Condensins are large protein complexes that play a central role in chromosome condensation and segregation during mitosis and meiosis (Figure 1). Their subunits were originally identified as major components of mitotic chromosomes assembled in Xenopus egg extracts.
Subunit composition and phylogeny
Eukaryotic types
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). 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). Each of the complexes contains a distinct set of non-SMC regulatory subunits (a kleisin subunit and a pair of HEAT repeat subunits). Both complexes are large, having a total molecular mass of 650-700 kDa.
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.
For instance, the fruit fly Drosophila melanogaster does not have the gene for the CAP-G2 subunit of condensin II. Other insect species often lack the genes for the CAP-D3 and/or CAP-H subunits, too, indicating that the non-SMC subunits unique to condensin II have been under high selection pressure during insect evolution. The nematode Caenorhabditis elegans possesses both condensins I and II. This species is, however, unique in the sense that it has a third complex (closely related to condensin I) that participates in chromosome-wide gene regulation, i.e., dosage compensation. In this complex, known as condensin IDC, the authentic SMC4 subunit is replaced with its variant, DPY-27 (Figure 2). Furthermore, in this organism, condensin I appears to play a role in interphase chromosome organization that is functionally analogous to that of cohesin in vertebrates. Some species, like fungi (e.g., the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe), lack all regulatory subunits unique to condensin II. On the other hand, the unicellular, primitive red alga Cyanidioschyzon merolae, whose genome size is comparable to those of the yeast, has both condensins I and II. Thus, there is no apparent relationship between the occurrence of condensin II and the size of eukaryotic genomes. Arabidopsis thaliana possesses two SMC2 paralogs, CAP-E1 and CAP-E2. While mutations in either gene alone do not significantly impair development, the double mutant is embryonic lethal. The ciliate Tetrahymena thermophila has condensin I only. Nevertheless, there are multiple paralogs for two of its regulatory subunits (CAP-D2 and CAP-H), and some of them specifically localize to either the macronucleus (responsible for gene expression) or the micronucleus (responsible for reproduction). Thus, this species has multiple condensin I complexes that have different regulatory subunits and display distinct nuclear localization. This is a very unique property that is not found in other species.
The following table summarizes the names of SMC complex subunits in representative eukaryotic model organisms.
Complex Subunit Vertebrate D. melanogaster C. elegans S. cerevisiae S. pombe A. thalianaT. thermophila condensin I & II SMC2 ATPase CAP-E/ SMC2 Smc2 MIX-1 Smc2 Cut14 CAP-E1 & -E2 Smc2 SMC4 ATPase CAP-C/ SMC4 Smc4/ Gluon SMC-4 Smc4 Cut3 CAP-C Smc4 condensin I kleisin CAP-H CAP-H/ Barren DPY-26 Brn1 Cnd2 CAP-H Cph1,2,3,4 & 5 HEAT-IA CAP-D2 CAP-D2 DPY-28 Ycs4 Cnd1 CAP-D2 Cpd1 & 2 HEAT-IB CAP-G CAP-G CAPG-1 Ycg1 Cnd3 CAP-G Cpg1 condensin II kleisin CAP-H2 CAP-H2 KLE-2 - - CAP-H2/ HEB2 - HEAT-IIA CAP-D3 CAP-D3 HCP-6 - - CAP-D3 - HEAT-IIB CAP-G2 - CAP-G2 - - CAP-G2/ HEB1 - condensin I DC SMC4 variant - - DPY-27 - - - -
Condensin is one of the three major SMC protein complexes found in eukaryotes. The other two are: cohesin, which is involved in sister chromatid cohesion and interphase chromosome organization; and the SMC5/6 complex, which functions in DNA repair and chromosome segregation.
Prokaryotic types
SMC-ScpAB: Condensin-like protein complexes also exist in prokaryotes, where they contribute to the organization and segregation of chromosomes (nucleoids). The best-studied example is the SMC–ScpAB complex (Figure 3, left), which is considered the evolutionary ancestor of the eukaryotic condensin complexes. Compared to its eukaryotic counterparts, SMC–ScpAB has a simpler architecture. For instance, while eukaryotic condensins contain an SMC heterodimer, prokaryotic SMC proteins form a homodimer. Among the regulatory subunits, ScpA belongs to the kleisin family, suggesting that the basic SMC–kleisin trimeric structure is conserved across prokaryotes and eukaryotes. By contrast, ScpB is classified as a member of the kite (Kleisin Interacting Tandem Elements) family, which is structurally distinct from the HEAT-repeat subunits found in eukaryotic condensins.
MukBEF: While most bacteria and archaea possess the SMC–ScpAB complex, a subset of gammaproteobacteria, including Escherichia coli, instead have a distinct SMC complex known as MukBEF. MukBEF forms a "dimer-of-dimers" through dimerization mediated by the kleisin subunit MukF (Figure 3, center). The third subunit, MukE, belongs to the kite family. Although sequence similarity between the subunits of MukBEF and those of SMC–ScpAB is low, their overall molecular architecture observed by electron microscopy and phenotypic defects in mutants suggest that the two are functional homologs. As such, they are often collectively referred to as prokaryotic condensins.
MksBEF/Wadjet: More recently, a third type of bacterial SMC complex (called MksBEF), structurally similar to MukBEF, has been reported. Pseudomonas aeruginosa have both SMC–ScpAB and MksBEF, which contribute to chromosome organization and segregation through distinct mechanisms. In contrast, in Corynebacterium glutamicum, SMC–ScpAB is responsible for chromosome architecture and segregation, whereas MksBEF, together with the nuclease subunit MksG, is specialized for plasmid defense. The MksBEFG complex is orthologous to the JetABCD complex in Bacillus cereus and the EptABCD complex in Mycobacterium smegmatis. These complexes, which serve a common function in plasmid defense, are collectively referred to as the Wadjet complexes (Figure 3, right).
The following table summarizes the names of SMC complex subunits in representative prokaryotic model organisms.
Complex Subunit B. subtilis C. crescentus E. coli P. aeruginosaC. glutamicum B. cereus SMC-ScpAB SMC ATPase SMC SMC - SMC SMC SMC kleisin ScpA ScpA - ScpA ScpA ScpA kite ScpB ScpB - ScpB ScpB ScpB MukBEF SMC ATPase - - MukB - - - kleisin - - MukF - - - kite - - MukE - - - MksBEF & Wadjet SMC ATPase - - - MksB MksB JetC kleisin - - - MksF MksF JetA kite - - - MksE MksE JetB nuclease - - - - MksG JetD
Molecular structures
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 4; see SMC proteins for details). The length of each coiled-coil arm reaches ~50 nm, which corresponds to the length of ~150 bp of double-stranded DNA (dsDNA). 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.
The formation of a condensin or condensin-like complex involves the association of an SMC dimer with non-SMC subunits (Figure 4). First, the N-terminal domain of the kleisin subunit binds to the neck region (a segment of the coiled coil near the head domain) of one SMC protein, while its C-terminal domain binds to the cap region (part of the head domain) of the other SMC subunit. These interactions result in the formation of a asymmetric ring-like architecture. Finally, two HEAT-repeat subunits (or two kite subunits depending on the complex) associate with the central region of the kleisin, completing the assembly of the holo-complex. MukBEF and Wadjet form higher-order assemblies through dimerization mediated by their kleisin subunits, a configuration often referred to as a "dimer-of-dimers" (Figure 3).
Structural information on individual complexes or their subcomplexes has been reported as follows: Prokaryotic SMC-ScpAB: Early X-ray crystallography studies revealed partial structures of ScpAB as well as the interaction interface between SMC and kleisin subunits. Prokaryotic MukBEF: In addition to early X-ray crystallography studies, more recent analyses using cryo-EM have visualized the steps of dissociation from DNA and of loading onto DNA. Prokaryotic Wadjet: The structure of the Wadjet complex, involved in plasmid defense, has been resolved by cryo-EM. Eukaryotic condensins: Several structures of subcomplexes and subdomains have been reported, including the hinge and arm domains of an SMC2-SMC4 dimer, a CAP-G(ycg1)/CAP-H(brn1) subcomplex, and a CAP-D2(ycs4)/CAP-H(brn1) subcomplex. More recently, a series of cryo-EM studies has shown that condensin undergoes large conformational changes that are coupled with ATP-binding and hydrolysis by its SMC subunits. A comparative analysis of human condensin I and condensin II has also been reported.
Molecular activities DNA compaction Among the various molecular activities attributed to condensins, perhaps the most intuitive is its ability to compact DNA by folding it, thereby reducing its effective length. Indeed, an early single-molecule experiment using magnetic tweezers have shown that condensin I purified from Xenopus egg metaphase extracts actively shortens the length of DNA in an ATP hydrolysis-dependent manner, and this process can be observed in real time. More recently, a comparable yet less dynamic compaction process mediated by budding yeast condensin was observed in the same experimental setup Furthermore, optical tweezers–based assays combining single-molecule DNA manipulation with Xenopus egg extracts have revealed that, among the multiple DNA-compacting activities present in mitotic extracts, condensins make the dominant contribution.
DNA supercoiling Early studies using condensin I purified from Xenopus egg extracts demonstrated that the complex introduces positive supercoils into double-stranded DNA in an ATP hydrolysis–dependent manner, in the presence of type I topoisomerases. Although this activity is often described as positive DNA supercoiling, it differs fundamentally from that of topoisomerases, since condensin I lacks DNA cleavage and re-ligation activity. Similar activities have also been observed with condensin complexes from nematodes and budding yeast. Furthermore, a modified assay combined with a type II topoisomerase has shown that Xenopus condensin I can generate "two oriented" supercoils in an ATP hydrolysis-dependent manner. These activities are stimulated by Cdk1-mediated phosphorylation in vitro, suggesting that they may constitute an essential mechanism underlying mitotic chromosome condensation. Through this supercoiling activity, condensin may not only facilitate chromatin compaction but also promote the resolution and separation of sister chromatids by aiding the action of topoisomerase II.
DNA loop extrusion