Condensin

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Figure 1. An interphase nucleus (left) and a set of mitotic chromosomes (right) from human tissue culture cells. Bar, 10 mm. Condensation1.png
Figure 1. An interphase nucleus (left) and a set of mitotic chromosomes (right) from human tissue culture cells. Bar, 10 μm.

Condensins are large protein complexes that play a central role in chromosome assembly and segregation during mitosis and meiosis (Figure 1). [1] [2] Their subunits were originally identified as major components of mitotic chromosomes assembled in Xenopus egg extracts. [3]

Contents

Subunit composition

Eukaryotic types

Figure 2. Subunit composition of condensin complexes 3condensins2(en).png
Figure 2. Subunit composition of condensin complexes

Many eukaryotic cells possess two different types of condensin complexes, known as condensin I and condensin II, each of which is composed of five subunits (Figure 2). [4] Condensins I and II share the same pair of core subunits, SMC2 and SMC4, both belonging to a large family of chromosomal ATPases, known as SMC proteins (SMC stands for Structural Maintenance of Chromosomes). [5] [6] Each of the complexes contains a distinct set of non-SMC regulatory subunits (a kleisin subunit [7] and a pair of HEAT repeat subunits). [8] Both complexes are large, having a total molecular mass of 650-700 kDa.

ComplexSubunitClassificationVertebrates D. melanogaster C. elegans S. cerevisiae S. pombe A. thaliana C. merolae T. thermophila
condensin I & IISMC2 SMC ATPase CAP-E/SMC2 SMC2MIX-1Smc2Cut14CAP-E1&-E2SMC2Scm2
condensin I & IISMC4 SMC ATPase CAP-C/SMC4 SMC4/GluonSMC-4Smc4Cut3CAP-CSMC4Smc4
condensin ICAP-D2 HEAT-IA CAP-D2 CAP-D2DPY-28Ycs4Cnd1CAB72176CAP-D2Cpd1&2
condensin ICAP-G HEAT-IB CAP-G CAP-GCAP-G1Ycg1Cnd3BAB08309CAP-GCpg1
condensin ICAP-Hkleisin CAP-H CAP-H/BarrenDPY-26Brn1Cnd2AAC25941CAP-HCph1,2,3,4&5
condensin IICAP-D3 HEAT-IIA CAP-D3 CAP-D3HCP-6--At4g15890.1CAP-D3-
condensin IICAP-G2 HEAT-IIB CAP-G2 -CAP-G2--CAP-G2/HEB1CAP-G2-
condensin IICAP-H2kleisin CAP-H2 CAP-H2KLE-2--CAP-H2/HEB2CAP-H2-
condensin IDCSMC4 variant SMC ATPase --DPY-27-----

The core subunits condensins (SMC2 and SMC4) are conserved among all eukaryotic species that have been studied to date. The non-SMC subunits unique to condensin I are also conserved among eukaryotes, but the occurrence of the non-SMC subunits unique to condensin II is highly variable among species.

Prokaryotic types

Prokaryotic species also have condensin-like complexes that play an important role in chromosome (nucleoid) organization and segregation. The prokaryotic condensins can be classified into two types: SMC-ScpAB [17] and MukBEF. [18] Many eubacterial and archaeal species have SMC-ScpAB, whereas a subgroup of eubacteria (known as Gammaproteobacteria) including Escherichia coli has MukBEF. ScpA and MukF belong to a family of proteins called "kleisins", [7] whereas ScpB and MukE have recently been classified into a new family of proteins named "kite". [19]

ComplexSubunitClassification B. subtilis Caulobacter E.coli
SMC-ScpABSMC ATPase SMC/BsSMCSMC-
SMC-ScpABScpAkleisinScpAScpA-
SMC-ScpABScpBkiteScpBScpB-
MukBEFMukB ATPase --MukB
MukBEFMukEkite--MukE
MukBEFMukFkleisin--MukF

Despite highly divergent primary structures of their corresponding subunits between SMC-ScpAB and MukBEF, it is reasonable to consider that the two complexes play similar if not identical functions in prokaryotic chromosome organization and dynamics, based on their molecular architecture and their defective cellular phenotypes. Both complexes are therefore often called prokaryotic (or bacterial) condensins. Recent studies report the occurrence of a third complex related to MukBEF (termed MksBEF) in some bacterial species. [20]

Molecular mechanisms

Molecular structures

Figure 3. Structure of an SMC dimer SMCfolding(en).png
Figure 3. Structure of an SMC dimer

SMC dimers that act as the core subunits of condensins display a highly characteristic V-shape, each arm of which is composed of anti-parallel coiled-coils (Figure 3; see SMC proteins for details). [21] [22] The length of each coiled-coil arm reaches ~50 nm, which corresponds to the length of ~150 bp of double-stranded DNA (dsDNA). In eukaryotic condensin I and II complexes, a kleisin subunit bridges the two head domains of an SMC dimer, and binds to two HEAT repeat subunits (Figure 1). [23] [24]

Early studies elucidated the structure of parts of bacterial condensins, such as MukBEF [25] [26] and SMC-ScpA. [27] [28] In eukaryotic complexes, several structures of subcomplexes and subdomains have been reported, including the hinge and arm domains of an SMC2-SMC4 dimer, [29] [30] a CAP-G(ycg1)/CAP-H(brn1) subcomplex, [31] [32] and a CAP-D2(ycs4)/CAP-H(brn1) subcomplex. [24] A recent cryo-EM study has shown that condensin undergoes large conformational changes that are coupled with ATP-binding and hydrolysis by its SMC subunits. [33] On the other hand, fast-speed atomic force microscopy has demonstrated that the arms of an SMC dimer is far more flexible than was expected. [34]

Molecular activities

Condensin I purified from Xenopus egg extracts is a DNA-stimulated ATPase and displays the ability to introduce positive superhelical tension into dsDNA in an ATP-hydrolysis-dependent manner (positive supercoiling activity). [35] [36] Similar activities have been detected in condensins from other organisms. [37] [38] The positive supercoiling activity is activated in vitro by Cdk1 phosphorylation, suggesting that it is likely one of the physiological activities directly involved in mitotic chromosome assembly. [39] It is postulated that this activity of condensin I helps fold DNA and promotes topoisomerase II-mediated resolution of sister chromatids. [40] Early single-DNA-molecule experiments also demonstrated in real time that condensin I is able to compact DNA in an ATP-hydrolysis dependent manner. [41]

Most recently, single-molecule experiments have demonstrated that budding yeast condensin I is able to translocate along dsDNA (motor activity) [42] and to "extrude" DNA loops (loop extrusion activity) [43] in an ATP hydrolysis-dependent manner. In the latter experiments, the activity of individual condensin complexes on DNA was visualized by real-time fluorescence imaging, revealing that condensin I indeed is a fast loop-extruding motor and that a single condensin I complex can extrude 1,500 bp of DNA per second in a strictly ATP-dependent manner. It has been proposed that condensin I anchors DNA between Ycg1-Brn1 subunits [31] and pulls DNA asymmetrically to form large loops. Moreover, it has been shown that condensin complexes can traverse each other, forming dynamic loop structures and changing their sizes. [44]

It is unknown how condensins might act on nucleosomal DNA. Recent development of a reconstitution system has identified the histone chaperone FACT as an essential component of condensin I-mediated chromosome assembly in vitro, providing an important clue to this problem. [45] It has also been shown that condensins can assemble chromosome-like structures in cell-free extracts even under the condition where nucleosome assembly is largely suppressed. [46] This observation indicates that condensins can work at least in part on non-nucleosomal DNA in a physiological setting.

How similar and how different are the molecular activities of condensin I and condensin II? Both share two SMC subunits, but each has three unique non-SMC subunits (Figure 2). A fine-tuned balance between the actions of these non-SMC subunits could determine the differences in the rate of loop extrusion [47] and the activity of mitotic chromosome assembly [48] [49] [50] [51] of the two complexes. By introducing different mutations, it is possible to convert condensin I into a complex with condensin II-like activities and vice versa. [51]

Mathematical modeling

Several attempts on mathematical modeling and computer simulation of mitotic chromosome assembly, based on molecular activities of condensins, have been reported. Representative ones include modeling based on loop extrusion, [52] stochastic pairwise contacts [53] and a combination of looping and inter-condensin attractions. [54]

Functions in chromosome assembly and segregation

Mitosis

Figure 4. Chromosome dynamics during mitosis in eukaryotes Resolution9E'.png
Figure 4. Chromosome dynamics during mitosis in eukaryotes
Figure 5. Distribution of condensin I (green) and condensin II (red) in human metaphase chromosomes. Bar, 1 mm. CondensinI&II.png
Figure 5. Distribution of condensin I (green) and condensin II (red) in human metaphase chromosomes. Bar, 1 μm.

In human tissue culture cells, the two condensin complexes are regulated differently during the mitotic cell cycle (Figure 4). [55] [56] Condensin II is present within the cell nucleus during interphase and participates in an early stage of chromosome condensation within the prophase nucleus. On the other hand, condensin I is present in the cytoplasm during interphase, and gains access to chromosomes only after the nuclear envelope breaks down (NEBD) at the end of prophase. During prometaphase and metaphase, condensin I and condensin II cooperate to assemble rod-shaped chromosomes, in which two sister chromatids are fully resolved. Such differential dynamics of the two complexes is observed in Xenopus egg extracts, [57] mouse oocytes, [58] and neural stem cells, [59] indicating that it is part of a fundamental regulatory mechanism conserved among different organisms and cell types. It is most likely that this mechanism ensures the ordered action of the two complexes, namely, condensin II first and condensin I later. [60]

On metaphase chromosomes, condensins I and II are both enriched in the central axis in a non-overlapping fashion (Figure 5). Depletion experiments in vivo [4] [59] [61] and immunodepletion experiments in Xenopus egg extracts [57] demonstrate that the two complexes have distinct functions in assembling metaphase chromosomes. Cells deficient in condensin functions are not arrested at a specific stage of cell cycle, displaying chromosome segregation defects (i.e., anaphase bridges) and progressing through abnormal cytokinesis. [62] [63]

The relative contribution of condensins I and II to mitosis varies among different eukaryotic species. For instance, each of condensins I and II plays an essential role in embryonic development in mice. [59] They have both overlapping and non-overlapping functions during the mitotic cell cycle. On the other hand, condensin II is non-essential for mitosis in the primitive alga C. merolae [14] and the land plant A. thaliana . [64] Curiously, condensin II plays a dominant role over condensin I in the C. elegans early embryos. [11] This peculiarity could be due to the fact that C. elegans has a specialized chromosome structure known as holocentric chromosomes. Fungi, such as S. cerevisiae [13] and S. pombe [12] have no condensin II from the first. These differences among eukaryotic species provide important implications in the evolution of chromosome architecture (see the section of "Evolutionary implications" below).

species M. musculus D. melanogaster C. elegans S. cerevisiae S. pombe A. thaliana C. merolae
genome size~2,500 Mb140 Mb100 Mb12 Mb14 Mb125 Mb16 Mb
condensin Iessentialessentialminoressentialessentialessentialessential
condensin IIessentialnon-essentialessential--non-essentialnon-essential

It has recently become possible that cell cycle-dependent structural changes of chromosomes are monitored by a genomics-based method known as Hi-C (High-throughput chromosome conformation capture). [65] The impact of condensin deficiency on chromosome conformation has been addressed in budding yeast, [66] [67] fission yeast, [68] [69] and the chicken DT40 cells. [70] The outcome of these studies strongly supports the notion that condensins play crucial roles in mitotic chromosome assembly and that condensin I and II have distinct functions in this process. Moreover, quantitative imaging analyses allow researchers to count the number of condensin complexes present on human metaphase chromosomes. [71]

Meiosis

Condensins also play important roles in chromosome assembly and segregation in meiosis. Genetic studies have been reported in S. cerevisiae, [72] D. melanogaster, [73] [74] and C. elegans . [75] In mice, requirements for condensin subunits in meiosis have been addressed by antibody-mediated blocking experiments [58] and conditional gene knockout analyses. [76] In mammalian meiosis I, the functional contribution of condensin II appears bigger than that of condensin I. As has been shown in mitosis, [59] however, the two condensin complexes have both overlapping and non-overlapping functions, too, in meiosis. Unlike cohesin, no meiosis-specific subunits of condensins have been identified so far.

Chromosomal functions outside of mitosis or meiosis

Recent studies have shown that condensins participate in a wide variety of chromosome functions outside of mitosis or meiosis. [60]

Posttranslational modifications and cell cycle regulation

Condensin subunits are subject to various post-translational modifications in a cell cycle-dependent manner. [89] Among these, phosphorylation in mitosis is the best studied. [90]

Phosphorylation by Cdk1 is essential for condensin I's supercoiling activity [39] [38] and chromosome assembly activity [45] in vitro. However, the target subunits and sites (and number) of phosphorylation essential for activation are not known. S/TP sequences, the primary targets of Cdk1, tend to be enriched in intrinsically disordered regions (IDRs) located at the ends of condensin subunits, [90] but their distribution and contribution to the regulation of condensin vary widely among different species. For example, in fission yeast, phosphorylation of the N-terminus of the SMC4 subunit regulates nuclear translocation of condensin during mitosis. [12] In budding yeast, condensin localizes to the nucleus throughout the cell cycle, and phosphorylation of the N-terminus of the SMC4 subunit is involved in the regulation of chromosome association dynamics of condensin. [91] [92] In vertebrates, it has been proposed that N-terminal phosphorylation of the CAP-H subunit promotes mitosis-specific loading of condensin I. [93] In addition to Cdk1, positive regulation by Aurora B [94] [95] and Polo [38] and negative regulation by CK2 (casein kinase 2) [96] have been reported.

Several mitotic kinases, Cdk1, [97] [98] [50] [51] polo [99] and Mps1 [100] are involved in condensin II regulation. It has been shown that the C-terminal tail of the CAP-D3 subunit is a major target for Cdk1 phosphorylation in the human condensin II complex. [51] Moreover, CAP-D3 has been identified as a substrate of the protein phosphatase PP2A-B55. [101]

It has been reported that the CAP-H2 subunit of condensin II is degraded in Drosophila through the action of the SCFSlimb ubiquitin ligase. [102]

Relevance to diseases

It was demonstrated that MCPH1, one of the proteins responsible for human primary microcephaly, has the ability to negatively regulate condensin II. [103] In mcph1 patient cells, condensin II (but not condensin I) is hyperactivated, leading to premature chromosome condensation in G2 phase (i.e., before entering mitosis). [104] There is no evidence, however, that misregulation of condensin II is directly related to the etiology of mcph1 microcephaly. More recently, it has been reported that hypomorphic mutations in condensin I or II subunits cause microcephaly in humans. [105] In mice, hypomorphic mutations in condensin II subunits cause specific defects in T cell development, [106] leading to T cell lymphoma. [107] It is interesting to note that cell types with specialized cell division modes, such as neural stem cells and T cells, are particularly susceptible to mutations in condensin subunits.

Evolutionary implications

Prokaryotes have primitive types of condensins, [17] [18] indicating that the evolutionary origin of condensins precede that of histones. The fact that condensins I and II are widely conserved among extant eukaryotic species strongly implicates that the last eukaryotic common ancestor (LECA) had both complexes. [60] It is therefore reasonable to speculate that some species such as fungi have lost condensin II during evolution.

Then why do many eukaryotes have two different condensin complexes? As discussed above, the relative contribution of condensins I and II to mitosis varies among different organisms. They play equally important roles in mammalian mitosis, whereas condensin I has a predominant role over condensin II in many other species. In those species, condensin II might have been adapted for various non-essential functions other than mitosis. [64] [82] Although there is no apparent relationship between the occurrence of condensin II and the size of genomes, it seems that the functional contribution of condensin II becomes big as the genome size increases. [14] [59] A recent, comprehensive Hi-C study argues from an evolutionary point of view that condensin II acts as a determinant that converts post-mitotic Rabl configurations into interphase chromosome territories. [108] The relative contribution of the two condensin complexes to mitotic chromosome architecture also change during development, making an impact on the morphology of mitotic chromosomes. [57] Thus, the balancing act of condensins I and II is apparently fine-tuned in both evolution and development.

Relatives

Eukaryotic cells have two additional classes of SMC protein complexes. Cohesin contains SMC1 and SMC3 and is involved in sister chromatid cohesion. The SMC5/6 complex contains SMC5 and SMC6 and is implicated in recombinational repair.

See also

Related Research Articles

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In cell biology, the spindle apparatus is the cytoskeletal structure of eukaryotic cells that forms during cell division to separate sister chromatids between daughter cells. It is referred to as the mitotic spindle during mitosis, a process that produces genetically identical daughter cells, or the meiotic spindle during meiosis, a process that produces gametes with half the number of chromosomes of the parent cell.

<span class="mw-page-title-main">Spindle checkpoint</span> Cell cycle checkpoint

The spindle checkpoint, also known as the metaphase-to-anaphase transition, the spindle assembly checkpoint (SAC), the metaphase checkpoint, or the mitotic checkpoint, is a cell cycle checkpoint during metaphase of mitosis or meiosis that prevents the separation of the duplicated chromosomes (anaphase) until each chromosome is properly attached to the spindle. To achieve proper segregation, the two kinetochores on the sister chromatids must be attached to opposite spindle poles. Only this pattern of attachment will ensure that each daughter cell receives one copy of the chromosome. The defining biochemical feature of this checkpoint is the stimulation of the anaphase-promoting complex by M-phase cyclin-CDK complexes, which in turn causes the proteolytic destruction of cyclins and proteins that hold the sister chromatids together.

SMC complexes represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics. SMC stands for Structural Maintenance of Chromosomes.

<span class="mw-page-title-main">Cohesin</span> Protein complex that regulates the separation of sister chromatids during cell division

Cohesin is a protein complex that mediates sister chromatid cohesion, homologous recombination, and DNA looping. Cohesin is formed of SMC3, SMC1, SCC1 and SCC3. Cohesin holds sister chromatids together after DNA replication until anaphase when removal of cohesin leads to separation of sister chromatids. The complex forms a ring-like structure and it is believed that sister chromatids are held together by entrapment inside the cohesin ring. Cohesin is a member of the SMC family of protein complexes which includes Condensin, MukBEF and SMC-ScpAB.

<span class="mw-page-title-main">Aurora kinase B</span> Protein

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<span class="mw-page-title-main">WAPAL</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">SMC4</span> Protein-coding gene in the species Homo sapiens

Structural maintenance of chromosomes protein 4 (SMC-4) also known as chromosome-associated polypeptide C (CAP-C) or XCAP-C homolog is a protein that in humans is encoded by the SMC4 gene. SMC-4 is a core subunit of condensin I and II, large protein complexes involved in high order chromosome organization, including condensation and segregation. SMC-4 protein is commonly associated with the SMC-2 protein, another protein complex within the SMC protein family. SMC-4 dimerizes with SMC-2, creating the flexible and dynamic structure of the condensin holocomplex. An over-expression of the SMC-4 protein is shown to impact carcinogenesis.

<span class="mw-page-title-main">SMC6</span> Protein-coding gene in the species Homo sapiens

Structural maintenance of chromosomes protein 6 is a protein that in humans is encoded by the SMC6 gene.

<span class="mw-page-title-main">NCAPD2</span> Protein-coding gene in the species Homo sapiens

Condensin complex subunit 1 also known as chromosome-associated protein D2 (CAP-D2) or non-SMC condensin I complex subunit D2 (NCAPD2) or XCAP-D2 homolog is a protein that in humans is encoded by the NCAPD2 gene. CAP-D2 is a subunit of condensin I, a large protein complex involved in chromosome condensation.

<span class="mw-page-title-main">SMC5</span> Protein-coding gene in the species Homo sapiens

Structural maintenance of chromosomes protein 5 is a protein encoded by the SMC5 gene in human.

<span class="mw-page-title-main">NCAPD3</span> Protein-coding gene in the species Homo sapiens

Condensin-2 complex subunit D3 (CAP-D3) also known as non-SMC condensin II complex subunit D3 (NCAPD3) is a protein that, in humans, is encoded by the NCAPD3 gene. CAP-D3 is a subunit of condensin II, a large protein complex involved in chromosome condensation.

<span class="mw-page-title-main">NCAPH</span> Protein-coding gene in the species Homo sapiens

Condensin complex subunit 2 also known as chromosome-associated protein H (CAP-H) or non-SMC condensin I complex subunit H (NCAPH) is a protein that in humans is encoded by the NCAPH gene. CAP-H is a subunit of condensin I, a large protein complex involved in chromosome condensation. Abnormal expression of NCAPH may be linked to various types of carcinogenesis as a prognostic indicator.

<span class="mw-page-title-main">NCAPG</span> Protein-coding gene in the species Homo sapiens

Condensin complex subunit 3 also known as condensin subunit CAP-G (CAP-G) or non-SMC condensin I complex subunit G (NCAPG) is a protein that in humans is encoded by the NCAPG gene. CAP-G is a subunit of condensin I, a large protein complex involved in chromosome condensation.

<span class="mw-page-title-main">NCAPG2</span> Protein-coding gene in the species Homo sapiens

Condensin-2 complex subunit G2 (CAP-G2) also known as chromosome-associated protein G2 (CAP-G2) or leucine zipper protein 5 (LUZP5) is a protein that in humans is encoded by the NCAPG2 gene. CAP-G2 is a subunit of condensin II, a large protein complex involved in chromosome condensation. It interacts with PLK1 through its C-terminal region during mitosis

<span class="mw-page-title-main">SMC2</span> Protein-coding gene in the species Homo sapiens

Structural maintenance of chromosomes protein 2 (SMC-2), also known as chromosome-associated protein E (CAP-E), is a protein that in humans is encoded by the SMC2 gene. SMC2 is part of the SMC protein family and is a core subunit of condensin I and II, large protein complexes involved in chromosome condensation, overall organization. Several studies have demonstrated the necessity of SMC2 for cell division and proliferation.

<span class="mw-page-title-main">NCAPH2</span> Protein-coding gene in the species Homo sapiens

Condensin-2 complex subunit H2, also known as chromosome-associated protein H2 (CAP-H2) or non-SMC condensin II complex subunit H2 (NCAPH2), is a protein that in humans is encoded by the NCAPH2 gene. CAP-H2 is a subunit of condensin II, a large protein complex involved in chromosome condensation.

<span class="mw-page-title-main">SMC1B</span> Protein-coding gene in the species Homo sapiens

Structural maintenance of chromosomes protein 1B (SMC-1B) is a protein that in humans is encoded by the SMC1B gene. SMC proteins engage in chromosome organization and can be broken into 3 groups based on function which are cohesins, condensins, and DNA repair. SMC-1B belongs to a family of proteins required for chromatid cohesion and DNA recombination during meiosis and mitosis. SMC1B protein appears to participate with other cohesins REC8, STAG3 and SMC3 in sister-chromatid cohesion throughout the whole meiotic process in human oocytes.

Xenopus egg extract is a lysate that is prepared by crushing the eggs of the African clawed frog Xenopus laevis. It offers a powerful cell-free system for studying various cell biological processes, including cell cycle progression, nuclear transport, DNA replication and chromosome segregation. It is also called Xenopus egg cell-free system or Xenopus egg cell-free extract.

In biology, the chromosome scaffold is the backbone that supports the structure of the chromosomes. It is composed of a group of non-histone proteins that are essential in the structure and maintenance of eukaryotic chromosomes throughout the cell cycle. These scaffold proteins are responsible for the condensation of chromatin during mitosis.

References

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