA replication stress in root meristem cells of Allium cepa

Two anticancer drugs, β-lapachone (β-lap, a naphthoquinone) and hydroxyurea (HU, an inhibitor of ribonucleotide reductase), differently affect nuclear morphology and cell cycle control mechanisms in root meristem cells of Allium cepa. The 18 h treatment with 100 μM β-lap results in a lowered number of M-phase cells, increased occurrence of mitotic abnormalities, including over-condensation of chromosomes, their enhanced stickiness, formation of anaphase bridges, micronucleation and reduced mitotic spindles. Following prolonged incubations using high doses of β-lap, cell nuclei reveal dark-red fluorescence evenly distributed in chromatin surrounding the unstained regions of nucleoli. Both drugs generate H2O2 and induce DNA double strand breaks, which is correlated with γ-phoshorylation of H2AX histones. However, the extent of H2AX phosphorylation (including the frequency of γ-H2AX foci and the relative number cells creating phospho-H2AX domains) is considerably reduced in root meristem cells treated jointly with the β-lap/HU mixture. Furthermore, various effects of caffeine (an inhibitor of ATM/ATR cell cycle checkpoint kinases) on β-lap- and HU-induced γ-phoshorylation of H2AX histones and the protective activity of HU against β-lap suggest that their genotoxic activities are largely dissimilar. β-Lap treatment results in the induction of apoptosis-like programmed cell death, while HU treatment leads to cell adaptation to replication stress and promotion of abnormal nuclear divisions with biphasic interphase/mitotic states of chromatin condensation.

Long-distance signaling in bypass1 mutants: bioassay development reveals the bps signal to be a metabolite

Root-to-shoot signaling is used by plants to coordinate shoot development with the conditions experienced by the roots. A mobile and biologically active compound, the bps signal, is over-produced in roots of an Arabidopsis thaliana mutant called bypass1 (bps1), and might also be a normally produced signaling molecule in wild-type plants. Our goal is to identify the bps signal chemically, which will then allow us to assess its production in normal plants. To identify any signaling molecule, a bioassay is required, and here we describe the development of a robust, simple, and quantitative bioassay for the bps signal. The developed bioassay follows the growth-reducing activity of the bps signal using the pCYCB1;1::GUS cell cycle marker. Wild-type plants carrying this marker, and provided the bps signal through either grafts or metabolite extracts, showed reduced cell division. By contrast, control grafts and treatment with control extracts showed no change in pCYCB1;1::GUS expression. To determine the chemical nature of the bps signal, extracts were treated with RNase A, Proteinase K, or heat. None of these treatments diminished the activity of bps1 extracts, suggesting that the active molecule might be a metabolite. This bioassay will be useful for future biochemical fractionation and analysis directed toward bps signal identification.

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.

Genome-wide analysis of cyclins in maize (Zea mays)

Cyclins are primary regulators of the activity of cyclin-dependent kinases and play crucial roles in cell cycle progression in eukaryotes. Although extensive studies have revealed the roles of some cyclins and underlying mechanisms in plants, relatively few cyclins have been functionally analyzed in maize. We identified 59 cyclins in the maize genome, distributed on 10 chromosomes; these were grouped into six types by phylogenetic analysis. The cyclin genes in the maize genome went through numerous tandem gene duplications on five chromosomes. However, no segmental duplications, which occur in rice, were found on maize chromosomes. This information allows us to assess the position of plant cyclin genes in terms of evolution and classification, which will be useful for functional studies of maize cyclins.

Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes

Cell division depends on the correct localization of the cyclin-dependent kinases that are regulated by phosphorylation, cyclin proteolysis, and protein-protein interactions. Although immunological assays can define cell cycle protein abundance and localization, they are not suitable for detecting the dynamic rearrangements of molecular components during cell division. Here, we applied an in vivo approach to trace the subcellular localization of 60 Arabidopsis (Arabidopsis thaliana) core cell cycle proteins fused to green fluorescent proteins during cell division in tobacco (Nicotiana tabacum) and Arabidopsis. Several cell cycle proteins showed a dynamic association with mitotic structures, such as condensed chromosomes and the preprophase band in both species, suggesting a strong conservation of targeting mechanisms. Furthermore, colocalized proteins were shown to bind in vivo, strengthening their localization-function connection. Thus, we identified unknown spatiotemporal territories where functional cell cycle protein interactions are most likely to occur.

A rice kinase-protein interaction map

Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

Transgenic tobacco plants overexpressing the Nicta; CycD3; 4 gene demonstrate accelerated growth rates

D-type cyclins control the onset of cell division and the response to extracellular signals during the G1 phase. In this study, we transformed a D-type cyclin gene, Nicta;CycD3;4, from Nicotiana tabacum using an Agrobacterium-mediated method. A predicted 1.1 kb cyclin gene was present in all of the transgenic plants, but not in wild-type. Northern analyses showed that the expression level of the Nicta;CycD3;4 gene in all of the transgenic plants was strong when compared to the wild-type plants, suggesting that Nicta;CycD3;4 gene driven by the CaMV 35S promoter was being overexpressed. Our results revealed that transgenic plants overexpressing Nicta;CycD3;4 had an accelerated growth rate when compared to wild-type plants, and that the transgenic plants exhibited a smaller cell size and a decreased cell population in young leaves when compared to wild-type plants.

Cell fate switch during in vitro plant organogenesis

Plant mature cells have the capability to reverse their state of differentiation and produce new organs under cultured conditions. Two phases, dedifferentiation and redifferentiation, are commonly characterized during in vitro organogenesis. In these processes, cells undergo fate switch several times regulated by both extrinsic and intrinsic factors, which are associated with reentry to the cell cycle, the balance between euchromatin and heterochromatin, reprogramming of gene expression, and so forth. This short article reviews the advances in the mechanism of organ regeneration from plant somatic cells in molecular, genomic and epigenetic aspects, aiming to provide important information on the mechanism underlying cell fate switch during in vitro plant organogenesis.

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.

The nanovirus-encoded Clink protein affects plant cell cycle regulation through interaction with the retinoblastoma-related protein

Nanoviruses, multicomponent single-stranded DNA plant viruses, encode a unique cell cycle link protein, Clink, that interacts with retinoblastoma-related proteins (RBR). We have established transgenic Arabidopsis thaliana lines that conditionally express Clink or a Clink variant deficient in RBR binding. By controlled induction of Clink expression, we demonstrated the capacity of the Clink protein to alter RBR function in vivo. We showed that transcription of both S-phase-specific and G2/M-phase-specific genes was up-regulated depending on the RBR-binding proficiency of Clink. Concomitantly, ploidy levels increased in a substantial fraction of leaf cell nuclei. Also, leaf epidermis cells of transgenic plants producing Clink were smaller and more numerous, indicating additional cell divisions in this tissue. Furthermore, cytogenetic analyses following induction of Clink expression in mature leaves revealed the presence of metaphasic and anaphasic nuclei, clear evidence that Clink-mediated RBR inactivation is sufficient to induce quiescent cells to reenter cell cycle progression and, for at least a fraction of them, to pass through mitosis. Expression of Clink had no effect on genes transcribed by RNA polymerases I and III, suggesting that, in contrast to its mammalian homologue, A. thaliana RBR is not involved in the repression of polymerase I and polymerase III transcription. The results of these in vivo analyses firmly establish Clink as a member of the diverse class of multifunctional cell cycle modulator proteins encoded by small DNA viruses.

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.

Genome-wide analysis of cyclin family in rice (Oryza Sativa L.)

The cyclins together with highly conserved cyclin-dependent kinases regulate cell cycle progression in plants. Although extensive and systematic study on cell cycle mechanisms and cyclin functions in yeasts and animals has been carried out, only a small number of plant cyclins have been characterized and classified functionally and phylogenetically. We identified several types of cyclin genes in the rice genome and characterized them by phylogenetic, tandem and segmental duplications analyses. Our results indicated that there were at least 49 predicted rice cyclin genes in the rice genome, and they were distributed on 12 chromosomes. Of these cyclins, one possessed only cyclin_C domain and no cyclin_N domain, and the remaining 48 cyclins with cyclin_N domains were classified as nine types based on evolutionary relationships. Eight of these nine types were common between rice and Arabidopsis, whereas only one, known as F-type cyclins, was unique to rice. No homologues of the F-type cyclins in plants could be retrieved from the public databases, and reverse transcription-PCR analysis supported an existence of the F-type cyclin genes. Sequence alignment suggested that the cyclin genes in the rice genome experienced a mass of gene tandem and segmental duplications occurred on seven chromosomes related to the origins of new cyclin genes. Our study provided an opportunity to facilitate assessment and classification of new members, serving as a guide for further functional elucidation of rice cyclins.

Overexpression of RAN1 in rice and Arabidopsis alters primordial meristem, mitotic progress, and sensitivity to auxin

Ran is an evolutionarily conserved eukaryotic GTPase. We previously identified a cDNA of TaRAN1, a novel Ran GTPase homologous gene in wheat (Triticum aestivum) and demonstrated that TaRAN1 is associated with regulation of genome integrity and cell division in yeast (Saccharomyces cerevisiae) systems. However, much less is known about the function of RAN in plant development. To analyze the possible biological roles of Ran GTPase, we overexpressed TaRAN1 in transgenic Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). TaRAN1 overexpression increased the proportion of cells in the G2 phase of the cell cycle, which resulted in an elevated mitotic index and prolonged life cycle. Furthermore, it led to increased primordial tissue, reduced number of lateral roots, and stimulated hypersensitivity to exogenous auxin. The results suggest that Ran protein was involved in the regulation of mitotic progress, either in the shoot apical meristem or the root meristem zone in plants, where auxin signaling is involved. This article determines the function of RAN in plant development mediated by the cell cycle and its novel role in meristem initiation mediated by auxin signaling.

The co-ordination of cell division, differentiation and morphogenesis in the shoot apical meristem: a perspective

Whether morphogenesis is cell division-driven or organismal-based has been a long-running debate in plant biology. This article is a summary of a series of experiments aimed at distinguishing these alternate views by local manipulation of parameters of cell division frequency, orientation, and growth within the shoot apical meristem. These data, put in the context of other investigations in this area, support an organismal view of plant morphogenesis and support the idea that the cell wall plays a key role in the mechanism by which this is achieved. At the same time, the data indicate that the intimate but variable relationship between cell growth and division within the organism means that cell proliferation can indirectly influence this process, leading to a context-dependent influence on morphogenesis. Finally, cell growth and proliferation are intimately related with the process of differentiation as cells exit the meristem. In the final part of the article the molecular mechanism by which these basic cellular parameters are intertwined is discussed.

Atypical regulation of a green lineage-specific B-type cyclin-dependent kinase

Cyclin-dependent kinases (CDKs) are the main regulators of cell cycle progression in eukaryotes. The role and regulation of canonical CDKs, such as the yeast (Saccharomyces cerevisiae) Cdc2 or plant CDKA, have been extensively characterized. However, the function of the plant-specific CDKB is not as well understood. Besides being involved in cell cycle control, Arabidopsis (Arabidopsis thaliana) CDKB would integrate developmental processes to cell cycle progression. We investigated the role of CDKB in Ostreococcus (Ostreococcus tauri), a unicellular green algae with a minimal set of cell cycle genes. In this primitive alga, at the basis of the green lineage, CDKB has integrated two levels of regulations: It is regulated by Tyr phosphorylation like cdc2/CDKA and at the level of synthesis-like B-type CDKs. Furthermore, Ostreococcus CDKB/cyclin B accounts for the main peak of mitotic activity, and CDKB is able to rescue a yeast cdc28(ts) mutant. By contrast, Ostreococcus CDKA is not regulated by Tyr phosphorylation, and it exhibits a low and steady-state activity from DNA replication to exit of mitosis. This suggests that from a major role in the control of mitosis in green algae, CDKB has evolved in higher plants to assume other functions outside the cell cycle.

A physiological overview of the genetics of flowering time control

Physiological studies on flowering time control have shown that plants integrate several environmental signals. Predictable factors, such as day length and vernalization, are regarded as 'primary', but clearly interfere with, or can even be substituted by, less predictable factors. All plant parts participate in the sensing of these interacting factors. In the case of floral induction by photoperiod, long-distance signalling is known to occur between the leaves and the shoot apical meristem (SAM) via the phloem. In the long-day plant, Sinapis alba, this long-distance signalling has also been shown to involve the root system and to include sucrose, nitrate, glutamine and cytokinins, but not gibberellins. In Arabidopsis thaliana, a number of genetic pathways controlling flowering time have been identified. Models now extend beyond 'primary' controlling factors and show an ever-increasing number of cross-talks between pathways triggered or influenced by various environmental factors and hormones (mainly gibberellins). Most of the genes involved are preferentially expressed in meristems (the SAM and the root tip), but, surprisingly, only a few are expressed preferentially or exclusively in leaves. However, long-distance signalling from leaves to SAM has been shown to occur in Arabidopsis during the induction of flowering by long days. In this review, we propose a model integrating physiological data and genes activated by the photoperiodic pathway controlling flowering time in early-flowering accessions of Arabidopsis. This model involves metabolites, hormones and gene products interacting as long- or short-distance signalling molecules.

Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins

Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.

Arabidopsis pdr2 reveals a phosphate-sensitive checkpoint in root development

Plants have evolved complex strategies to maintain phosphate (Pi) homeostasis and to maximize Pi acquisition when the macronutrient is limiting. Adjustment of root system architecture via changes in meristem initiation and activity is integral to the acclimation process. However, the mechanisms that monitor external Pi status and interpret the nutritional signal remain to be elucidated. Here, we present evidence that the Pi deficiency response, pdr2, mutation disrupts local Pi sensing. The sensitivity and amplitude of metabolic Pi-starvation responses, such as Pi-responsive gene expression or accumulation of anthocyanins and starch, are enhanced in pdr2 seedlings. However, the most conspicuous alteration of pdr2 is a conditional short-root phenotype that is specific for Pi deficiency and caused by selective inhibition of root cell division followed by cell death below a threshold concentration of about 0.1 mm external Pi. Measurements of general Pi uptake and of total phosphorus (P) in root tips exclude a defect in high-affinity Pi acquisition. Rescue of root meristem activity in Pi-starved pdr2 by phosphite (Phi), a non-metabolizable Pi analog, and divided-root experiments suggest that pdr2 disrupts sensing of low external Pi availability. Thus, PDR2 is proposed to function at a Pi-sensitive checkpoint in root development, which monitors environmental Pi status, maintains and fine-tunes meristematic activity, and finally adjusts root system architecture to maximize Pi acquisition.

Altered life cycle in Arabidopsis plants expressing PsUGT1, a UDP-glucuronosyltransferase-encoding gene from pea

Alfalfa (Medicago sativa) and Arabidopsis were used as model systems to examine molecular mechanisms underlying developmental effects of a microsomal UDP-glucuronosyltransferase-encoding gene from pea (Pisum sativum; PsUGT1). Alfalfa expressing PsUGT1 antisense mRNA under the control of the cauliflower mosaic virus (CaMV) 35S promoter exhibited delayed root emergence, reduced root growth, and increased lateral root development. The timing of root emergence in wild-type and antisense plants was correlated with the transient accumulation of auxin at the site of root emergence. Cell suspension cultures derived from the antisense alfalfa plants exhibited a delay in cell cycle from 24-h in the wild-type plants to 48-h in the antisense plants. PsUGT1::uidA was introduced into Arabidopsis to demonstrate that, as in alfalfa and pea, PsUGT1 expression occurs in regions of active cell division. This includes the root cap and root apical meristems, leaf primordia, tips of older leaves, and the transition zone between the hypocotyl and the root. Expression of PsUGT1::uidA colocalized with the expression of the auxin-responding reporter DR5::uidA. Co-expression of DR5::uidA in transgenic Arabidopsis lines expressing CaMV35S::PsUGT1 revealed that ectopic expression of CaMV35S::PsUGT1 is correlated with a change in endogenous auxin gradients in roots. Roots of ecotype Columbia expressing CaMV35S::PsUGT1 exhibited distinctive responses to exogenous naphthalene acetic acid. Completion of the life cycle occurred in 4 to 6 weeks compared with 6 to 7 weeks for wild-type Columbia. Inhibition of endogenous ethylene did not correct this early senescence phenotype.

Arabidopsis D-type cyclin CYCD4;1 is a novel cyclin partner of B2-type cyclin-dependent kinase

B-type cyclin-dependent kinases (CDKs) are unique to plants and are assumed to be involved in the control of the G2-to-M phase progression and mitotic events. However, little is known about their cyclin partners. In Arabidopsis, we isolated cDNA encoding the D-type cyclin CYCD4;1 by a yeast (Saccharomyces cerevisiae) two-hybrid screening using CDKB2;1 as bait. In vitro pull-down assay showed that CYCD4;1 bound to CDKB2;1 and CDKA;1. Protein complexes of CYCD4;1-CDKA;1 and CYCD4;1-CDKB2;1 in insect cells exhibited histone H1-kinase activity. Promoter analysis using the luciferase reporter gene showed that CDKB2;1 was expressed from early G2 to M phase, whereas CYCD4;1 was expressed throughout the cell cycle. In situ hybridization of plant tissues revealed that both CDKB2;1 and CYCD4;1 transcripts accumulated in the shoot apical meristem, leaf primordia, vasculature of leaves, and tapetal cells in anthers. Our results suggest that CDKB2;1 and CYCD4;1 may form an active kinase complex during G2/M phase and control the development of particular tissues.

Regulation of MSV and WDV virion-sense promoters by WDV nonstructural proteins: a role for their retinoblastoma protein-binding motifs

In this work we demonstrate that wheat dwarf virus (WDV) RepA can activate WDV and maize streak virus (MSV) virion (V)-sense expression in plant tissues. Rep alone does not have any effect on the silent WDV promoter and it represses the basal MSV promoter activity. MSV promoter activation by RepA depends on an intact RepA retinoblastoma protein (RB)-binding domain. Promoter repression by Rep also depends on this domain to some extent. Mutation of the RepA RB-binding domain has no effect on WDV promoter activation. The WDV promoter contains two sites that fit the consensus E2F-binding site. One, WDV1, binds human E2F-1 in one-hybrid assays in yeast. It also binds specifically to maize and wheat proteins in vitro and, when fused to a minimal 35S promoter, it confers responsiveness to RepA only when the RepA RB-binding domain and the WDV1 site are intact. In the whole WDV V-sense promoter context, mutations of this sequence have no effect, suggesting that additional sequences are important for RepA-mediated promoter activation.

Mitosis in plants: how far we have come at the molecular level?

The basic mechanism of mitosis is universally conserved in all eucaryotes, but specific solutions to achieve this process have been adapted by different organisms during evolution. Although cytological studies of plant cells have contributed to our understanding of chromatin dynamics during mitosis, many of the molecular mechanisms that control mitosis have been identified in yeast and animal cells. Nevertheless, recent advances have begun to fill the gaps in our understanding of how mitosis is regulated in plants, and raise intriguing questions to be answered in the future.