Editing Cell cycle (section)

===Role of cyclins and CDKs===
{| class=wikitable align=right
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|[[File:Paul Nurse portrait.jpg|120px]]<br />Nobel Laureate<br />[[Paul Nurse]]
|[[File:Tim hunt.jpg|132px]]<br />Nobel Laureate<br />[[Tim Hunt]]
|}

Two key classes of regulatory molecules, [[cyclin]]s and [[cyclin-dependent kinase]]s (CDKs), determine a cell's progress through the cell cycle.<ref name="pmid7575488">{{cite journal | vauthors = Nigg EA | title = Cyclin-dependent protein kinases: key regulators of the eukaryotic cell cycle | journal = BioEssays | volume = 17 | issue = 6 | pages = 471–480 | date = June 1995 | pmid = 7575488 | doi = 10.1002/bies.950170603 | s2cid = 44307473 }}</ref> [[Leland H. Hartwell]], [[R. Timothy Hunt]], and [[Paul M. Nurse]] won the 2001 [[Nobel Prize in Physiology or Medicine]] for their discovery of these central molecules.<ref>{{cite web| url=http://nobelprize.org/nobel_prizes/medicine/laureates/2001/press.html | publisher=Nobelprize.org | title=The Nobel Prize in Physiology or Medicine 2001 – Press release}}</ref> Many of the genes encoding cyclins and CDKs are [[conservation (genetics)|conserved]] among all eukaryotes, but in general, more complex organisms have more elaborate cell cycle control systems that incorporate more individual components. Many of the relevant genes were first identified by studying yeast, especially ''[[Saccharomyces cerevisiae]]'';<ref name="pmid9843569">{{cite journal | vauthors = Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B | display-authors = 6 | title = Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization | journal = Molecular Biology of the Cell | volume = 9 | issue = 12 | pages = 3273–3297 | date = December 1998 | pmid = 9843569 | pmc = 25624 | doi = 10.1091/mbc.9.12.3273 }}</ref> genetic nomenclature in yeast dubs many of these genes ''cdc'' (for "cell division cycle") followed by an identifying number, e.g. ''[[cdc25]]'' or ''[[cdc20]]''.

Cyclins form the regulatory subunits and CDKs the catalytic subunits of an activated [[heterodimer]]; cyclins have no catalytic activity and CDKs are inactive in the absence of a partner cyclin. When activated by a bound cyclin, CDKs perform a common biochemical reaction called [[phosphorylation]] that activates or inactivates target proteins to orchestrate coordinated entry into the next phase of the cell cycle. Different cyclin-CDK combinations determine the downstream proteins targeted. CDKs are constitutively expressed in cells whereas cyclins are synthesised at specific stages of the cell cycle, in response to various molecular signals.<ref name="Robbins">{{cite book | vauthors = Robbins SL, Cotran RS | veditors = Kumar V, Abbas AK, Fausto N | title = Pathological Basis of Disease | publisher = [[Elsevier]] |year=2004 |isbn=978-81-8147-528-2}}</ref>

====General mechanism of cyclin-CDK interaction====
Upon receiving a pro-mitotic extracellular signal, G<sub>1</sub> [[cyclin-CDK]] complexes become active to prepare the cell for S phase, promoting the expression of [[transcription factor]]s that in turn promote the expression of S cyclins and of enzymes required for [[DNA replication]]. The G<sub>1</sub> cyclin-CDK complexes also promote the degradation of molecules that function as S phase inhibitors by targeting them for [[ubiquitination]]. Once a protein has been ubiquitinated, it is targeted for proteolytic degradation by the [[proteasome]]. Results from a study of E2F transcriptional dynamics at the single-cell level argue that the role of G1 cyclin-CDK activities, in particular cyclin D-CDK4/6, is to tune the timing rather than the commitment of cell cycle entry.<ref name="Dong, P. 2014">{{cite journal | vauthors = Dong P, Maddali MV, Srimani JK, Thélot F, Nevins JR, Mathey-Prevot B, You L | title = Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control | journal = Nature Communications | volume = 5 | pages = 4750 | date = September 2014 | pmid = 25175461 | pmc = 4164785 | doi = 10.1038/ncomms5750 | bibcode = 2014NatCo...5.4750D }}</ref>

Active S cyclin-CDK complexes phosphorylate proteins that make up the [[pre-replication complex]]es assembled during G<sub>1</sub> phase on DNA [[origin of replication|replication origins]]. The phosphorylation serves two purposes: to activate each already-assembled pre-replication complex, and to prevent new complexes from forming. This ensures that every portion of the cell's [[genome]] will be replicated once and only once. The reason for prevention of gaps in replication is fairly clear, because daughter cells that are missing all or part of crucial genes will die. However, for reasons related to [[gene copy number]] effects, possession of extra copies of certain genes is also deleterious to the daughter cells.

Mitotic cyclin-CDK complexes, which are synthesized but inactivated during S and G<sub>2</sub> phases, promote the initiation of [[mitosis]] by stimulating downstream proteins involved in chromosome condensation and [[mitotic spindle]] assembly. A critical complex activated during this process is a [[ubiquitin ligase]] known as the [[anaphase-promoting complex]] (APC), which promotes degradation of structural proteins associated with the chromosomal [[kinetochore]]. APC also targets the mitotic cyclins for degradation, ensuring that telophase and cytokinesis can proceed.<ref>{{cite journal | vauthors = Mahmoudi M, Azadmanesh K, Shokrgozar MA, Journeay WS, Laurent S | title = Effect of nanoparticles on the cell life cycle | journal = Chemical Reviews | volume = 111 | issue = 5 | pages = 3407–3432 | date = May 2011 | pmid = 21401073 | doi = 10.1021/cr1003166 }}</ref>

====Specific action of cyclin-CDK complexes====
[[Cyclin D]] is the first cyclin produced in the cells that enter the cell cycle, in response to extracellular signals (e.g. [[growth factor]]s). Cyclin D levels stay low in resting cells that are not proliferating. Additionally, [[Cyclin-dependent kinase 4|CDK4/6]] and [[Cyclin-dependent kinase 2|CDK2]] are also inactive because CDK4/6 are bound by [[INK4]] family members (e.g., p16), limiting kinase activity. Meanwhile, CDK2 complexes are inhibited by the CIP/KIP proteins such as p21 and p27,<ref>{{cite journal | vauthors = Goel S, DeCristo MJ, McAllister SS, Zhao JJ | title = CDK4/6 Inhibition in Cancer: Beyond Cell Cycle Arrest | journal = Trends in Cell Biology | volume = 28 | issue = 11 | pages = 911–925 | date = November 2018 | pmid = 30061045 | pmc = 6689321 | doi = 10.1016/j.tcb.2018.07.002 }}</ref> When it is time for a cell to enter the cell cycle, which is triggered by a mitogenic stimuli, levels of cyclin D increase. In response to this trigger, cyclin D binds to existing [[Cyclin-dependent kinase 4|CDK4]]/6, forming the active cyclin D-CDK4/6 complex. Cyclin D-CDK4/6 complexes in turn mono-phosphorylates the [[retinoblastoma]] susceptibility protein ([[Retinoblastoma protein|Rb]]) to pRb. The un-phosphorylated Rb tumour suppressor functions in inducing cell cycle exit and maintaining G0 arrest (senescence).<ref>{{cite journal | vauthors = Burkhart DL, Sage J | title = Cellular mechanisms of tumour suppression by the retinoblastoma gene | journal = Nature Reviews. Cancer | volume = 8 | issue = 9 | pages = 671–682 | date = September 2008 | pmid = 18650841 | pmc = 6996492 | doi = 10.1038/nrc2399 }}</ref>

In the last few decades, a model has been widely accepted whereby pRB proteins are inactivated by cyclin D-Cdk4/6-mediated phosphorylation. Rb has 14+ potential phosphorylation sites. Cyclin D-Cdk 4/6 progressively phosphorylates Rb to hyperphosphorylated state, which triggers dissociation of pRB–[[E2F]] complexes, thereby inducing G1/S cell cycle gene expression and progression into S phase.<ref>{{cite book | vauthors = Morgan DO |title=The cell cycle : principles of control |date=2007 |publisher=New Science Press |isbn=978-0-19-920610-0 |location=London |oclc=70173205 }}</ref>

Scientific observations from a study have shown that Rb is present in three types of isoforms: (1) un-phosphorylated Rb in G0 state; (2) mono-phosphorylated Rb, also referred to as "hypo-phosphorylated' or 'partially' phosphorylated Rb in early G1 state; and (3) inactive hyper-phosphorylated Rb in late G1 state.<ref>{{cite journal | vauthors = Paternot S, Bockstaele L, Bisteau X, Kooken H, Coulonval K, Roger PP | title = Rb inactivation in cell cycle and cancer: the puzzle of highly regulated activating phosphorylation of CDK4 versus constitutively active CDK-activating kinase | journal = Cell Cycle | volume = 9 | issue = 4 | pages = 689–699 | date = February 2010 | pmid = 20107323 | doi = 10.4161/cc.9.4.10611 | doi-access = free | url = https://dipot.ulb.ac.be/dspace/bitstream/2013/57637/1/17-PaternotCC9-4.pdf }}</ref><ref>{{cite journal | vauthors = Henley SA, Dick FA | title = The retinoblastoma family of proteins and their regulatory functions in the mammalian cell division cycle | journal = Cell Division | volume = 7 | issue = 1 | pages = 10 | date = March 2012 | pmid = 22417103 | pmc = 3325851 | doi = 10.1186/1747-1028-7-10 | doi-access = free }}</ref><ref name=":0">{{cite journal | vauthors = Narasimha AM, Kaulich M, Shapiro GS, Choi YJ, Sicinski P, Dowdy SF | title = Cyclin D activates the Rb tumor suppressor by mono-phosphorylation | journal = eLife | volume = 3 | pages = e02872 | date = June 2014 | pmid = 24876129 | pmc = 4076869 | doi = 10.7554/eLife.02872 | doi-access = free }}</ref> In early G1 cells, mono-phosphorylated Rb exists as 14 different isoforms, one of each has distinct [[E2F]] binding affinity.<ref name=":0" /> Rb has been found to associate with hundreds of different proteins<ref>{{cite book | vauthors = Morris EJ, Dyson NJ | title = Retinoblastoma protein partners | volume = 82 | pages = [https://archive.org/details/advancesincancer0000unse_w5o8/page/1 1–54] | date = 2001-01-01 | pmid = 11447760 | doi = 10.1016/s0065-230x(01)82001-7 | publisher = Academic Press | isbn = 9780120066827 | series = Advances in Cancer Research | url = https://archive.org/details/advancesincancer0000unse_w5o8/page/1 }}</ref> and the idea that different mono-phosphorylated Rb isoforms have different protein partners was very appealing.<ref name="pmid27401552">{{cite journal | vauthors = Dyson NJ | title = RB1: a prototype tumor suppressor and an enigma | journal = Genes & Development | volume = 30 | issue = 13 | pages = 1492–1502 | date = July 2016 | pmid = 27401552 | pmc = 4949322 | doi = 10.1101/gad.282145.116 }}</ref> A later report confirmed that mono-phosphorylation controls Rb's association with other proteins and generates functional distinct forms of Rb.<ref name="Sanidas">{{cite journal | vauthors = Sanidas I, Morris R, Fella KA, Rumde PH, Boukhali M, Tai EC, Ting DT, Lawrence MS, Haas W, Dyson NJ | display-authors = 6 | title = A Code of Mono-phosphorylation Modulates the Function of RB | journal = Molecular Cell | volume = 73 | issue = 5 | pages = 985–1000.e6 | date = March 2019 | pmid = 30711375 | pmc = 6424368 | doi = 10.1016/j.molcel.2019.01.004 }}</ref> All different mono-phosphorylated Rb isoforms inhibit E2F transcriptional program and are able to arrest cells in G1-phase. Different mono-phosphorylated forms of Rb have distinct transcriptional outputs that are extended beyond E2F regulation.<ref name="Sanidas" />

In general, the binding of pRb to E2F inhibits the E2F target gene expression of certain G1/S and S transition genes including [[Cyclin E|E-type cyclins]]. The partial phosphorylation of Rb de-represses the Rb-mediated suppression of E2F target gene expression, begins the expression of cyclin E. The molecular mechanism that causes the cell switched to cyclin E activation is currently not known, but as cyclin E levels rise, the active cyclin E-CDK2 complex is formed, bringing Rb to be inactivated by hyper-phosphorylation.<ref name=":0" /> Hyperphosphorylated Rb is completely dissociated from E2F, enabling further expression of a wide range of E2F target genes are required for driving cells to proceed into S phase [1]. It has been identified that cyclin D-Cdk4/6 binds to a C-terminal alpha-helix region of Rb that is only distinguishable to cyclin D rather than other cyclins, [[cyclin E]], [[Cyclin A|A]] and [[Cyclin B|B]].<ref name=":1">{{cite journal | vauthors = Topacio BR, Zatulovskiy E, Cristea S, Xie S, Tambo CS, Rubin SM, Sage J, Kõivomägi M, Skotheim JM | display-authors = 6 | title = Cyclin D-Cdk4,6 Drives Cell-Cycle Progression via the Retinoblastoma Protein's C-Terminal Helix | journal = Molecular Cell | volume = 74 | issue = 4 | pages = 758–770.e4 | date = May 2019 | pmid = 30982746 | pmc = 6800134 | doi = 10.1016/j.molcel.2019.03.020 }}</ref> This observation based on the structural analysis of Rb phosphorylation supports that Rb is phosphorylated in a different level through multiple Cyclin-Cdk complexes. This also makes feasible the current model of a simultaneous switch-like inactivation of all mono-phosphorylated Rb isoforms through one type of Rb hyper-phosphorylation mechanism. In addition, mutational analysis of the cyclin D- Cdk 4/6 specific Rb C-terminal helix shows that disruptions of cyclin D-Cdk 4/6 binding to Rb prevents Rb phosphorylation, arrests cells in G1, and bolsters Rb's functions in tumor suppressor.<ref name=":1" /> This cyclin-Cdk driven cell cycle transitional mechanism governs a cell committed to the cell cycle that allows cell proliferation. A cancerous cell growth often accompanies with deregulation of Cyclin D-Cdk 4/6 activity.

The hyperphosphorylated Rb dissociates from the E2F/DP1/Rb complex (which was bound to the [[E2F]] responsive genes, effectively "blocking" them from transcription), activating E2F. Activation of E2F results in transcription of various genes like [[cyclin E]], [[cyclin A]], [[DNA polymerase]], [[thymidine kinase]], etc. Cyclin E thus produced binds to [[Cyclin-dependent kinase 2|CDK2]], forming the cyclin E-CDK2 complex, which pushes the cell from G<sub>1</sub> to S phase (G<sub>1</sub>/S, which initiates the G<sub>2</sub>/M transition).<ref name="isbn0-12-324719-5">{{cite book | vauthors = Norbury C | veditors = Hardie DG, Hanks S | title = Protein kinase factsBook | publisher = Academic Press | location = Boston | year = 1995 | pages = [https://archive.org/details/proteinkinasefac0000unse/page/184 184] | chapter = Cdk2 protein kinase (vertebrates) | isbn = 978-0-12-324719-3 | chapter-url = https://archive.org/details/proteinkinasefac0000unse/page/184 }}</ref> [[Cyclin B]]-cdk1 complex activation causes breakdown of [[nuclear envelope]] and initiation of [[prophase]], and subsequently, its deactivation causes the cell to exit mitosis.<ref name="Robbins" /> A quantitative study of E2F transcriptional dynamics at the single-cell level by using engineered fluorescent reporter cells provided a quantitative framework for understanding the control logic of cell cycle entry, challenging the canonical textbook model. Genes that regulate the amplitude of E2F accumulation, such as Myc, determine the commitment in cell cycle and S phase entry. G1 cyclin-CDK activities are not the driver of cell cycle entry. Instead, they primarily tune the timing of E2F increase, thereby modulating the pace of cell cycle progression.<ref name="Dong, P. 2014" />