Cell cycle

The cell cycle is the sequence of events by which a biological cell prepares for and completes division, including DNA replication and distribution of chromosomes. In Saccharomyces cerevisiae, changing bud appearance provides an accessible readout; see the Burgess, Powers and Mell account and Hartwell, Culotti and Reid's primary study cited there.

For a typical cycling diploid eukaryotic biological cell, the order is G1 phase, S phase, G2 phase, then M phase. DNA replication doubles nuclear DNA amount during S phase; mitosis distributes the copies, and cytokinesis separates the daughters. The useful distinction is between copying a library and allocating its copies: DNA replication changes how much material exists, whereas division changes which biological cell contains it.

Gene expression continues to supply RNA and proteins as the biological cell grows; it is different from duplicating the genome. In the yeast cross-species complementation experiment, restored growth requires successful repeated cell cycles, but growth alone does not locate a defect within a phase. Bud appearance in Saccharomyces cerevisiae provides another readout, while a flow cytometric DNA-content assay asks how much nuclear DNA is present and DNA pulse labeling asks whether new DNA was synthesized during an exposure.

The budding-yeast signalling network promoting sustained Cdc14 activity and completion of mitosis. Its upstream Tem1 activity is restrained during an active spindle position checkpoint.

A mechanism delaying mitotic entry when interphase centrosomes are misoriented relative to the niche in fly male germline stem cells. It couples geometry to the timing of an oriented division.

A surveillance mechanism that restrains mitotic exit when the budding-yeast spindle is mispositioned. It is distinct from kinetochore-attachment surveillance by the spindle checkpoint.

The bipartite GTPase-activating complex that inhibits Tem1 in budding yeast. Its localization and phosphorylation connect the spindle position checkpoint to mitotic exit.

A cell-division-cycle mutant identified by a defect in cycle progression. A conditional growth defect alone does not establish a stage-specific cycle function.

A regulatory coactivator of the anaphase-promoting complex. Its activity helps maintain low mitotic-cyclin abundance during late mitosis and G1, before the next cell-cycle programme.

The retinoblastoma tumour-suppressor protein, which restrains E2F-dependent proliferation when appropriately active. Regulation by cyclin-dependent kinases couples this restraint to cell-cycle signals.

A pause or block in progression through the cell cycle. It can permit repair or become durable; arrest is not itself proof that molecular damage has been repaired.

A durable cell state involving proliferative arrest and additional cellular changes. Its secretory effects can influence immune clearance and neighbouring tissue, so arrest and tissue-level benefit should be assessed separately.

A cyclin-dependent-kinase inhibitor induced in many p53-dependent arrest responses. Lower kinase activity helps restrain proliferation while stress is assessed.

A budding-yeast cyclin-dependent-kinase inhibitor. Phosphorylation-dependent recognition by an SCF ubiquitin ligase couples its destruction to S-phase entry.

Division with a preferred spindle or daughter-placement direction relative to tissue axes. An association with organ elongation requires causal tests before division orientation can be assigned the shaping role.

An SKP1–cullin–F-box ubiquitin ligase complex directing substrate-selective ubiquitination. Recognition of degradation signals couples substrate destruction to cellular state.

A replication-control protein whose regulated degradation motif is used in the original Fucci reporters.

A fluorescent ubiquitination-based cell-cycle indicator using phase-dependent stability of reporter fusions. The original Cdt1 and geminin reporters distinguish much of G1 phase from S phase/G2 phase/M phase, rather than reporting all phase boundaries independently.^[ref]

Cytostatic factor denotes activity maintaining the meiotic arrest of an unfertilized vertebrate egg. Calcium-dependent release of arrest permits the regulated destruction of mitotic cyclins and completion of meiosis.

The anaphase-promoting complex is a regulated ubiquitin ligase that uses regulatory cofactors to target selected cell cycle proteins for destruction. Degradation of mitotic cyclins helps reset kinase activity during exit, while other substrates coordinate chromosome separation.

Maturation-promoting factor is the cyclin–CDK activity that can drive meiotic maturation and mitotic events. A mitotic cyclin–CDK1 complex connects changing cyclin availability to phosphorylation-dependent cell-cycle transitions.

A regulatory system involving retinoblastoma protein and E2F-associated control of cell-cycle gene expression and entry into DNA replication.

An APC/C-associated regulatory protein controlled by the spindle checkpoint and involved in triggering destruction of anaphase substrates.

A surveillance and response system coordinating replication stress with fork protection, origin use and subsequent cell-cycle events.

A control system that changes cell-cycle progression in response to damaged DNA. Checkpoint activation is a response to damage rather than a guarantee that every lesion will be repaired.

Replication of nuclear DNA without a corresponding normal mitotic division, producing increased genome copy number. It illustrates that replication and cell division can be developmentally uncoupled.

An early embryonic division that partitions the egg's contents among blastomeres, initially with little overall growth relative to later development.

Interphase comprises G1 phase, S phase and G2 phase, including growth and DNA replication.

During G1 phase, growth and preparation precede DNA replication. The ordinary diploid nuclear state is $2n,2C$.

During S phase, nuclear DNA replication produces paired sister chromatids. DNA content rises from $2C$ to $4C$, while the chromosome count remains $2n$.

G2 phase follows completed nuclear DNA replication and precedes mitosis. The ordinary diploid state is $2n,4C$. ^[ref]

M phase includes mitosis and ordinarily cytokinesis, which can overlap in time.

Mitosis allocates copied chromosomes to daughter cell nuclei. The spindle apparatus aligns sister chromatids before separation in anaphase.

The copying has already occurred during S phase, before mitosis. Nuclear chromosome segregation and cytokinesis, the partition of the cytoplasm, are distinct processes: two daughter cell nuclei can form inside one undivided biological cell.^[ref]

The original cartoon follows a hypothetical diploid animal biological cell with $2n=4$. Its two homologous chromosome pairs are $A,a$ and $B,b$; upper- and lower-case letters identify homologues, not dominant and recessive alleles. In prophase and metaphase, each replicated chromosome contains two sister chromatids: four replicated chromosomes contain eight chromatids, rather than eight replicated chromosomes. The X shape depicts two associated copies, not the shape of every chromosome throughout the cell cycle.

This open mitosis cartoon shows nuclear envelope breakdown and reassembly. Closed mitosis in some yeasts retains the nuclear envelope while daughter chromosomes separate inside it; the cartoon is therefore not a universal cellular architecture.^[ref]

In prophase, replicated chromosomes condense and the spindle apparatus begins to organize.

In open mitosis, nuclear envelope breakdown permits spindle apparatus microtubules to reach kinetochores at centromere regions.

In metaphase, replicated chromosomes align near the spindle apparatus equator, with their two sister chromatids connected through kinetochores toward opposite poles.

In mitotic anaphase, sister chromatids separate into daughter chromosomes moving toward opposite poles.

Release of cohesin-mediated association permits the sister centromere regions to separate. Each former chromatid is then counted as an independent daughter chromosome. This changes the counting convention without making additional DNA copies. For the $2n=4$ example, the whole undivided biological cell transiently contains eight daughter chromosomes, four moving toward each pole. Movement toward poles and separation of the poles both contribute to partition in the illustrated animal setting.^[ref]

In open mitosis, telophase includes reassembly of nuclear envelopes around the separated chromosome groups and relaxation of their condensation.^[ref]

Count the same hypothetical diploid animal biological cell in three ways: chromosomes, double-stranded DNA molecules, and nuclear DNA amount. Assume one continuous double-stranded DNA molecule per unreplicated chromosome or replicated chromatid, complete S phase, and no losses or mutations. Exclude mitochondrion DNA. Here $n=2$ is the size of one haploid set, and $C$ is its unreplicated nuclear DNA amount, as defined in cell-cycle DNA content. A double-stranded DNA molecule counts as one, despite containing two strands.

The allocation can be checked copy by copy. DNA replication turns $A$ into $A_1,A_2$, $a$ into $a_1,a_2$, and similarly for $B,b$. One daughter receives $A_1,a_1,B_1,b_1$ and the other $A_2,a_2,B_2,b_2$. Each therefore inherits the same four chromosome identities and the same gene and allele content as the unreplicated parent, under the stated assumptions. Across both daughters there are $4+4=8$ DNA molecules and $2C+2C=4C$: partition conserves the material present after S phase.

The transient whole-cell count of eight does not mean that each daughter's ploidy has doubled. Each completed daughter is diploid, containing both homologues of each homologous chromosome pair. This differs from separating homologous chromosomes during meiosis I. Faithful mitosis preserves a nuclear genome through growth and renewal; equal inherited genes need not imply equal gene expression or equal cell fate. Mutations or chromosome segregation errors can break the ideal inheritance pattern.

The spindle checkpoint can delay anaphase while kinetochore attachment is incomplete. This couples progression to the state of the spindle apparatus, rather than requiring every biological cell to separate its sister chromatids after a fixed waiting time. Alignment in a picture alone is not a demonstration that this control is satisfied.^[ref]

A checkpoint component participating in kinetochore-associated signalling and mitotic checkpoint complexes.

A checkpoint regulator involved in attachment surveillance and inhibitory complexes controlling anaphase-promoting complex–Cdc20.

A checkpoint component participating in inhibition of Cdc20 as part of the mitotic checkpoint complex.

A protein assembly that inhibits productive anaphase-promoting complex–Cdc20 activity while kinetochore-associated checkpoint signalling remains active.

In 1995, Conly L. Rieder, Richard W. Cole, Alexey Khodjakov and Greenfield Sluder tested whether an unattached kinetochore supplies the inhibitory signal delaying anaphase. Living PtK1 biological cells on glass coverslips were mounted in Rose chambers at $35$–$37{}^{\circ }\mathrm{C}$. An inverted microscope with a $60\times$ objective recorded differential interference contrast microscopy video. A pulsed $532\mathrm{nm}$ laser focused through that objective destroyed selected chromosome regions. The readout was chromosome movement and anaphase onset before and after surgery.^[ref]

Destroying the last unattached kinetochore permitted anaphase without that chromosome aligning. Cutting chromosome arms served as a damage control: progression still awaited attachment of the last naturally one-pole-attached chromosome. Correlative electron microscopy checked the absence of the targeted kinetochore. Together these results located an inhibitory activity in or near the unattached kinetochore, rather than establishing a requirement for alignment itself.^[ref]

This intervention localized control; it did not identify every signaling molecule or guarantee faithful inheritance after damage. The cultured PtK1 preparation differs from the hypothetical $2n=4$ cartoon. Neither the cartoon nor this experiment establishes identical control in every species.

Cytokinesis partitions the cytoplasm. Without cytokinesis, two cell nuclei can share one biological cell. ^[ref]

Cytokinesis makes physically separate daughter biological cells by partitioning their cytoplasm and completing their cell membrane boundaries. Mitosis divides nuclear material. These processes can overlap during M phase, but completion of one does not imply completion of the other.^[ref]

For an original compartment-counting example, consider a hypothetical diploid biological cell after two daughter cell nuclei have formed. Let $n=5$ be the number of chromosomes in one haploid set, and let $C$ be that set's unreplicated nuclear DNA amount, as in cell-cycle DNA content. Assume faithful mitosis, no nuclear DNA replication during the partition, and no loss of nuclear DNA; exclude mitochondrion DNA.

The check is to follow the two existing cell nuclei: initially one boundary encloses both; finally each daughter boundary encloses one. The total remains two cell nuclei, twenty chromosomes and $2C+2C=4C$ of nuclear DNA. Thus the amount per biological cell halves because the counting boundary changes, without any new DNA replication or change of nuclear ploidy. Doubling the number of biological cells need not double their combined material.

Coordinating chromosome segregation with cytoplasm partition lets descendants inherit nuclear information inside separate working compartments. Equal nuclear DNA allocations do not require equal daughter sizes or equal allocations of every organelle. The geometry of cytokinesis connects an internal allocation to the creation of two independently bounded biological cells.

The final membrane-separation event that resolves the intercellular bridge between daughter cells, distinct from earlier furrow ingression.

A structure within the late intercellular bridge that organises events associated with final cell separation.

An actomyosin ring is a contractile assembly containing actin filaments and myosin II. In typical animal cytokinesis, it forms in the cell cortex beneath the cell membrane. Its contraction draws the boundary inward to produce a cleavage furrow; an inward groove is not yet complete separation of the daughters.^[ref]

A cleavage furrow is the inward indentation of the cell membrane during cytokinesis. It is the visible deformation; the actomyosin ring is machinery beneath that boundary.^[ref]

In 1961, Raymond Rappaport gently removed membrane and jelly from sand dollar ova with a constricted pipette. After fertilization, he used an inverted optical microscope and rack-and-pinion manipulator to press a needle-mounted glass sphere through an egg onto the chamber floor, producing a torus-shaped biological cell. Visible spindle apparatus positions and cleavage furrow progression were the readout.^[ref]

First cytokinesis opened one side into a horseshoe containing two cell nuclei. During the next division, daughters separated from its free ends; an additional cleavage furrow crossed between mitotic asters of different spindle apparatuses. Control eggs supplied the timing comparison. This region lacked intervening chromosomes or a previous nearby spindle apparatus. This supported mitotic aster-associated positioning, without identifying the signal or establishing universal necessity.^[ref]

A cell plate is an internal partition assembled during plant cytokinesis by fusion of transport vesicles. It grows outward to join the parental cell membrane, providing daughter boundaries and material for a new plant cell wall.^[ref]

G0 phase describes withdrawal from the division cycle. Some biological cells re-enter G1 phase; others remain nondividing. Metabolism and gene expression can continue. ^[ref] In the ordinary diploid case, $2C$ alone cannot distinguish G0 phase from G1 phase.

Let $n$ count chromosomes in one complete set, and let $C$ denote the nuclear DNA amount in one unreplicated haploid set of this organism. Ploidy counts sets, whereas $C$ units count material; $C$ is not a universal mass shared by all species. Here we count a paired replicated chromosome as one until its sister chromatids separate. A copied diploid genome is therefore still diploid through S phase: $2n$ persists even as $2C$ becomes $4C$.

An original bookkeeping example uses a hypothetical diploid biological cell with $n=3$. Name its three homologous chromosome pairs $A,a$, $B,b$ and $D,d$. Assume ordinary nuclear DNA replication, no chromosome loss, and one continuous double-stranded DNA molecule per unreplicated chromosome or replicated chromatid. Count nuclear material only, excluding mitochondrion DNA.

For example, $A$ becomes the paired copies $A_1,A_2$ during S phase. They remain one replicated chromosome until separation. Each completed daughter receives one $A$ copy and one $a$ copy, and similarly for the other two pairs. Across both daughters, $2\times 6=12$ double-stranded DNA molecules and $2(2C)=4C$: division allocates the copied material without another round of DNA replication.

The whole undivided anaphase biological cell transiently contains $4n$ separately counted daughter chromosomes. This counting change does not establish a four-set ploidy in a completed daughter genome: each pole receives $2n$, and each completed daughter cell nucleus is diploid. Always state whether a number refers to one cell nucleus, one pole, or the entire undivided biological cell. Compare meiotic DNA content: after meiosis I, a haploid cell nucleus can contain $2C$, so amount alone cannot determine ploidy.

Cell cycle analysis assigns evidence to stages of the cell cycle. A flow cytometric DNA-content assay measures accumulated nuclear DNA, whereas DNA pulse labeling detects synthesis over an exposure window. Agreement between these readouts is useful because an amount and a synthesis event answer different questions.

DNA pulse labeling exposes biological cells to a detectable precursor for a bounded interval. After removal, later sampling can follow the labeled material and descendants. A short pulse asks about synthesis during that interval; overnight labeling instead accumulates evidence across many hours. Detectable synthesis does not by itself prove completion of a cell cycle, and DNA repair can also incorporate precursors.

EdU labeling uses a modified nucleoside, 5-ethynyl-2'-deoxyuridine, incorporated into newly synthesized DNA, then chemically couples it to a fluorescent reporter.

A 2008 experiment injected adult mice with $100\mu \mathrm{g}$ of this label and inspected intestinal sections 96 hours later. Fixed sections on slides received $10\mu \mathrm{M}$ Alexa568-azide for 10 minutes. Imaging with a fluorescence microscope combined the reporter image with a Hoechst DNA counterstain and a transmitted-light view. Labeled cell nuclei marked descendants of biological cells synthesizing DNA during exposure, rather than identifying current S phase at collection. ^[ref]

The same study's cultured-cell controls compared overnight $10\mu \mathrm{M}$ label, no label, and label with $10\mathrm{mM}$ hydroxyurea. No-label samples had little reporter background; hydroxyurea strongly suppressed incorporation. The camera detected residual signal with a 3-second exposure versus 40 milliseconds under otherwise identical settings, demonstrating why acquisition settings matter. These controls support synthesis-dependent labeling, without proving that every labeled biological cell completes division. ^[ref]

The spindle apparatus distributes chromosomes during division of a cell nucleus.

The microtubule-organizing structure at a yeast spindle pole. Its location relative to mother and bud contributes to spatial regulation of mitotic exit.

The overlapping spindle microtubule array assembled between segregating chromosome masses during anaphase, contributing to cytokinetic organisation.

A mitotic aster is a radial array of microtubules around a pole of the spindle apparatus.