Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice

Forty-one rice cDNAs encoding protein kinases were fused to the tandem affinity purification (TAP) tag and expressed in transgenic rice plants. The TAP-tagged kinases and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by mass spectrometry. Ninety-five percent of the TAP-tagged kinases were recovered. Fifty-six percent of the TAP-tagged kinases were found to interact with other rice proteins. A number of these interactions were consistent with known protein complexes found in other species, validating the TAP-tag method in rice plants. Phosphorylation sites were identified on four of the kinases that interacted with either 14-3-3 proteins or cyclins.     

Cyclin E ablation in the mouse

E type cyclins (E1 and E2) are believed to drive cell entry into the S phase. It is widely assumed that the two E type cyclins are critically required for proliferation of all cell types. Here, we demonstrate that E type cyclins are largely dispensable for mouse development. However, endoreplication of trophoblast giant cells and megakaryocytes is severely impaired in the absence of cyclin E. Cyclin E-deficient cells proliferate actively under conditions of continuous cell cycling but are unable to reenter the cell cycle from the quiescent G(0) state. Molecular analyses revealed that cells lacking cyclin E fail to normally incorporate MCM proteins into DNA replication origins during G(0)-->S progression. We also found that cyclin E-deficient cells are relatively resistant to oncogenic transformation. These findings define a molecular function for E type cyclins in cell cycle reentry and reveal a differential requirement for cyclin E in normal versus oncogenic proliferation.     

Immunodetection of four mitotic cyclins and the Cdc2a protein kinase in the maize root: Their distribution in cell development and dedifferentiation

Summary Cyclin proteins and cyclin-dependent kinases play a key role in the regulation of cell division. We have therefore studied the relationship of the level of four mitotic cyclin proteins and the Cdc2a kinase protein to cell division in maize root tissue with respect to cessation of division as cells leave the primary meristem region, resumption of division in formation of lateral-root primordia, and induced division following wounding. All four mitotic cyclins and Cdc2a were most abundant in dividing cells. The only examined cell cycle protein which was restricted to dividing tissue was cyclin ZmCycB1;2 (previously ZmIb) and may thus be a limiting factor for cell division. All other cyclin proteins, i.e., ZmCycB1;1 (previously ZmIa), ZmCycA1;1 (previously ZmII), and ZmCycB2;1 (previously ZmIII), and the Cdc2a kinase declined shortly after cells had ceased division. The distance from the root tip at which cells ceased division was tissue-specific and reflected the distance at which decrease of cell cycle proteins was detected. Whereas cyclin ZmCycB1;2 rapidly declined to a hardly detectable level in either nucleus or cytoplasm, in the nuclei of nondividing cells there was persistence of Cdc2a and of cyclins ZmCycB1;1, ZmCycCA1;1, and ZmCycB2;1, indicating that there are plant cyclins which are tightly linked to cell division and others that persist, especially in the nuclei, in nondividing cells. The transition from division to differentiation may thus partly be triggered and enforced by the decrease of the cell cycle proteins and especially the decline of cyclins in the cytoplasm. In the resumption of cell division, both in lateral-root formation and in wound response, high nuclear and low cytoplasmic accumulation of cyclin ZmCycB2;1 was the first visible sign of cell dedifferentiation, implying a role for cyclin ZmCycB2;1 in the G₀–G₁ phase transition. Next, cytoplasmic accumulation of cyclin ZmCycA1;1, followed by a rearrangement of cortical microtubules, was observed and since both the cyclins ZmCycA1;1 and ZmCycB2;1 were found at places of high tubulin concentration, they may function in the microtubule rearrangement for cell division. When the nuclei of dedifferentiating cells had visibly enlarged, all cyclins and Cdc2a accumulated there, possibly contributing to DNA replication and preparation for mitosis. Later, presumably during G₂ phase, cytoplasmic accumulation was observed for Cdc2a at low levels, as observed in G₂ phase cells of the primary meristem, and for cyclins ZmCycB1;1 and ZmCycB1;2 accumulation was observed above the levels found in undisturbed meristems, suggesting special contributions to late dedifferentiation processes in both wound-induced and lateral meristems.Abbreviations CDK cyclin-dependent kinase - LRP lateral-root primordium - Mt microtubule - FITC fluorescein isothiocyanate - TRITC tetramethylrhodamine isothiocyanate Dedicated to Professor Walter Gustav Url on the occasion of his 70th birthday     

Threshold expression of cyclin E but not D type cyclins characterizes normal and tumour cells entering S phase

Complexes of cyclin-dependent kinases (cdk) and their partner cyclins drive the cell through the cell cycle, each such complex phosphorylating a distinct set of proteins at a particular check-point or phase of the cycle. Immunocytochemical detection of cyclins combined with measurement of cellular DNA content by flow cytometry makes it possible to relate expression of each of these proteins with the actual cell cycle position, without the necessity of cell synchronization. In the present study, we have investigated expression of E and D type cyclins in G₁ cells and in cells entering S phase, in eight different human hematopoietic and solid tumour cell lines (two leukaemias, a lymphoma, three breast carcinomas, a colon carcinoma and a bladder transitional cell carcinoma) during their exponential phase of growth, as well as in normal mitogen stimulated lymphocytes. In all the cell types studied, the average level of D type cyclin expression was invariable throughout the cell cycle. A great intercellular variability, in particular of the G₁ cell subpopulations, and the presence of a large fraction of G₁, S and G₂+ M cells that were cyclin D negative (20–40% in tumour cell lines and about 80% among lymphocytes), were other characteristic features of D type cyclin expression. In contrast to D type cyclins, the expression of cyclin E was discontinuous during the cycle, peaking at the time of cell entrance to S. Also, a well defined threshold in expression of cyclin E characterized cells that were entering S phase, and virtually no cyclin E negative cells were seen during the early portion of S phase. The data indicate that while cell entrance to S phase is unrelated to expression of D type cyclins (at the time of entrance), accumulation of cyclin E up to critical level is a prerequisite for initiation of DNA replication. The great intercellular variability in expression of D type cyclins and their invariant average level across the cell cycle suggest that these cyclins, in addition to their acknowledged function in promoting cell progression through mid- to late-G₁ may have other role(s), related or unrelated to the cell cycle progression. The presence of a large number of D type cyclin negative cells in all phases of the cycle suggests that during exponential growth the cells may not express this protein and yet may traverse the cycle, including G₁ phase.     

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.     

Saccharomyces cerevisiae cell cycle: cdc28 and the G1 cyclins.

Two families of cyclin-like proteins have been found in S. cerevisiae. The clb proteins are the mitotic cyclins. The cln proteins provide an essential function, are required for the G1/S transition, and appear to be rate-limiting for START, but have no obvious role elsewhere in the cycle. The cln proteins are unstable; they form complexes with cdc28; the complexes have protein kinase activity; and at least one of the clns oscillates in abundance through the cell cycle. The action of the cln cyclins at START suggests that they may be 'G1 cyclins'.     

A method for analyzing the ubiquitination and degradation of aurora-A

The cell cycle machinery consists of regulatory proteins that control the progression through the cell cycle ensuring that DNA replication alternates with DNA segregation in mitosis to maintain cell integrity. Some of these key regulators have to be degraded at each cell cycle to prevent cellular dysfunction. Mitotic exit requires the inactivation of cyclin dependent kinase1 (cdk1) and it is the degradation of the cyclin subunit that inactivates the kinase. Cyclin degradation has been well characterized and it was shown that it is ubiquitin proteasome pathway that leads to the elimination of cyclins. By now, many other regulatory proteins were shown to be degraded by the same pathway, among them members of the aurora kinase family, degraded many other regulatory proteins. Aurora kinases are involved in mitotic spindle formation as well as in cytokinesis. The abundance and activity of the kinase is precisely regulated during the cell cycle. To understand how proteolysis regulates transitions through the cell cycle we describe two assays for ubiquitination and degradation of xenopus aurora kinase A using extracts from xenopus eggs or somatic cell lines. Published: November 11, 2002     

Identification of the structural and functional human homolog of the yeast ubiquitin conjugating enzyme UBC9.

Ubiquitin conjugating enzymes (UBCs) are a family of proteins directly involved in ubiquitination of proteins. Ubiquitination is known to be involved in control of a variety of cellular processes, including cell proliferation, through the targeting of key regulatory proteins for degradation. The ubc9 gene of the yeast Saccharomyces cerevisiae (Scubc9) is an essential gene which is required for cell cycle progression and is involved in the degradation of S phase and M phase cyclins. We have identified a human homolog of Scubc9 (termed hubc9) using the two hybrid screen for proteins that interact with the human papillomavirus type 16 E1 replication protein. The hubc9 encoded protein shares a very high degree of amino acid sequence similarity with ScUBC9 and with the homologous hus5+ gene product of Schizosaccharomyces pombe. Genetic complementation experiments in a S.cerevisiae ubc9ts mutant reveal that hUBC9 can substitute for the function of ScUBC9 required for cell cycle progression.     

Mechanisms of the anticancer effects of plant polyphenols. II. Suppression of tumor growth

Mechanisms of suppression of carcinogenesis promotion/progression by plant polyphenols have been considered. They can exhibit antiproliferative activity by decreasing cyclins and cyclin dependent kinases and by activating their inhibitor proteins in tumor cells. Plant polyphenols can also induce apoptosis by modulating activity of proteins involved in apoptosis and thus exhibit proapoptotic effect. They may inhibit tumor metastasis and angiogenesis. Polyphenols act through the regulation of cell signal transduction and gene expression and exhibit either up or down regulation of genes controlling tumor development.     

P. gingivalis accelerates gingival epithelial cell progression through the cell cycle

P. gingivalis, an opportunistic pathogen in periodontal disease, can reside within the epithelial cells that line the gingival crevice. A proteomic analysis revealed that infection of gingival epithelial cells with P. gingivalis induces broadly based changes in the level and phosphorylation status of proteins that exert multi-level control on the eukaryotic cell cycle. Pathways that were impacted by P. gingivalis included those involving cyclins, p53 and PI3K. The predicted infection-dependent phenotype was confirmed by cytofluorimetry that showed an enhanced proliferation rate of gingival epithelial cells infected with P. gingivalis associated with accelerated progression through the S-phase. Elevated cell proliferation was dependent on the presence of the long fimbriae of P. gingivalis. The ability of P. gingivalis, a common inhabitant of the subgingival crevice, to accelerate cell cycling could have biological consequences for barrier and signaling functions, and for physiological status, of the gingival epithelium.     

Stability, chromatin association and functional activity of mammalian pre-replication complex proteins during the cell cycle

We have examined the behavior of pre-replication complex (pre-RC) proteins in relation to key cell cycle transitions in Chinese Hamster Ovary (CHO) cells. ORC1, ORC4 and Cdc6 were stable (T1/2 >2 h) and associated with a chromatin-containing fraction throughout the cell cycle. Green fluorescent protein-tagged ORC1 associated with chromatin throughout mitosis in living cells and co-localized with ORC4 in metaphase spreads. Association of Mcm proteins with chromatin took place during telophase, approximately 30 min after the destruction of geminin and cyclins A and B, and was coincident with the licensing of chromatin to replicate in geminin-supplemented Xenopus egg extracts. Neither Mcm recruitment nor licensing required protein synthesis throughout mitosis. Moreover, licensing could be uncoupled from origin specification in geminin-supplemented extracts; site-specific initiation within the dihydrofolate reductase locus required nuclei from cells that had passed through the origin decision point (ODP). These results demonstrate that mammalian pre-RC assembly takes place during telophase, mediated by post-translational modifications of pre-existing proteins, and is not sufficient to select specific origin sites. A subsequent, as yet undefined, step selects which pre-RCs will function as replication origins.     

The starch granule associated proteomes of commercially purified starch reference materials from rice and maize

Commercially available reference materials are integral components of many experimental protocols, as it is critical to compare one's results to those derived from well-characterized standards. Most reference materials are well defined, with all their components being cataloged. However, certain reference materials, such as commercially prepared starch samples, can have undefined components, potentially limiting their usefulness as standards. The proteome of commercially prepared starch has not been documented, and to that end, we initiated a mass spectrometry-based survey of the proteins associated with starch granules in commercially prepared rice and maize starch samples. We performed direct trypsin treatments of starch samples and sequenced both the water-soluble peptides liberated into the aqueous supernatant and the peptides released from the starch granule surface by isopropanol solvent washing. We discovered that the majority of proteins, in both rice and maize samples, were involved in either carbohydrate metabolism or storage. We also documented proteins that are markers for seed maturity and for starch mobilization.     

Cell specification in the Arabidopsis root epidermis requires the activity of ECTOPIC ROOT HAIR 3--a katanin-p60 protein.

The Arabidopsis root is composed of radial cell layers, each with distinct identities. The epidermal layer is composed of rows of hair cells flanked on either side by rows of non-hair epidermal cells. The development of hair and non-hair cells is dependent on domains of positional information with strict boundaries. The pattern of cell differentiation and the expression of molecular markers of cell fate is altered in the ectopic root hair 3 (erh3) mutant epidermis indicating that ERH3 is required for the specification of cell fates from early in development (in the meristem) through differentiation. Furthermore the expression of molecular markers indicates that the specification of cell identities is defective within other radial cell layers. ERH3 encodes a p60 katanin protein that is expressed throughout the plant. Katanin proteins are known to sever microtubules, and have a role in the organisation of the plant cell wall since mutants with decreased katanin activity have been shown to have defective walls. We suggest that microtubules are involved in the specification of cell identities in cells of the Arabidopsis root. Microtubules may be required for the localization of positional cues in the wall that have previously been shown to operate in the development of the root epidermis. Alternatively microtubules may be involved in another as yet undefined process required for the specification of cell identity in plants.     

Lipid droplet-organelle interactions; sharing the fats

Lipid droplets (LDs) are key cellular organelles involved in lipid storage and mobilisation. While the major signalling cascades and many of the regulators of lipolysis have been identified, the cellular interactions involved in lipid mobilisation and release remain largely undefined. In non-adipocytes, LDs are small, mobile and interact with other cellular compartments. In contrast, adipocytes primarily contain very large, immotile LDs. The striking morphological differences between LDs in adipocytes and non-adipocytes suggest that key differences must exist in the manner in which LDs in different cell types interact with other organelles. Recent studies have highlighted the complexity of LD interactions, which can be both homotypic, with each other, and heterotypic, with other organelles. The molecules involved in these interactions are also now emerging, including Rab proteins, key regulators of membrane traffic, and caveolin, an integral membrane protein providing a functional link between the cell surface and LDs. Here we summarise recent insights into the cell biology of the LD particularly focussing on the homotypic and heterotypic interactions in both adipocytes and non-adipocytes. We speculate that these interactions may involve inter-organelle membrane contact sites or a hemi-fusion type mechanism to facilitate lipid transfer.