Activation of an alfalfa cyclin-dependent kinase inhibitor by calmodulin-like domain protein kinase

Identification of short protein-destabilizing sequences in Arabidopsis cyclin-dependent kinase inhibitors, ICKs

Plants have a family of cyclin-dependent kinase (CDK) inhibitors called interactors/inhibitors of CDK (ICKs) or Kip-related proteins (KRPs). ICK proteins have important functions in cell proliferation, endoreduplication, plant growth, and reproductive development, and their functions depend on the protein levels. However, understanding of how ICK protein levels are regulated is very limited. We fused Arabidopsis ICK sequences to green fluorescent protein (GFP) and determined their effects on the fusion proteins in plants, yeast, and Escherichia coli. The N-terminal regions of ICKs drastically reduced GFP fusion protein levels in Arabidopsis plants. A number of short sequences of 10-20 residues were found to decrease GFP fusion protein levels when fused at the N-terminus or C-terminus. Three of the four short sequences from ICK3 showed a similar function in yeast. Intriguingly, three short sequences from ICK1 and ICK3 caused the degradation of the fusion proteins in E. coli. In addition, computational analyses showed that ICK proteins were mostly disordered and unstructured except for the conserved C-terminal region, suggesting that ICKs are intrinsically disordered proteins. This study has identified a number of short protein-destabilizing sequences, and evidence suggests that some of them may cause protein degradation through structural disorder and instability.

Characterization of the soybean KRP gene family reveals a key role for GmKRP2a in root development

Kip-related proteins (KRPs), as inhibitory proteins of cyclin-dependent kinases, are involved in the growth and development of plants by regulating the activity of the CYC-CDK complex to control cell cycle progression. The KRP gene family has been identified in several plants, and several KRP proteins from Arabidopsis thaliana have been functionally characterized. However, there is little research on KRP genes in soybean, which is an economically important crop. In this study, we identified nine GmKRP genes in the Glycine max genome using HMM modeling and BLASTP searches. Protein subcellular localization and conserved motif analysis showed soybean KRP proteins located in the nucleus, and the C-terminal protein sequence was highly conserved. By investigating the expression patterns in various tissues, we found that all GmKRPs exhibited transcript abundance, while several showed tissue-specific expression patterns. By analyzing the promoter region, we found that light, low temperature, an anaerobic environment, and hormones-related cis-elements were abundant. In addition, we performed a co-expression analysis of the GmKRP gene family, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) set enrichment analysis. The co-expressing genes were mainly involved in RNA synthesis and modification and energy metabolism. Furthermore, the GmKRP2a gene, a member of the soybean KRP family, was cloned for further functional analysis. GmKRP2a is located in the nucleus and participates in root development by regulating cell cycle progression. RNA-seq results indicated that GmKRP2a is involved in cell cycle regulation through ribosome regulation, cell expansion, hormone response, stress response, and plant pathogen response pathways. To our knowledge, this is the first study to identify and characterize the KRP gene family in soybean.

Increasing yield on dry fields: molecular pathways with growing potential

Drought stress constitutes one of the major constraints to agriculture all over the world, and its devastating effect is only expected to increase in the following years due to climate change. Concurrently, the increasing food demand in a steadily growing population requires a proportional increase in yield and crop production. In the past, research aimed to increase plant resilience to severe drought stress. However, this often resulted in stunted growth and reduced yield under favorable conditions or moderate drought. Nowadays, drought tolerance research aims to maintain plant growth and yield under drought conditions. Overall, recently deployed strategies to engineer drought tolerance in the lab can be classified into a 'growth-centered' strategy, which focuses on keeping growth unaffected by the drought stress, and a 'drought resilience without growth penalty' strategy, in which the main aim is still to boost drought resilience, while limiting the side effects on plant growth. In this review, we put the scope on these two strategies and some molecular players that were successfully engineered to generate drought-tolerant plants: abscisic acid, brassinosteroids, cytokinins, ethylene, ROS scavenging genes, strigolactones, and aquaporins. We discuss how these pathways participate in growth and stress response regulation under drought. Finally, we present an overview of the current insights and future perspectives in the development of new strategies to improve drought tolerance in the field.

Exogenously-supplied trehalose inhibits the growth of wheat seedlings under high temperature by affecting plant hormone levels and cell cycle processes

High temperature reduces the yield of crops, and exogenous trehalose can improve the stress resistance of plants. However, the mechanism by which trehalose causes phenotypic changes in plants is still unknown. Here we investigated the effects of exogenously supplied trehalose (1.5 mM) during high-temperature stress and subsequent recovery on plant hormones and cell cycle in wheat seedlings. Our results showed that after high-temperature stress, exogenously supplied trehalose reduced the root length, vertical height, leaf area, and leaf length of wheat seedlings, thereby reducing their growth. However, the content of hormones, such as abscisic acid, auxin (IAA), gibberellin (GA₃), and cytokinin in seedlings pretreated with trehalose and high-temperature stress was lower than that under high-temperature stress alone. Our further experiments showed that the levels of these hormones were affected by genes involved in hormone biosynthesis and decomposition pathways in trehalose-pretreated seedlings. Compared with control plants, the activity of IAA oxidase is also higher. In addition, exogenous trehalose decreased the transcriptional levels of CycD2 and CDC2 (two genes regulating cell cycle progression) under heat stress, and reduced the activity of vacuolar invertase after recovery from heat stress, thereby shortening the cell length. These results indicate that trehalose inhibits wheat growth at high temperature by affecting plant hormone levels and the cell cycle process.AbbreviationsABA, abscisic acid; CDK, cyclin-dependent kinase; CycD, D-type cyclins; GA₃, gibberellin; IAA, auxin; KRP, KIP-related protein; T6P, trehalsoe-6-phosphate; VIN, vacuolar invertase.

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.

Cyclin-Dependent Kinase Inhibitor Gene TaICK1 acts as a Potential Contributor to Wheat Male Sterility induced by a Chemical Hybridizing Agent

Heterosis has been widely accepted as an effective strategy to increase yields in plant breeding. Notably, the chemical hybridization agent SQ-1 induces male sterility in wheat, representing a critical potential tool in hybrid seed production. However, the mechanisms underlying the male sterility induced by SQ-1 still remain poorly understood. In this study, a cyclin-dependent kinase inhibitor gene, TaICK1, which encodes a 229 amino acid protein, was identified as a potential contributor to male sterility in common wheat. The expression of TaICK1 was upregulated during the development of anthers in Xinong1376 wheat treated with SQ-1. Meanwhile, the seed setting rate was found to be significantly decreased in TaICK1 transgenic rice. Furthermore, we identified two cyclin proteins, TaCYCD2;1 and TaCYCD6;1, as interactors through yeast two-hybrid screening using TaICK1 as the bait, which were validated using bimolecular fluorescence complementation. Subcellular localization revealed that the proteins encoded by TaICK1, TaCYCD2;1, and TaCYCD6;1 were localized in the cell nucleus. The expression levels of TaCYCD2;1 and TaCYCD6;1 were lower in Xinong1376 treated with SQ-1. A further analysis demonstrated that the expression levels of OsCYCD2;1 and OsCYCD6;1 were lower in transgenic TaICK1 rice lines as well. Taken together, these results suggest that the upregulation of TaICK1, induced by SQ-1, may subsequently suppress the expression of TaCYCD2;1 and TaCYCD6;1 in anthers, resulting in male sterility. This study provides new insights into the understanding of SQ-1-induced wheat male sterility, as well as the developmental mechanisms of anthers.

Local endoreduplication as a feature of intracellular fungal accommodation in arbuscular mycorrhizas

The intracellular accommodation of arbuscular mycorrhizal (AM) fungi is a paradigmatic feature of this plant symbiosis that depends on the activation of a dedicated signaling pathway and the extensive reprogramming of host cells, including striking changes in nuclear size and transcriptional activity. By combining targeted sampling of early root colonization sites, detailed confocal imaging, flow cytometry and gene expression analyses, we demonstrate that local, recursive events of endoreduplication are triggered in the Medicago truncatula root cortex during AM colonization. AM colonization induces an increase in ploidy levels and the activation of endocycle specific markers. This response anticipates the progression of fungal colonization and is limited to arbusculated and neighboring cells in the cortical tissue. Furthermore, endoreduplication is not induced in M. truncatula mutants for symbiotic signaling pathway genes. On this basis, we propose endoreduplication as part of the host cell prepenetration responses that anticipate AM fungal accommodation in the root cortex.

Proteins with calmodulin-like domains: structures and functional roles

The appearance of modular proteins is a widespread phenomenon during the evolution of proteins. The combinatorial arrangement of different functional and/or structural domains within a single polypeptide chain yields a wide variety of activities and regulatory properties to the modular proteins. In this review, we will discuss proteins, that in addition to their catalytic, transport, structure, localization or adaptor functions, also have segments resembling the helix-loop-helix EF-hand motifs found in Ca2+-binding proteins, such as calmodulin (CaM). These segments are denoted CaM-like domains (CaM-LDs) and play a regulatory role, making these CaM-like proteins sensitive to Ca2+ transients within the cell, and hence are able to transduce the Ca2+ signal leading to specific cellular responses. Importantly, this arrangement allows to this group of proteins direct regulation independent of other Ca2+-sensitive sensor/transducer proteins, such as CaM. In addition, this review also covers CaM-binding proteins, in which their CaM-binding site (CBS), in the absence of CaM, is proposed to interact with other segments of the same protein denoted CaM-like binding site (CLBS). CLBS are important regulatory motifs, acting either by keeping these CaM-binding proteins inactive in the absence of CaM, enhancing the stability of protein complexes and/or facilitating their dimerization via CBS/CLBS interaction. The existence of proteins containing CaM-LDs or CLBSs substantially adds to the enormous versatility and complexity of Ca2+/CaM signaling.

Proliferating cell nuclear antigen associates to protein complexes containing cyclins/cyclin dependent kinases susceptible of inhibition by KRPs during maize germination

The Proliferating Cell Nuclear Antigen, PCNA, has roles in both G1 and S phases of the cell cycle. Here we show that maize PCNA can be found in cells in structures of a trimer or a dimer of trimer, in complexes of high molecular mass that change in size as germination proceeds, co-eluting with cell cycle proteins as CycD3;1 and CDKs (A/B1;1). Using different methodological strategies, we show that PCNA actually interacts with CycD3;1, CDKA, CDKB1;1, KRP1;1 and KRP4;1, all of which contain PIP or PIP-like motifs. Anti-PCNA immunoprecipitates show kinase activity that is inhibited by KRP1;1 and KRP4;2, indicating the formation of quaternary complexes PCNA-CycD/CDKs-KRPs in which PCNA would act as a platform. This inhibitory effect seems to be differential during the germination process, more pronounced as germination advances, suggesting a complex regulatory mechanism in which PCNA could bind different sets of cyclins/CDKs, some more susceptible to inhibition by KRPs than others.

Multiple mechanisms explain how reduced KRP expression increases leaf size of Arabidopsis thaliana

Although cell number generally correlates with organ size, the role of cell cycle control in growth regulation is still largely unsolved. We studied kip related protein (krp) 4, 6 and 7 single, double and triple mutants of Arabidopsis thaliana to understand the role of cell cycle inhibitory proteins in leaf development. We performed leaf growth and seed size analysis, kinematic analysis, flow cytometery, transcriptome analysis and mathematical modeling of G1/S and G2/M checkpoint progression of the mitotic and endoreplication cycle. Double and triple mutants progressively increased mature leaf size, because of elevated expression of cell cycle and DNA replication genes stimulating progression through the division and endoreplication cycle. However, cell number was also already increased before leaf emergence, as a result of an increased cell number in the embryo. We show that increased embryo and seed size in krp4/6/7 results from seed abortion, presumably reducing resource competition, and that seed size differences contribute to the phenotype of several large-leaf mutants. Our results provide a new mechanistic understanding of the role of cell cycle regulation in leaf development and highlight the contribution of the embryo to the development of leaves after germination in general.

Identification and functional analysis of the ICK gene family in maize

Inhibitors of cyclin-dependent kinases (ICKs) are key regulators of cyclin-dependent kinase activities and cell division. Herein, we identified eight ICKs in maize, which we named Zeama;ICKs (ZmICKs). Primary sequencing and phylogenetic analyses were used to divide the ZmICK family into two classes: group B and group C. Subcellular localization analysis of ZmICK:enhanced green fluorescent protein (eGFP) fusion constructs in tobacco leaf cells indicated that ZmICKs are principally nuclear. Co-localization analysis of the ZmICKs and maize A-type cyclin-dependent kinase (ZmCDKA) was also performed using enhanced green fluorescent protein (eGFP) and red fluorescent protein (RFP) fusion constructs. The ZmICKs and ZmCDKA co-localized in the nucleus. Semi-quantitative RT-PCR analysis of the ZmICKs showed that they were expressed at different levels in all tissues examined and shared similar expression patterns with cell cycle-related genes. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that ZmICK1, ZmICK2, ZmICK3, and ZmICK4 interact with ZmCDKA1 and ZmCDKA3. Interestingly, ZmICK7 interacts with D-type cyclins. Transformed and expressed ZmCDKA1 and ZmICKs together in fission yeast revealed that ZmICK1, ZmICK3, and ZmICK4 can affect ZmCDKA1 function. Moreover, the C-group of ZmICKs could interact with ZmCDKA1 directly and affect ZmCDKA1 function, suggesting that C-group ZmICKs are important for cell division regulation.

Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D-cyclin-dependent kinase complexes

The family of maize Kip-related proteins (KRPs) has been studied and a nomenclature based on the relationship to rice KRP genes is proposed. Expression studies of KRP genes indicate that all are expressed at 24 h of seed germination but expression is differential in the different tissues of maize plantlets. Recombinant KRP1;1 and KRP4;2 proteins, members of different KRP classes, were used to study association to and inhibitory activity on different maize cyclin D (CycD)-cyclin-dependent kinase (CDK) complexes. Kinase activity in CycD2;2-CDK, CycD4;2-CDK, and CycD5;3-CDK complexes was inhibited by both KRPs; however, only KRP1;1 inhibited activity in the CycD6;1-CDK complex, not KRP4;2. Whereas KRP1;1 associated with either CycD2;2 or CycD6;1, and to cyclin-dependent kinase A (CDKA) recombinant proteins, forming ternary complexes, KRP4;2 bound CDKA and CycD2;2 but did not bind CycD6;1, establishing a differential association capacity. All CycD-CDK complexes included here phosphorylated both the retinoblastoma-related (RBR) protein and the two KRPs; interestingly, while KRP4;2 phosphorylated by the CycD2;2-CDK complex increased its inhibitory capacity, when phosphorylated by the CycD6;1-CDK complex the inhibitory capacity was reduced or eliminated. Evidence suggests that the phosphorylated residues in KRP4;2 may be different for every kinase, and this would influence its performance as a cyclin-CDK inhibitor.

A short motif in Arabidopsis CDK inhibitor ICK1 decreases the protein level, probably through a ubiquitin-independent mechanism

The ICK/KRP family of cyclin-dependent kinase (CDK) inhibitors modulates the activity of plant CDKs through protein binding. Previous work has shown that changing the levels of ICK/KRP proteins by overexpression or downregulation affects cell proliferation and plant growth, and also that the ubiquitin proteasome system is involved in degradation of ICK/KRPs. We show in this study that the region encompassing amino acids 21 to 40 is critical for ICK1 levels in both Arabidopsis and yeast. To determine how degradation of ICK1 is controlled, we analyzed the accumulation of hemagglutinin (HA) epitope-tagged ICK1 proteins in yeast mutants defective for two ubiquitin E3 ligases. The highest level of HA-ICK1 protein was observed when both the N-terminal 1-40 sequence was removed and the SCF (SKP1-Cullin1-F-box complex) function disrupted, suggesting the involvement of both SCF-dependent and SCF-independent mechanisms in the degradation of ICK1 in yeast. A short motif consisting of residues 21-30 is sufficient to render green fluorescent protein (GFP) unstable in plants and had a similar effect in plants regardless of whether it was fused to the N-terminus or C-terminus of GFP. Furthermore, results from a yeast ubiquitin receptor mutant rpn10Δ indicate that protein ubiquitination is not critical in the degradation of GFP-ICK1(1-40) in yeast. These results thus identify a protein-destabilizing sequence motif that does not contain a typical ubiquitination residue, suggesting that it probably functions through an SCF-independent mechanism.

Core cell cycle regulatory genes in rice and their expression profiles across the growth zone of the leaf

Rice (Oryza sativa L.) as a model and crop plant with a sequenced genome offers an outstanding experimental system for discovering and functionally analyzing the major cell cycle control elements in a cereal species. In this study, we identified the core cell cycle genes in the rice genome through a hidden Markov model search and multiple alignments supported with the use of short protein sequence probes. In total we present 55 rice putative cell cycle genes with locus identity, chromosomal location, approximate chromosome position and EST accession number. These cell cycle genes include nine cyclin dependent-kinase (CDK) genes, 27 cyclin genes, one CKS gene, two RBR genes, nine E2F/DP/DEL genes, six KRP genes, and one WEE gene. We also provide characteristic protein sequence signatures encoded by CDK and cyclin gene variants. Promoter analysis by the FootPrinter program discovered several motifs in the regulatory region of the core cell cycle genes. As a first step towards functional characterization we performed transcript analysis by RT-PCR to determine gene specific variation in transcript levels along the rice leaves. The meristematic zone of the leaves where cells are actively dividing was identified based on kinematic analysis and flow cytometry. As expected, expression of the majority of cell cycle genes was exclusively associated with the meristematic region. However genes such as different D-type cyclins, DEL1, KRP1/3, and RBR2 were also expressed in leaf segments representing the transition zone in which cells start differentiation.

Differential response of cell-cycle and cell-expansion regulators to heat stress in apple (Malus domestica) fruitlets

Temperature is one of the most significant factors affecting physiological and biochemical aspects of fruit development. Current and progressing global warming is expected to change climate in the traditional deciduous fruit tree cultivation regions. In this study, 'Golden Delicious' trees, grown in a controlled environment or commercial orchard, were exposed to different periods of heat treatment. Early fruitlet development was documented by evaluating cell number, cell size and fruit diameter for 5-70 days after full bloom. Normal activities of molecular developmental and growth processes in apple fruitlets were disrupted under daytime air temperatures of 29°C and higher as a result of significant temporary declines in cell-production and cell-expansion rates, respectively. Expression screening of selected cell cycle and cell expansion genes revealed the influence of high temperature on genetic regulation of apple fruitlet development. Several core cell-cycle and cell-expansion genes were differentially expressed under high temperatures. While expression levels of B-type cyclin-dependent kinases and A- and B-type cyclins declined moderately in response to elevated temperatures, expression of several cell-cycle inhibitors, such as Mdwee1, Mdrbr and Mdkrps was sharply enhanced as the temperature rose, blocking the cell-cycle cascade at the G1/S and G2/M transition points. Moreover, expression of several expansin genes was associated with high temperatures, making them potentially useful as molecular platforms to enhance cell-expansion processes under high-temperature regimes. Understanding the molecular mechanisms of heat tolerance associated with genes controlling cell cycle and cell expansion may lead to the development of novel strategies for improving apple fruit productivity under global warming.

Endogenous abscisic acid promotes hypocotyl growth and affects endoreduplication during dark-induced growth in tomato (Solanum lycopersicum L.)

Dark-induced growth (skotomorphogenesis) is primarily characterized by rapid elongation of the hypocotyl. We have studied the role of abscisic acid (ABA) during the development of young tomato (Solanum lycopersicum L.) seedlings. We observed that ABA deficiency caused a reduction in hypocotyl growth at the level of cell elongation and that the growth in ABA-deficient plants could be improved by treatment with exogenous ABA, through which the plants show a concentration dependent response. In addition, ABA accumulated in dark-grown tomato seedlings that grew rapidly, whereas seedlings grown under blue light exhibited low growth rates and accumulated less ABA. We demonstrated that ABA promotes DNA endoreduplication by enhancing the expression of the genes encoding inhibitors of cyclin-dependent kinases SlKRP1 and SlKRP3 and by reducing cytokinin levels. These data were supported by the expression analysis of the genes which encode enzymes involved in ABA and CK metabolism. Our results show that ABA is essential for the process of hypocotyl elongation and that appropriate control of the endogenous level of ABA is required in order to drive the growth of etiolated seedlings.

The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis

In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita-induced galls of KRP6-overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6-overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.

Salicylic acid antagonizes abscisic acid inhibition of shoot growth and cell cycle progression in rice

We analysed effects of abscisic acid (ABA, a negative regulatory hormone), alone and in combination with positive or neutral hormones, including salicylic acid (SA), on rice growth and expression of cell cycle-related genes. ABA significantly inhibited shoot growth and induced expression of OsKRP4, OsKRP5, and OsKRP6. A yeast two-hybrid assay showed that OsKRP4, OsKRP5, and OsKRP6 interacted with OsCDKA;1 and/or OsCDKA;2. When SA was simultaneously supplied with ABA, the antagonistic effect of SA completely blocked ABA inhibition. SA also blocked ABA inhibition of DNA replication and thymidine incorporation in the shoot apical meristem. These results suggest that ABA arrests cell cycle progression by inducing expression of OsKRP4, OsKRP5, and OsKRP6, which inhibit the G₁/S transition, and that SA antagonizes ABA by blocking expression of OsKRP genes.

Modelling cell division and endoreduplication in tomato fruit pericarp

In many developing plant tissues and organs, differentiating cells switch from the classical cell cycle to an alternative partial cycle. This partial cycle bypasses mitosis and allows for multiple rounds of genome duplication without cell division, giving rise to cells with high ploidy numbers. This partial cycle is referred to as endoreduplication. Cell division and endoreduplication are important processes for biomass allocation and yield in tomato. Quantitative trait loci for tomato fruit size or weight are frequently associated with variations in the pericarp cell number, and due to the tight connection between endoreduplication and cell expansion and the prevalence of polyploidy in storage tissues, a functional correlation between nuclear ploidy number and cell growth has also been implicated (karyoplasmic ratio theory). In this paper, we assess the applicability of putative mechanisms for the onset of endoreduplication in tomato pericarp cells via development of a mathematical model for the cell cycle gene regulatory network. We focus on targets for regulation of the transition to endoreduplication by the phytohormone auxin, which is known to play a vital role in the onset of cell expansion and differentiation in developing tomato fruit. We show that several putative mechanisms are capable of inducing the onset of endoreduplication. This redundancy in explanatory mechanisms is explained by analysing system behaviour as a function of their combined action. Namely, when all these routes to endoreduplication are used in a combined fashion, robustness of the regulation of the transition to endoreduplication is greatly improved.

PaKRP, a cyclin-dependent kinase inhibitor from avocado, may facilitate exit from the cell cycle during fruit growth

Previous studies using 'Hass' avocado cultivar showed that its small-fruit (SF) phenotype is limited by cell number. To explore the molecular components affecting avocado cell production, we isolated four cDNAs encoding: an ICK/KRP protein, known to play cell cycle-regulating roles through modulation of CDK function; two CDK proteins and a D-type cyclin, and monitored their expression patterns, comparing NF (normal fruit) versus SF profiles. The accumulation of PaKRP gradually deceased during growth in both fruit populations. Despite these similarities, SF exhibited higher levels of PaKRP accumulation at early stages of growth. Moreover, in NF, augmented PaKRP expression coincided with a decrease in CDK and PaCYCD1 levels, whereas in SF, enhanced PaKPR expression was coupled with an earlier decline of CDK and PaCYCD1 levels. For both NF and SF, enhanced mesocarp PaKRP transcript accumulation, was associated with elevated abscisic acid (ABA) and ABA catabolites content. Nevertheless, the collective ABA levels, including catabolites, were substantially higher in SF tissues, as compared with NF tissues. Finally, additional expression analysis revealed that in cultured cells, PaKRP could be induced by ABA. Together, our data links PaKRP with exit from the fruit cell cycle and suggest a role for ABA in controlling its expression.

Downregulation of multiple CDK inhibitor ICK/KRP genes upregulates the E2F pathway and increases cell proliferation, and organ and seed sizes in Arabidopsis

The ICK/KRP cyclin-dependent kinase (CDK) inhibitors are important plant cell cycle factors sharing only limited similarity with the metazoan CIP/KIP family of CDK inhibitors. Little is known about the specific functions of different ICK/KRP genes in planta. In this study, we created double and multiple mutants from five single Arabidopsis ICK/KRP T-DNA mutants, and used a set of 20 lines for the functional investigation of the important gene family. There were gradual increases in CDK activity from single to multiple mutants, indicating that ICK/KRPs act as CDK inhibitors under normal physiological conditions in plants. Whereas lower-order mutants showed no morphological phenotypes, the ick1 ick2 ick6 ick7 and ick1 ick2 ick5 ick6 ick7 mutants had a slightly altered leaf shape. The quintuple mutant had larger cotyledons, leaves, petals and seeds than the wild-type control. At the cellular level, the ICK/KRP mutants had more but smaller cells in all the organs examined. These phenotypic effects became more apparent as more ICK/KRPs were downregulated, suggesting that to a large extent ICK/KRPs function in plants redundantly in a dosage-dependent manner. Analyses also revealed increased expression of E2F-dependent genes, and elevated RBR1 as well as an increased level of phospho-RBB1 protein in the quintuple mutant. Thus, downregulation of multiple ICK/KRP genes increases CDK activity, upregulates the E2F pathway and stimulates cell proliferation, resulting in increased cell numbers, and larger organs and seeds.

Ectopic expression of Kip-related proteins restrains root-knot nematode-feeding site expansion

The development of nematode feeding sites induced by root-knot nematodes involves the synchronized activation of cell cycle processes such as acytokinetic mitoses and DNA amplification. A number of key cell cycle genes are reported to be critical for nematode feeding site development. However, it remains unknown whether plant cyclin-dependent kinase (CDK) inhibitors such as the Arabidopsis interactor/inhibitor of CDK (ICK)/Kip-related protein (KRP) family are involved in nematode feeding site development. This study demonstrates the involvement of Arabidopsis ICK2/KRP2 and ICK1/KRP1 in the control of mitosis to endoreduplication in galls induced by the root-knot nematode Meloidogyne incognita. Using ICK/KRP promoter-GUS fusions and mRNA in situ hybridizations, we showed that ICK2/KRP2, ICK3/KRP5 and ICK4/KRP6 are expressed in galls after nematode infection. Loss-of-function mutants have minor effects on gall development and nematode reproduction. Conversely, overexpression of both ICK1/KRP1 and ICK2/KRP2 impaired mitosis in giant cells and blocked neighboring cell proliferation, resulting in a drastic reduction of gall size. Studying the dynamics of protein expression demonstrated that protein levels of ICK2/KRP2 are tightly regulated during giant cell development and reliant on the presence of the nematode. This work demonstrates that impeding cell cycle progression by means of ICK1/KRP1 and ICK2/KRP2 overexpression severely restricts gall development, leading to a marked limitation of root-knot nematode development and reduced numbers of offspring.

Control of the plant cell cycle by developmental and environmental cues

Plant morphogenesis relies on cell proliferation and differentiation strictly controlled in space and time. As in other eukaryotes, progression through the plant cell cycle is governed by cyclin-dependent kinases (CDKs) that associate with their activator proteins called cyclins (CYCs), and the activity of CYC-CDK is modulated at both transcriptional and post-translational levels. Compared with animals and yeasts, plants generally possess many more genes encoding core cell cycle regulators and it has been puzzling how their functions are specified or overlapped in development or in response to various environmental changes. Thanks to the recent advances in high-throughput, genome-wide transcriptome and proteomic technologies, we are finally beginning to see how core regulators are assembled during the cell cycle and how their activities are modified by developmental and environmental cues. In this review we will summarize the latest progress in plant cell cycle research and provide an overview of some of the emerging molecular interfaces that link upstream signaling cascades and cell cycle regulation.

DELLA signaling mediates stress-induced cell differentiation in Arabidopsis leaves through modulation of anaphase-promoting complex/cyclosome activity

Drought is responsible for considerable yield losses in agriculture due to its detrimental effects on growth. Drought responses have been extensively studied, but mostly on the level of complete plants or mature tissues. However, stress responses were shown to be highly tissue and developmental stage specific, and dividing tissues have developed unique mechanisms to respond to stress. Previously, we studied the effects of osmotic stress on dividing leaf cells in Arabidopsis (Arabidopsis thaliana) and found that stress causes early mitotic exit, in which cells end their mitotic division and start endoreduplication earlier. In this study, we analyzed this phenomenon in more detail. Osmotic stress induces changes in gibberellin metabolism, resulting in the stabilization of DELLAs, which are responsible for mitotic exit and earlier onset of endoreduplication. Consequently, this response is absent in mutants with altered gibberellin levels or DELLA activity. Mitotic exit and onset of endoreduplication do not correlate with an up-regulation of known cell cycle inhibitors but are the result of reduced levels of DP-E2F-LIKE1/E2Fe and UV-B-INSENSITIVE4, both inhibitors of the developmental transition from mitosis to endoreduplication by modulating anaphase-promoting complex/cyclosome activity, which are down-regulated rapidly after DELLA stabilization. This work fits into an emerging view of DELLAs as regulators of cell division by regulating the transition to endoreduplication and differentiation.

Analyses of two rice (Oryza sativa) cyclin-dependent kinase inhibitors and effects of transgenic expression of OsiICK6 on plant growth and development

BACKGROUND AND AIMS

Plants have a family of proteins referred to as ICKs (inhibitors of cyclin-dependent kinase, CDK) or KRPs (Kip-related proteins) that function to regulate the activities of CDK. Knowledge of these plant CDK inhibitors has been gained mostly from studies of selected members in dicotyledonous plants, particularly Arabidopsis. Much remains to be learned regarding the differences among various members of the ICK/KRP family, and regarding the function and regulation of these proteins in monocotyledonous plants.

METHODS

We analysed ICK-related sequences in the rice (Orysa sativa L. subsp. indica) genome and determined that there are six members with the conserved C-terminal signature region for ICK/KRP proteins. They are referred to as OsiICKs and further analyses were performed. The interactions with CDKs and cyclins were determined by a yeast two-hybrid assay, and cellular localization by fusion with the enhanced green fluorescence protein (EGFP). The expression of OsiICK6 in different tissues and in response to several treatments was analysed by reverse transcriptase-mediated polymerase chain reaction (RT-PCR) and real-time PCR. Furthermore, OsiICK6 was over-expressed in transgenic rice plants and significant phenotypes were observed.

KEY RESULTS AND CONCLUSIONS

Based on putative protein sequences, the six OsiICKs are grouped into two classes, with OsiICK1 and OsiICK6 in each of the two classes, respectively. Results showed that OsiICK1 and OsiICK6 interacted with OsCYCD, but differed in their interactions with CDKA. Both EGFP:OsiICK1 and EGFP:OsiICK6 were localized in the nucleus. Whereas EGFP:OsiICK6 showed a punctuate subnuclear distribution, OsiICK1 had a homogeneous pattern. Over-expression of OsiICK6 resulted in multiple phenotypic effects on plant growth, morphology, pollen viability and seed setting. In OsiICK6-over-expressing plants, leaves rolled toward the abaxial side, suggesting that cell proliferation is critical in maintaining an even growth along the dorsal-ventral plane of leaf blades.

Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest

Despite its relevance for agricultural production, environmental stress-induced growth inhibition, which is responsible for significant yield reductions, is only poorly understood. Here, we investigated the molecular mechanisms underlying cell cycle inhibition in young proliferating leaves of the model plant Arabidopsis thaliana when subjected to mild osmotic stress. A detailed cellular analysis demonstrated that as soon as osmotic stress is sensed, cell cycle progression rapidly arrests, but cells are kept in a latent ambivalent state allowing a quick recovery (pause). Remarkably, cell cycle arrest coincides with an increase in 1-aminocyclopropane-1-carboxylate levels and the activation of ethylene signaling. Our work showed that ethylene acts on cell cycle progression via inhibition of cyclin-dependent kinase A activity independently of EIN3 transcriptional control. When the stress persists, cells exit the mitotic cell cycle and initiate the differentiation process (stop). This stop is reflected by early endoreduplication onset, in a process independent of ethylene. Nonetheless, the potential to partially recover the decreased cell numbers remains due to the activity of meristemoids. Together, these data present a conceptual framework to understand how environmental stress reduces plant growth.

Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors

BACKGROUND AND AIMS

The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.

METHODS

We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.

KEY RESULTS AND CONCLUSIONS

Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.

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.

Functional characterization of the tomato cyclin-dependent kinase inhibitor SlKRP1 domains involved in protein-protein interactions

• Cyclin-dependent kinase (CDK) inhibitors (kip-related proteins, KRPs) play a major role in the regulation of plant cell cycle in antagonizing its progression, and are thus regulators of development. The primary sequence of KRPs is characterized by the existence of conserved motifs, for which we have limited information on their functional significance. • We performed a functional analysis of various domains present in KRPs from tomato. A series of deletion mutants of SlKRP1 was generated and used in transient expression assays to define the relevance of conserved protein domains in subcellular and subnuclear localizations. Specific interactions of SlKRP1 and its deletion variants with cell cycle proteins were investigated using two-hybrid assays and bimolecular fluorescent complementation. • Plant KRPs are distributed into two phylogenetic subgroups according to the presence of conserved motifs. Members of subgroup 1 represented by SlKRP1 share 6 conserved motifs whose function in protein localization and protein-protein interactions could be identified. A new interaction motif was localized in the central part of SlKRP1 that targets SlCDKA1 and SlCYCD3;1 to the nucleus. • Our results bring new insights to the functional role of particular domains in KRPs relative to subcellular localization or proteolytic degradation.

A proposed conserved role for an avocado FW2.2-like gene as a negative regulator of fruit cell division

Previous studies using 'Hass' avocado and its small fruit (SF) phenotype as a model showed that SF is limited by cell number, not by cell size. In an attempt to explore the molecular mechanisms regulating avocado fruit cell division, we isolated four distinct avocado cell proliferation-related genes and investigated their expression characteristics, comparing normal fruit (NF) and SF developmental patterns. Three cDNAs termed PaCYCA1, PaCYCB1 and PaPCNA, encoding two mitotic cyclins and a proliferating cell nuclear antigen (PCNA), were first isolated from young NF tissues. The accumulation of their transcripts was predominant in mitotically active organs, including young fruitlets, leaves and roots. Furthermore, a fourth full-length cDNA, designated Pafw2.2-like, encoding a FW2.2 (fruit-weight)-like protein, was isolated from SF tissues. FW2.2 is postulated to function as a negative regulator of cell division in tomato fruit. Remarkably, northern analysis revealed that the accumulation of the mitotic cyclins and of PCNA transcripts gradually decreased in NF tissues during growth, whereas in SF, their levels had already decreased at earlier stages of fruit development, concomitant with an earlier arrest of fruit cell division activity. In contrast, parallel sq-RT-PCR analysis showed that Pafw2.2-like mRNA accumulation was considerably higher in SF tissues than in the same NF tissues essentially at all examined stages of fruit growth. Together, our data suggest essential roles for the two mitotic cyclins genes and the PCNA gene in regulating avocado fruit development. Furthermore, the possibility that Pafw2.2-like acts as does fw2.2 in tomato, is discussed.

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.

Functions, regulation and cellular localization of plant cyclin-dependent kinase inhibitors

The cell cycle is regulated by the cyclin-dependent kinase (CDK), and CDK inhibitors can bind to CDKs and inhibit their activities. This review examines plant CDK inhibitors, with particular emphasis on their molecular and cellular functions, regulation and cellular localization. In plants, a family of ICK/KRP CDK inhibitors represented by ICK1 is known and another type of CDK inhibitor represented by the SIMESE (SIM) has recently been reported. Considerable understanding has been gained with the ICK/KRP CDK inhibitors. These plant CDK inhibitors share only limited sequence similarity in the C-terminal region with the KIP/CIP family of mammalian CDK inhibitors. The ICK/KRP CDK inhibitors thus provide good tools to understand the basic machinery as well as the unique aspects of the plant cell cycle. The ICK/KRP CDK inhibitors interact with D-type cyclins or A-type CDKs or both. Several functional regions and motifs have been identified in ICK1 for CDK inhibition, nuclear localization and protein instability. Clear evidence shows that ICK/KRP proteins are important for the cell cycle and endoreduplication. Preliminary evidence suggests that they may also be involved in cell differentiation and cell death. Results so far show that plant CDK inhibitors are exclusively localized in the nucleus. The molecular sequences regulating the localization and functional significance will be discussed.

The ins and outs of the plant cell cycle

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

T-loop phosphorylation of Arabidopsis CDKA;1 is required for its function and can be partially substituted by an aspartate residue

As in other eukaryotes, progression through the cell cycle in plants is governed by cyclin-dependent kinases. Phosphorylation of a canonical Thr residue in the T-loop of the kinases is required for high enzyme activity in animals and yeast. We show that the Arabidopsis thaliana Cdc2(+)/Cdc28 homolog CDKA;1 is also phosphorylated in the T-loop and that phosphorylation at the conserved Thr-161 residue is essential for its function. A phospho-mimicry T161D substitution restored the primary defect of cdka;1 mutants, and although the T161D substitution displayed a dramatically reduced kinase activity with a compromised ability to bind substrates, homozygous mutant plants were recovered. The rescue by the T161D substitution, however, was not complete, and the resulting plants displayed various developmental abnormalities. For instance, even though flowers were formed, these plants were completely sterile as a result of a failure of the meiotic program, indicating that different requirements for CDKA;1 function are needed during plant development.

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

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

Analysis of the subcellular localization, function, and proteolytic control of the Arabidopsis cyclin-dependent kinase inhibitor ICK1/KRP1

Recent studies have shown that cyclin-dependent kinase (CDK) inhibitors can have a tremendous impact on cell cycle progression in plants. In animals, CDK inhibitors are tightly regulated, especially by posttranslational mechanisms of which control of nuclear access and regulation of protein turnover are particularly important. Here we address the posttranslational regulation of INHIBITOR/INTERACTOR OF CDK 1 (ICK1)/KIP RELATED PROTEIN 1 (KRP1), an Arabidopsis (Arabidopsis thaliana) CDK inhibitor. We show that ICK1/KRP1 exerts its function in the nucleus and its presence in the nucleus is controlled by multiple nuclear localization signals as well as by nuclear export. In addition, we show that ICK1/KRP1 localizes to different subnuclear domains, i.e. in the nucleoplasm and to the chromocenters, hinting at specific actions within the nuclear compartment. Localization to the chromocenters is mediated by an N-terminal domain, in addition we find that this domain may be involved in cyclin binding. Further we demonstrate that ICK1/KRP1 is an unstable protein and degraded by the 26S proteasome in the nucleus. This degradation is mediated by at least two domains indicating the presence of at least two different pathways impinging on ICK1/KRP1 protein stability.