Journal articles: 'Cell cycle protein'

1

Farley, John, Laurent Ozbun, Goli Samimi, and Michael J. Birrer. "Cell Cycle and Related Protein." Disease Markers 23, no. 5-6 (2007): 433–43. http://dx.doi.org/10.1155/2007/464712.

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Vázquez-Ramos, Jorge M., and María de la Paz Sánchez. "The cell cycle and seed germination." Seed Science Research 13, no. 2 (June 2003): 113–30. http://dx.doi.org/10.1079/ssr2003130.

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AbstractThe cell cycle is the series of molecular events that allows cells to duplicate and segregate their chromosomes to form new cells. The finding that a protein kinase, the product of the yeastcdc2gene, was fundamental in the regulation of the G2/M and G1/S transitions, associated with unstable proteins named cyclins, opened a very exciting and dynamic research area. The number of gene products that participate in the development and regulation of the cell cycle may be in the hundreds, and there is a high degree of conservation in protein sequences and regulatory pathways among eukaryotes. Although there are clear differences between plants and animals in cell structure, organization, growth, development and differentiation, the same types of proteins and very similar regulatory pathways seem to exist. Seed germination appears to be an excellent model system for studying the cell cycle in plants. Imbibition will reactivate meristematic cells – most initially with a G1DNA content – into the cell cycle in preparation for seedling establishment. Early events include a thorough survey of DNA status, since the drying process and seed storage conditions reduce chromosomal integrity. The initiation of cell cycle events leading to G1and S phases, and of the germination process itself, may depend on a G1checkpoint control. Most, if not all, cell cycle proteins appear to be already present in unimbibed embryos, although there is evidence of protein turnover in the early hours, suggesting the need forde novoprotein synthesis. Regulation also may occur at the level of protein modification, because existing G1, S and G2cell cycle proteins appear to be activated at precise times during germination. Thus, cell cycle control during seed germination may be exerted at multiple levels; however, knowledge of cell cycle events and their importance for germination is still scarce and fragmentary, and different species may have developed unique control mechanisms, more suited to specific germination characteristics and habitat.

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Evanko, Daniel. "Protein suicide highlights the cell cycle." Nature Methods 5, no. 4 (April 2008): 283. http://dx.doi.org/10.1038/nmeth0408-283.

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Wong, W. "Not Just a Cell Cycle Protein." Science Signaling 3, no. 106 (January 26, 2010): ec27-ec27. http://dx.doi.org/10.1126/scisignal.3106ec27.

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Hollingsworth, Robert E., Carmel E. Hensey, and Wen-Hwa Lee. "Retinoblastoma protein and the cell cycle." Current Opinion in Genetics & Development 3, no. 1 (February 1993): 55–62. http://dx.doi.org/10.1016/s0959-437x(05)80341-7.

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Wirth, Anna J., and Martin Gruebele. "Protein Folding across the Cell Cycle." Biophysical Journal 104, no. 2 (January 2013): 573a. http://dx.doi.org/10.1016/j.bpj.2012.11.3182.

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Pines, Jonathon. "Protein kinases and cell cycle control." Seminars in Cell Biology 5, no. 6 (December 1994): 399–408. http://dx.doi.org/10.1006/scel.1994.1047.

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Westwood, J. Tim, Robert B. Church, and Emile B. Wagenaar. "Patterns of protein synthesis during the cell cycle of Chinese hamster ovary cells." Biochemistry and Cell Biology 65, no. 3 (March 1, 1987): 219–29. http://dx.doi.org/10.1139/o87-028.

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The protein synthesis patterns at various stages of the cell cycle of Chinese hamster ovary cells were examined by labelling cells with [35S]methionine and then separating the proteins by isoelectric focussing and two-dimensional, nonequilibrium pH gradient gel electrophoresis. We have observed a number of proteins which display quantitative differences in synthesis at specific cell cycle stages and of these the α- and β-tubulins have been identified. A few proteins appear to be uniquely synthesized at specific times during the cell cycle. These include the histones and a modified version of them, which are synthesized only in S phase, and a pair of 21 kilodalton (kDa), pI 5.5 proteins, which appear only in late G2 and mitosis. We have also identified a 58-kDa, pI 7.5 protein which is present at all cell cycle stages except during late G2. This protein appears to have the same temporal properties as a 57-kDa protein called "cyclin" originally described in sea urchin embryos.

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Murphy, Eain A., Daniel N. Streblow, Jay A. Nelson, and Mark F. Stinski. "The Human Cytomegalovirus IE86 Protein Can Block Cell Cycle Progression after Inducing Transition into the S Phase of Permissive Cells." Journal of Virology 74, no. 15 (August 1, 2000): 7108–18. http://dx.doi.org/10.1128/jvi.74.15.7108-7118.2000.

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ABSTRACT Human cytomegalovirus (HCMV) infection of permissive cells has been reported to induce a cell cycle halt. One or more viral proteins may be involved in halting progression at different stages of the cell cycle. We investigated how HCMV infection, and specifically IE86 protein expression, affects the cell cycles of permissive and nonpermissive cells. We used a recombinant virus that expresses the green fluorescent protein (GFP) to determine the effects of HCMV on the cell cycle of permissive cells. Fluorescence by GFP allowed us to select for only productively infected cells. Replication-defective adenovirus vectors expressing the IE72 or IE86 protein were also used to efficiently transduce 95% or more of the cells. The adenovirus-expressed IE86 protein was determined to be functional by demonstrating negative autoregulation of the major immediate-early promoter and activation of an early viral promoter in the context of the viral genome. To eliminate adenovirus protein effects, plasmids expressing GFP for fluorescent selection of only transfected cells and wild-type IE86 protein or a mutant IE86 protein were tested in permissive and nonpermissive cells. HCMV infection induced the entry of U373 cells into the S phase. All permissive cells infected with HCMV were blocked in cell cycle progression and could not divide. After either transduction or transfection and IE86 protein expression, the number of all permissive or nonpermissive cell types in the S phase increased significantly, but the cells could no longer divide. The IE72 protein did not have a significant effect on the S phase. Since IE86 protein inhibits cell cycle progression, the IE2 gene in a human fibroblast IE86 protein-expressing cell line was sequenced. The IE86 protein in these retrovirus-transduced cells has mutations in a critical region of the viral protein. The locations of the mutations and the function of the IE86 protein in controlling cell cycle progression are discussed.

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Gookin, Sara, Mingwei Min, Harsha Phadke, Mingyu Chung, Justin Moser, Iain Miller, Dylan Carter, and Sabrina L. Spencer. "A map of protein dynamics during cell-cycle progression and cell-cycle exit." PLOS Biology 15, no. 9 (September 11, 2017): e2003268. http://dx.doi.org/10.1371/journal.pbio.2003268.

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11

Ivanova, Aneliya, Aleksandar Atemin, Sonya Uzunova, Georgi Danovski, Radoslav Aleksandrov, Stoyno Stoynov, and Marina Nedelcheva-Veleva. "The Effect of Dia2 Protein Deficiency on the Cell Cycle, Cell Size, and Recruitment of Ctf4 Protein in Saccharomyces cerevisiae." Molecules 27, no. 1 (December 24, 2021): 97. http://dx.doi.org/10.3390/molecules27010097.

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Cells have evolved elaborate mechanisms to regulate DNA replication machinery and cell cycles in response to DNA damage and replication stress in order to prevent genomic instability and cancer. The E3 ubiquitin ligase SCFDia2 in S. cerevisiae is involved in the DNA replication and DNA damage stress response, but its effect on cell growth is still unclear. Here, we demonstrate that the absence of Dia2 prolongs the cell cycle by extending both S- and G2/M-phases while, at the same time, activating the S-phase checkpoint. In these conditions, Ctf4—an essential DNA replication protein and substrate of Dia2—prolongs its binding to the chromatin during the extended S- and G2/M-phases. Notably, the prolonged cell cycle when Dia2 is absent is accompanied by a marked increase in cell size. We found that while both DNA replication inhibition and an absence of Dia2 exerts effects on cell cycle duration and cell size, Dia2 deficiency leads to a much more profound increase in cell size and a substantially lesser effect on cell cycle duration compared to DNA replication inhibition. Our results suggest that the increased cell size in dia2∆ involves a complex mechanism in which the prolonged cell cycle is one of the driving forces.

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Liu, Boyang, Han Zhao, Keliang Wu, and Jörg Großhans. "Temporal Gradients Controlling Embryonic Cell Cycle." Biology 10, no. 6 (June 9, 2021): 513. http://dx.doi.org/10.3390/biology10060513.

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Cell proliferation in early embryos by rapid cell cycles and its abrupt pause after a stereotypic number of divisions present an attractive system to study the timing mechanism in general and its coordination with developmental progression. In animals with large eggs, such as Xenopus, zebrafish, or Drosophila, 11–13 very fast and synchronous cycles are followed by a pause or slowdown of the cell cycle. The stage when the cell cycle is remodeled falls together with changes in cell behavior and activation of the zygotic genome and is often referred to as mid-blastula transition. The number of fast embryonic cell cycles represents a clear and binary readout of timing. Several factors controlling the cell cycle undergo dynamics and gradual changes in activity or concentration and thus may serve as temporal gradients. Recent studies have revealed that the gradual loss of Cdc25 protein, gradual depletion of free deoxyribonucleotide metabolites, or gradual depletion of free histone proteins impinge on Cdk1 activity in a threshold-like manner. In this review, we will highlight with a focus on Drosophila studies our current understanding and recent findings on the generation and readout of these temporal gradients, as well as their position within the regulatory network of the embryonic cell cycle.

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Herr, Patrick, Johan Boström, Eric Rullman, Sean G. Rudd, Mattias Vesterlund, Janne Lehtiö, Thomas Helleday, Gianluca Maddalo, and Mikael Altun. "Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics." Molecular & Cellular Proteomics 19, no. 4 (February 12, 2020): 608–23. http://dx.doi.org/10.1074/mcp.ra120.001938.

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The cell cycle is a highly conserved process involving the coordinated separation of a single cell into two daughter cells. To relate transcriptional regulation across the cell cycle with oscillatory changes in protein abundance and activity, we carried out a proteome- and phospho-proteome-wide mass spectrometry profiling. We compared protein dynamics with gene transcription, revealing many transcriptionally regulated G2 mRNAs that only produce a protein shift after mitosis. Integration of CRISPR/Cas9 survivability studies further highlighted proteins essential for cell viability. Analyzing the dynamics of phosphorylation events and protein solubility dynamics over the cell cycle, we characterize predicted phospho-peptide motif distributions and predict cell cycle-dependent translocating proteins, as exemplified by the S-adenosylmethionine synthase MAT2A. Our study implicates this enzyme in translocating to the nucleus after the G1/S-checkpoint, which enables epigenetic histone methylation maintenance during DNA replication. Taken together, this data set provides a unique integrated resource with novel insights on cell cycle dynamics.

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Fujita, Masatoshi, Chieko Yamada, Hidemasa Goto, Naoaki Yokoyama, Kiyotaka Kuzushima, Masaki Inagaki, and Tatsuya Tsurumi. "Cell Cycle Regulation of Human CDC6 Protein." Journal of Biological Chemistry 274, no. 36 (September 3, 1999): 25927–32. http://dx.doi.org/10.1074/jbc.274.36.25927.

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15

Cookson, Natalie A., Scott W. Cookson, Lev S. Tsimring, and Jeff Hasty. "Cell cycle-dependent variations in protein concentration." Nucleic Acids Research 38, no. 8 (December 17, 2009): 2676–81. http://dx.doi.org/10.1093/nar/gkp1069.

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16

Weinberg, Robert A. "The retinoblastoma protein and cell cycle control." Cell 81, no. 3 (May 1995): 323–30. http://dx.doi.org/10.1016/0092-8674(95)90385-2.

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17

Hamel, P. "The retinoblastoma protein and cell cycle regulation." Trends in Genetics 8, no. 1 (1992): 180–85. http://dx.doi.org/10.1016/0168-9525(92)90092-i.

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Hamel, P. A., B. L. Gallie, and R. A. Phillips. "The retinoblastoma protein and cell cycle regulation." Trends in Genetics 8, no. 5 (May 1992): 180–85. http://dx.doi.org/10.1016/0168-9525(92)90221-o.

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19

Jia, Min, Claudia Mateoiu, and Serhiy Souchelnytskyi. "Protein tyrosine nitration in the cell cycle." Biochemical and Biophysical Research Communications 413, no. 2 (September 2011): 270–76. http://dx.doi.org/10.1016/j.bbrc.2011.08.084.

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20

Shi, Yan, Zhi Rong Qian, Sui Zhang, Wanwan Li, Yohei Masugi, Tingting Li, Jennifer A. Chan, et al. "Cell Cycle Protein Expression in Neuroendocrine Tumors." Pancreas 46, no. 10 (2017): 1347–53. http://dx.doi.org/10.1097/mpa.0000000000000944.

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21

Rosner, Margit, and Markus Hengstschläger. "mTOR protein localization is cell cycle-regulated." Cell Cycle 10, no. 20 (October 15, 2011): 3608–10. http://dx.doi.org/10.4161/cc.10.20.17855.

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Frykman, Scott, and Friedrich Srienc. "Cell cycle-dependent protein secretion bySaccharomyces cerevisiae." Biotechnology and Bioengineering 76, no. 3 (2001): 259–68. http://dx.doi.org/10.1002/bit.10003.

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23

Preininger, A. M., and H. E. Hamm. "Heterotrimeric G Protein Cycle." Science Signaling 2004, no. 218 (February 3, 2004): tr1. http://dx.doi.org/10.1126/stke.2182004tr1.

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Kulartz, Monika, Ekkehard Hiller, Ferdinand Kappes, Lorenzo A. Pinna, and Rolf Knippers. "Protein kinase CK2 phosphorylates the cell cycle regulatory protein Geminin." Biochemical and Biophysical Research Communications 315, no. 4 (March 2004): 1011–17. http://dx.doi.org/10.1016/j.bbrc.2004.01.164.

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25

Evers, B. M., T. C. Ko, J. Li, and E. A. Thompson. "Cell cycle protein suppression and p21 induction in differentiating Caco-2 cells." American Journal of Physiology-Gastrointestinal and Liver Physiology 271, no. 4 (October 1, 1996): G722—G727. http://dx.doi.org/10.1152/ajpgi.1996.271.4.g722.

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Despite intensive efforts, the exact cellular mechanisms leading to gut differentiation and development remain largely undefined. The cyclins, the cyclin-dependent kinases (Cdks), and the Cdk inhibitors (e.g., p21 and p27) are proteins that are important for cell cycle progression, subsequent growth inhibition, and differentiation of various cell types. The purpose of our study was to better define the role of these cell cycle proteins in gut differentiation using the Caco-2 human cell line, which spontaneously differentiates to a small bowel phenotype, as demonstrated by induction of sucrase-isomaltase (SI) gene expression. We found that protein levels of the cyclins (both D- and E-type) and the Cdks (both Cdk2 and Cdk4) progressively decreased in postconfluent Caco-2 cells. Moreover, cyclin E-associated histone H1 kinase activity decreased in an analogous fashion as the cyclins and Cdks. In contrast, induction of the Cdk inhibitor p21 occurred by 3 days postconfluency, which was before the increase in SI mRNA levels. These changes in the cell cycle proteins, which include a progressive decrease of the cyclins and Cdks and a concomitant induction of p21, suggest an important role for these proteins in Caco-2 cell differentiation. Identifying the cell cycle mechanisms responsible for intestinal cell differentiation will be important to our understanding of both normal gut development as well as gut neoplasia, which involves aberrant regulation of cell cycle arrest.

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Harbauer, Angelika B., Magdalena Opalińska, Carolin Gerbeth, Josip S. Herman, Sanjana Rao, Birgit Schönfisch, Bernard Guiard, Oliver Schmidt, Nikolaus Pfanner, and Chris Meisinger. "Cell cycle–dependent regulation of mitochondrial preprotein translocase." Science 346, no. 6213 (November 6, 2014): 1109–13. http://dx.doi.org/10.1126/science.1261253.

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Mitochondria play central roles in cellular energy conversion, metabolism, and apoptosis. Mitochondria import more than 1000 different proteins from the cytosol. It is unknown if the mitochondrial protein import machinery is connected to the cell division cycle. We found that the cyclin-dependent kinase Cdk1 stimulated assembly of the main mitochondrial entry gate, the translocase of the outer membrane (TOM), in mitosis. The molecular mechanism involved phosphorylation of the cytosolic precursor of Tom6 by cyclin Clb3-activated Cdk1, leading to enhanced import of Tom6 into mitochondria. Tom6 phosphorylation promoted assembly of the protein import channel Tom40 and import of fusion proteins, thus stimulating the respiratory activity of mitochondria in mitosis. Tom6 phosphorylation provides a direct means for regulating mitochondrial biogenesis and activity in a cell cycle-specific manner.

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Wu, Hsuan-Chen, Colin G. Hebert, Chi-Wei Hung, David N. Quan, Karen K. Carter, and William E. Bentley. "Tuning cell cycle of insect cells for enhanced protein production." Journal of Biotechnology 168, no. 1 (October 2013): 55–61. http://dx.doi.org/10.1016/j.jbiotec.2013.08.017.

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Endicott, J. A., P. Nurse, and L. N. Johnson. "Mutational analysis supports a structural model for the cell cycle protein kinase p34." "Protein Engineering, Design and Selection" 7, no. 2 (1994): 243–57. http://dx.doi.org/10.1093/protein/7.2.243.

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de Lichtenberg, Ulrik, Thomas S. Jensen, Lars J. Jensen, and Søren Brunak. "Protein Feature Based Identification of Cell Cycle Regulated Proteins in Yeast." Journal of Molecular Biology 329, no. 4 (June 2003): 663–74. http://dx.doi.org/10.1016/s0022-2836(03)00490-x.

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30

Widlak, Piotr. "The DNA Damage-Induced Cell Cycle Checkpoints." Journal of Theoretical Medicine 2, no. 4 (2000): 237–43. http://dx.doi.org/10.1080/10273660008833051.

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The proliferation of eukaryotic cells is driven by a process called the cell cycle. Proper regulation of this process, leading to orderly execution of sequential steps within the cycle, ensures normal development and homeostasis of the organism. On the other hand, perturbations of the cell cycle are frequently attributed to cancer cells. Mechanisms that ensure the order and fidelity of events in the cell cycle are called checkpoints. The checkpoints induced by damaged DNA delay the cell cycle progression, providing more time for repair of lesion before DNA replication and segregation. The DNA damage-induced checkpoints can be recognized as signal transduction pathways that communicate information between DNA lesion and components of the cell cycle. Proteins involved in the cell cycle, as well as components of the signal transduction pathways communicating with the cell cycle, are frequently products of oncogenes and tumor suppressor genes. Malfunction of these genes plays a critical role in the development of human cancers. The key component in the checkpoint machinery is tumor suppressor gene p53, involved in either regulation of the cell cycle progression (e.g. Gl arrest of cells treated with DNA damaging factor) or activation of programmed cell death (apoptosis). It is postulated that p53 protein is activated by DNA damage detectors. One of the candidates for this role is DNA-dependent protein kinase (DNA-PK) which recognizes DNA strand breaks and phosphorylates p53 protein.

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Pelech, Steven L., Jasbinder S. Sanghera, and Maleki Daya-Makin. "Protein kinase cascades in meiotic and mitotic cell cycle control." Biochemistry and Cell Biology 68, no. 12 (December 1, 1990): 1297–330. http://dx.doi.org/10.1139/o90-194.

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Eukaryotic cell cycle progression during meiosis and mitosis is extensively regulated by reversible protein phosphorylation. Many cell surface receptors for mitogens are ligand-stimulated protein-tyrosine kinases that control the activation of a network of cytoplasmic and nuclear protein-serine(threonine) kinases. Over 30 plasma membrane associated protein-tyrosine kinases are encoded by proto-oncogenes, i.e., genes that have the potential to facilitate cancer when disregulated. Proteins such as ribosomal protein S6, microtubule-associated protein-2, myelin basic protein, and casein have been used to detect intracellular protein-serine(threonine) kinases that are activated further downstream in growth factor signalling transduction cascades. Genetic analysis of yeast cell division control (cdc) mutants has revealed another 20 or so protein-serine(threonine) kinases. One of these, specified by the cdc-2 gene in Schizosaccharomyces pombe, has homologs that are stimulated during M phase in maturing sea star and frog oocytes and mammalian somatic cells. Furthermore, during meiotic maturation in these echinoderm and amphibian oocytes, this is followed by activation of many of the same protein-serine(threonine) kinases that are stimulated when quiescent mammalian somatic cells are prompted with mitogens to traverse from G0 to G1 phase. These findings imply that a similar protein kinase cascade may oversee progression at multiple points in the cell cycle.Key words: protein kinases, mitosis, meiosis, oncogenes, cell division control.

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Palladino, Giuseppe, Tiziana Notarangelo, Giuseppe Pannone, Annamaria Piscazzi, Olga Lamacchia, Lorenza Sisinni, Girolamo Spagnoletti, et al. "TRAP1 regulates cell cycle and apoptosis in thyroid carcinoma cells." Endocrine-Related Cancer 23, no. 9 (September 2016): 699–709. http://dx.doi.org/10.1530/erc-16-0063.

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Tumor necrosis factor receptor-associated protein 1 (TRAP1) is a heat shock protein 90 (HSP90) molecular chaperone upregulated in several human malignancies and involved in protection from apoptosis and drug resistance, cell cycle progression, cell metabolism and quality control of specific client proteins. TRAP1 role in thyroid carcinoma (TC), still unaddressed at present, was investigated by analyzing its expression in a cohort of 86 human TCs and evaluating its involvement in cancer cell survival and proliferationin vitro. Indeed, TRAP1 levels progressively increased from normal peritumoral thyroid gland, to papillary TCs (PTCs), follicular variants of PTCs (FV-PTCs) and poorly differentiated TCs (PDTCs). By contrast, anaplastic thyroid tumors exhibited a dual pattern, the majority being characterized by high TRAP1 levels, while a small subgroup completely negative. Consistently with a potential involvement of TRAP1 in thyroid carcinogenesis, TRAP1 silencing resulted in increased sensitivity to paclitaxel-induced apoptosis, inhibition of cell cycle progression and attenuation of ERK signaling. Noteworthy, the inhibition of TRAP1 ATPase activity by pharmacological agents resulted in attenuation of cell proliferation, inhibition of ERK signaling and reversion of drug resistance. These data suggest that TRAP1 inhibition may be regarded as potential strategy to target specific features of human TCs, i.e., cell proliferation and resistance to apoptosis.

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Schroeder, Matthew D., Jaime Symowicz, and Linda A. Schuler. "PRL Modulates Cell Cycle Regulators in Mammary Tumor Epithelial Cells." Molecular Endocrinology 16, no. 1 (January 1, 2002): 45–57. http://dx.doi.org/10.1210/mend.16.1.0762.

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Abstract PRL is essential for normal lobulo-alveolar growth of the mammary gland and may contribute to mammary cancer development or progression. However, analysis of the mechanism of action of PRL in these processes is complicated by the production of PRL within mammary epithelia. To examine PRL actions in a mammary cell-specific context, we selected MCF-7 cells that lacked endogenous PRL synthesis, using PRL stimulation of interferon-γ-activated sequence-related PRL response elements. Derived clones exhibited a greater proliferative response to PRL than control cells. To understand the mechanism, we examined, by Western analysis, levels of proteins essential for cell cycle progression as well as phosphorylation of retinoblastoma protein. The expression of cyclin D1, a critical regulator of the G1/S transition, was significantly increased by PRL and was associated with hyperphosphorylation of retinoblastoma protein at Ser780. Cyclin B1 was also increased by PRL. In contrast, PRL decreased the Cip/Kip family inhibitor, p21, but not p16 or p27. These studies demonstrate that PRL can stimulate the cell cycle in mammary epithelia and identify specific targets in this process. This model system will enable further molecular dissection of the pathways involved in PRL-induced proliferation, increasing our understanding of this hormone and its interactions with other factors in normal and pathogenic processes.

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Inostroza, Daniel, Cecilia Hernández, Diego Seco, Gonzalo Navarro, and Alvaro Olivera-Nappa. "Cell cycle and protein complex dynamics in discovering signaling pathways." Journal of Bioinformatics and Computational Biology 17, no. 03 (June 2019): 1950011. http://dx.doi.org/10.1142/s0219720019500112.

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Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data available and the recent discoveries showing that many diseases are related to the disruption of cellular signal transduction cascades, in silico discovery of signaling pathways in cell biology has become an active research topic in past years. However, reconstruction of signaling pathways remains a challenge mainly because of the need for systematic approaches for predicting causal relationships, like edge direction and activation/inhibition among interacting proteins in the signal flow. We propose an approach for predicting signaling pathways that integrates protein interactions, gene expression, phenotypes, and protein complex information. Our method first finds candidate pathways using a directed-edge-based algorithm and then defines a graph model to include causal activation relationships among proteins, in candidate pathways using cell cycle gene expression and phenotypes to infer consistent pathways in yeast. Then, we incorporate protein complex coverage information for deciding on the final predicted signaling pathways. We show that our approach improves the predictive results of the state of the art using different ranking metrics.

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Soltani, Mohammad, and Abhyudai Singh. "Effects of cell-cycle-dependent expression on random fluctuations in protein levels." Royal Society Open Science 3, no. 12 (December 2016): 160578. http://dx.doi.org/10.1098/rsos.160578.

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Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We analyse a model where a stable protein is synthesized in random bursts, and the frequency with which bursts occur varies within the cell cycle. Formulae quantifying the extent of fluctuations in the protein copy number are derived and decomposed into components arising from the cell cycle and stochastic processes. The latter stochastic component represents contributions from bursty expression and errors incurred during partitioning of molecules between daughter cells. These formulae reveal an interesting trade-off: cell-cycle dependencies that amplify the noise contribution from bursty expression also attenuate the contribution from partitioning errors. We investigate the existence of optimum strategies for coupling expression to the cell cycle that minimize the stochastic component. Intriguingly, results show that a zero production rate throughout the cell cycle, with expression only occurring just before cell division, minimizes noise from bursty expression for a fixed mean protein level. By contrast, the optimal strategy in the case of partitioning errors is to make the protein just after cell division. We provide examples of regulatory proteins that are expressed only towards the end of the cell cycle, and argue that such strategies enhance robustness of cell-cycle decisions to the intrinsic stochasticity of gene expression.

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Todd, R., P. W. Hinds, K. Munger, A. K. Rustgi, O. G. Opitz, Y. Suliman, and D. T. Wong. "Cell Cycle Dysregulation in Oral Cancer." Critical Reviews in Oral Biology & Medicine 13, no. 1 (January 2002): 51–61. http://dx.doi.org/10.1177/154411130201300106.

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The dysregulation of the molecular events governing cell cycle control is emerging as a central theme of oral carcinogenesis. Regulatory pathways responding to extracellular signaling or intracellular stress and DNA damage converge on the cell cycle apparatus. Abrogation of mitogenic and anti-mitogenic response regulatory proteins, such as the retinoblastoma tumor suppressor protein (pRB), cyclin D1, cyclin-dependent kinase (CDK) 6, and CDK inhibitors (p21WAF1/CIP1, p27KIP1, and p16INK4a), occur frequently in human oral cancers. Cellular responses to metabolic stress or genomic damage through p53 and related pathways that block cell cycle progression are also altered during oral carcinogenesis. In addition, new pathways and cell cycle regulatory proteins, such as p12DOC-1, are being discovered. The multistep process of oral carcinogenesis likely involves functional alteration of cell cycle regulatory members combined with escape from cellular senescence and apoptotic signaling pathways. Detailing the molecular alterations and understanding the functional consequences of the dysregulation of the cell cycle apparatus in the malignant oral keratinocyte will uncover novel diagnostic and therapeutic approaches.

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Gudi, Siva R. P., Ann A. Lee, Craig B. Clark, and John A. Frangos. "Equibiaxial strain and strain rate stimulate early activation of G proteins in cardiac fibroblasts." American Journal of Physiology-Cell Physiology 274, no. 5 (May 1, 1998): C1424—C1428. http://dx.doi.org/10.1152/ajpcell.1998.274.5.c1424.

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Cardiac fibroblasts are responsible for the production of the extracellular matrix of the heart, with alterations of fibroblast function implicated in myocardial infarction and cardiac hypertrophy. Here the role of heterotrimeric GTP-binding proteins (G proteins) in the mechanotransduction of strain in rat cardiac fibroblasts was investigated. Cells in an equibiaxial stretch device were incubated with the photoreactive GTP analog azidoanalido [α-32P]GTP (AAGTP) and were subjected to various regimens of strain. Autoradiographic analysis showed a 42-kDa protein labeled for cells exposed to 12 cycles of 3% strain or 6 cycles of 6% strain over 60 s (strain rate of 1.2%/s), whereas 6 cycles of 3% strain (0.6%/s) elicited no measurable response. To further investigate the role of strain rate, a single 6% cycle over 10 or 60 s (1.2% and 0.2%/s, respectively) was applied, with the more rapid cycle stimulating AAGTP binding, whereas the lower strain rate showed no response. In cells subjected to a single 6% cycle/10 s, immunoprecipitation identified the AAGTP-labeled 42-kDa band as the G protein subunits Gαq and Gαi1. These results demonstrate that G protein activation represents one of the early mechanotransduction events in cardiac fibroblasts subjected to mechanical strain, with the rate at which the strain is applied modulating this response.

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Poli, Alessandro, Sara Mongiorgi, Lucio Cocco, and Matilde Y. Follo. "Protein kinase C involvement in cell cycle modulation." Biochemical Society Transactions 42, no. 5 (September 18, 2014): 1471–76. http://dx.doi.org/10.1042/bst20140128.

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Protein kinases C (PKCs) are a family of serine/threonine kinases which act as key regulators in cell cycle progression and differentiation. Studies of the involvement of PKCs in cell proliferation showed that their role is dependent on cell models, cell cycle phases, timing of activation and localization. Indeed, PKCs can positively and negatively act on it, regulating entry, progression and exit from the cell cycle. In particular, the targets of PKCs resulted to be some of the key proteins involved in the cell cycle including cyclins, cyclin-dependent kinases (Cdks), Cip/Kip inhibitors and lamins. Several findings described roles for PKCs in the regulation of G1/S and G2/M checkpoints. As a matter of fact, data from independent laboratories demonstrated PKC-related modulations of cyclins D, leading to effects on the G1/S transition and differentiation of different cell lines. Moreover, interesting data were published on PKC-mediated phosphorylation of lamins. In addition, PKC isoenzymes can accumulate in the nuclei, attracted by different stimuli including diacylglycerol (DAG) fluctuations during cell cycle progression, and target lamins, leading to their disassembly at mitosis. In the present paper, we briefly review how PKCs could regulate cell proliferation and differentiation affecting different molecules related to cell cycle progression.

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39

Carlomagno, Francesca. "Ferritinophagy and Cell Cycle Control." Blood 128, no. 22 (December 2, 2016): SCI—20—SCI—20. http://dx.doi.org/10.1182/blood.v128.22.sci-20.sci-20.

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Abstract The autophagic degradation of the iron-storage macromolecule ferritin, called ferritinophagy, is critical to restore the appropriate cellular iron levels and influences systemic iron homeostasis. Under low iron conditions, nuclear receptor coactivator 4 (NCOA4) protein accumulates and promotes, as cargo receptor, ferritinophagy. We have recently demonstrated that mice carrying genetic ablation of NCOA4 were unable to mobilize iron from deposits, featuring tissue iron overload as well as mild anemia. Because of impaired ferritinophagy, NCOA4 null mice displayed a severe microcytic hypochromic anemia and ineffective erythropoiesis when fed with an iron low diet. Conversely, they poorly tolerated an iron rich diet, dying prematurely from iron toxicity. Since in previous studies we discovered that nuclear NCOA4 is a chromatin binding protein that acts as a negative regulator of DNA replication origin activation, inhibiting the MCM2-7 DNA helicase, we also investigated whether NCOA4 could regulate DNA replication as a function of iron bioavailability. Treatment with iron chelators promoted a G1 phase cell cycle arrest, blocking DNA replication origins activation. In cell fractionation experiments, we observed that iron depletion induced not only cytosolic but also nuclear NCOA4 stabilization, and by chromatin immunoprecipitation (CHIP) and co-immunoprecipitation assays, we demonstrated that NCOA4 enriches at canonical DNA replication origins increasing the binding to MCM2-7 complex. Silencing of NCOA4 induced an unscheduled activation of DNA replication under iron-depleted conditions that promotes replication stress and impairs cell viability. In conclusion, our data indicate NCOA4 as a novel key iron responsive protein able to couple DNA replication origin activation to cellular iron levels. Disclosures No relevant conflicts of interest to declare.

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Livneh, Etta, and Daniel D. Fishman. "Linking Protein Kinase C to Cell-Cycle Control." European Journal of Biochemistry 248, no. 1 (August 15, 1997): 1–9. http://dx.doi.org/10.1111/j.1432-1033.1997.t01-4-00001.x.

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Wheeler, Robert T., James W. Gober, and Lucy Shapiro. "Protein localization during the Caulobacter crescentus cell cycle." Current Opinion in Microbiology 1, no. 6 (December 1998): 636–42. http://dx.doi.org/10.1016/s1369-5274(98)80108-2.

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Hall, Frederick L., and P. Richard Vulliet. "Proline-directed protein phosphorylation and cell cycle regulation." Current Opinion in Cell Biology 3, no. 2 (April 1991): 176–84. http://dx.doi.org/10.1016/0955-0674(91)90136-m.

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43

Ewen, Mark E. "The cell cycle and the retinoblastoma protein family." Cancer and Metastasis Reviews 13, no. 1 (March 1994): 45–66. http://dx.doi.org/10.1007/bf00690418.

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MacCorkle, Rebecca A., and Tse-Hua Tan. "Mitogen-Activated Protein Kinases in Cell-Cycle Control." Cell Biochemistry and Biophysics 43, no. 3 (2005): 451–62. http://dx.doi.org/10.1385/cbb:43:3:451.

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Hicke, Brian, Rachel Rempel, James Mailer, Richard A. Swank, Joyce R. Hamaguchi, E. Morton Bradbury, David M. Prescott, and Thomas R. Cech. "Phosphorylation of theOxytrichatelomere protein: possible cell cycle regulation." Nucleic Acids Research 23, no. 11 (1995): 1887–93. http://dx.doi.org/10.1093/nar/23.11.1887.

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Ang, Xiaolu L., and J. Wade Harper. "SCF-mediated protein degradation and cell cycle control." Oncogene 24, no. 17 (April 2005): 2860–70. http://dx.doi.org/10.1038/sj.onc.1208614.

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47

Koga, Shinichiro, Nobuhiro Yamaguchi, Tomoko Abe, Masayoshi Minegishi, Shigeru Tsuchiya, Masayuki Yamamoto, and Naoko Minegishi. "Cell-cycle–dependent oscillation of GATA2 expression in hematopoietic cells." Blood 109, no. 10 (January 25, 2007): 4200–4208. http://dx.doi.org/10.1182/blood-2006-08-044149.

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Abstract In vitro manipulation of hematopoietic stem cells (HSCs) is a key issue in both transplantation therapy and regenerative medicine, and thus new methods are required to achieve HSC expansion with self-renewal. GATA2 is a transcription factor controlling pool size of HSCs. Of interest, continuous overexpression of GATA2 does not induce HSC proliferation. In this report, we demonstrate that GATA2 expression, in leukemic and normal hematopoietic cells, oscillates during the cell cycle, such that expression is high in S phase but low in G1/S and M phase. GATA2 binding to target Bcl-X gene also oscillates in accordance with GATA2 expression. Using a green fluorescent protein (GFP)–GATA2 fusion protein, we demonstrate cell-cycle–specific activity of proteasome-dependent degradation of GATA2. Immunoprecipitation/immunoblotting analysis demonstrated phosphorylation of GATA2 at cyclin-dependent kinase (Cdk)–consensus motifs, S/T0P+1, and interaction of GATA2 with Cdk2/cyclin A2–, Cdk2/cyclin A2–, and Cdk4/cyclin D1–phosphorylated GATA2 in vitro. Mutants in phosphorylation motifs exhibited altered expression profiles of GFP-GATA2 domain fusion proteins. These results indicate that GATA2 phosphorylation by Cdk/cyclin systems is responsible for the cell-cycle–dependent regulation of GATA2 expression, and suggest the possibility that a cell-cycle–specific “on-off” response of GATA2 expression may control hematopoietic-cell proliferation and survival.

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Kelliher, Christina M., Matthew W. Foster, Francis C. Motta, Anastasia Deckard, Erik J. Soderblom, M. Arthur Moseley, and Steven B. Haase. "Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae." Molecular Biology of the Cell 29, no. 22 (November 2018): 2644–55. http://dx.doi.org/10.1091/mbc.e18-04-0255.

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In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the periodic expression of many genes during the cell cycle, including gene products required for progression through cell-cycle events. Experimental evidence coupled with quantitative models suggests that a network of interconnected TFs is capable of regulating periodic genes over the cell cycle. Importantly, these dynamical models were built on transcriptomics data and assumed that TF protein levels and activity are directly correlated with mRNA abundance. To ask whether TF transcripts match protein expression levels as cells progress through the cell cycle, we applied a multiplexed targeted mass spectrometry approach (parallel reaction monitoring) to synchronized populations of cells. We found that protein expression of many TFs and cell-cycle regulators closely followed their respective mRNA transcript dynamics in cycling wild-type cells. Discordant mRNA/protein expression dynamics was also observed for a subset of cell-cycle TFs and for proteins targeted for degradation by E3 ubiquitin ligase complexes such as SCF (Skp1/Cul1/F-box) and APC/C (anaphase-promoting complex/cyclosome). We further profiled mutant cells lacking B-type cyclin/CDK activity ( clb1-6) where oscillations in ubiquitin ligase activity, cyclin/CDKs, and cell-cycle progression are halted. We found that a number of proteins were no longer periodically degraded in clb1-6 mutants compared with wild type, highlighting the importance of posttranscriptional regulation. Finally, the TF complexes responsible for activating G1/S transcription (SBF and MBF) were more constitutively expressed at the protein level than at periodic mRNA expression levels in both wild-type and mutant cells. This comprehensive investigation of cell-cycle regulators reveals that multiple layers of regulation (transcription, protein stability, and proteasome targeting) affect protein expression dynamics during the cell cycle.

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Malumbres, Marcos. "Physiological Relevance of Cell Cycle Kinases." Physiological Reviews 91, no. 3 (July 2011): 973–1007. http://dx.doi.org/10.1152/physrev.00025.2010.

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The basic biology of the cell division cycle and its control by protein kinases was originally studied through genetic and biochemical studies in yeast and other model organisms. The major regulatory mechanisms identified in this pioneer work are conserved in mammals. However, recent studies in different cell types or genetic models are now providing a new perspective on the function of these major cell cycle regulators in different tissues. Here, we review the physiological relevance of mammalian cell cycle kinases such as cyclin-dependent kinases (Cdks), Aurora and Polo-like kinases, and mitotic checkpoint regulators (Bub1, BubR1, and Mps1) as well as other less-studied enzymes such as Cdc7, Nek proteins, or Mastl and their implications in development, tissue homeostasis, and human disease. Among these functions, the control of self-renewal or asymmetric cell division in stem/progenitor cells and the ability to regenerate injured tissues is a central issue in current research. In addition, many of these proteins play previously unexpected roles in metabolism, cardiovascular function, or neuron biology. The modulation of their enzymatic activity may therefore have multiple therapeutic benefits in human disease.

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Girard, F., U. Strausfeld, J. C. Cavadore, P. Russell, A. Fernandez, and N. J. Lamb. "cdc25 is a nuclear protein expressed constitutively throughout the cell cycle in nontransformed mammalian cells." Journal of Cell Biology 118, no. 4 (August 15, 1992): 785–94. http://dx.doi.org/10.1083/jcb.118.4.785.

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A family of proteins homologous to the cdc25 gene product of the fission yeast bear specific protein tyrosine phosphatase activity involved in the activation of the p34cdc2-cyclin B kinase. Using affinity-purified antibodies raised against a synthetic peptide corresponding to the catalytic site of the cdc25 phosphatase, we show that cdc25 protein is constitutively expressed throughout the cell cycle of nontransformed mammalian fibroblasts and does not undergo major changes in protein level. By indirect immunofluorescence, cdc25 protein is found essentially localized in the nucleus throughout interphase and during early prophase. Just before the complete nuclear envelope breakdown at the prophase-prometaphase boundary, cdc25 proteins are redistributed throughout the cytoplasm. During metaphase and anaphase, cdc25 staining remains distributed throughout the cell and excludes the condensed chromosomes. The nuclear locale reappears during telophase. In light of the recent data describing the cytoplasmic localization of cyclin B protein (Pines, J., and T. Hunter. 1991. J. Cell Biol. 115:1-17), the data presented here suggest that separation in two distinct cellular compartments of the cdc25 phosphatase and its substrate p34cdc2-cyclin B may be of importance in the regulation of the cdc2 kinase activity.

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Journal articles on the topic 'Cell cycle protein'

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