Evidence for binary Smc complexes lacking kite subunits in archaea

Abstract

SMC complexes play a central role in chromosome organization in all domains of life. The bacterial Smc–ScpAB complex is a three-subunit complex composed of Smc, ScpA and ScpB. ScpA bridges the two ATPase domains of the Smc homodimer, while ScpB, which belongs to the kite family of proteins, interacts with ScpA. The three subunits are known to be equally important for the function of Smc–ScpAB in bacteria. From crystallographic and biochemical studies, evidence is provided that six archaeal ScpA proteins are unable to interact with the only putative ScpB found in these species. Structure-based sequence alignment reveals that these archaeal ScpAs lack the ScpB-binding segment that is commonly present in the middle of bacterial ScpA sequences, which is thus responsible for their inability to interact with ScpB. ScpA proteins lacking the ScpB-binding segment are found to prevail in archaea. Moreover, two archaeal ScpA proteins with a longer middle region also failed to bind their putative ScpB partner. Furthermore, all or most species belonging to five out of 14 euryarchaeotal orders contain Smc and ScpA but not a detectable ScpB homologue. These data support the notion that archaeal Smc-based complexes generally function as a two-subunit complex composed of only Smc and ScpA.

Structure-function relationships of SMC protein complexes for DNA loop extrusion

“…ScpB was regarded as a DNA-binding protein because it contains a WH domain, which is one of the representative DNAbinding motifs, but its DNA-binding affinity seems very low and not necessary for the function of Smc-ScpAB complexes in prokaryotes (Jeon et al, 2020;Kim et al, 2006). A DNA-binding capability of MukE has also not been reported.…”

SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path

“…Next, we turn to the problem of modeling the full-length prokaryotic SMC complex 38,39 . A previous biochemical study showed that in several archaea, such as Pyrococcus yayanosii ( Py ), a binary complex (SMC-ScpA) is more likely to form than a tripartite complex (SMC-ScpAB) due to the absence of the ScpB (KITE) binding segment in the ScpA subunit 40 . Therefore, our current study focuses on the SMC-ScpA binary complex as a minimal configuration to investigate the translocation of SMC complexes.…”

Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

“…28,29 Most archaea (with the notable exception of Crenarchaeota) possess homologs of the bacterial Smc- ScpAB subunits, namely the Smc ATPase, the Kleisin protein ScpA, and the Kite protein ScpB. 30,31 Recent in vitro experiments failed to detect a physical interaction between ScpA and ScpB from some archaea including Pyrococcus yayanosii, Thermococcus onnurineus, Methanosalsum zhilinae and Methanothrix soehngenii , despite the fact that their bacterial homologs form a stable subcomplex. 30,32,33 Genomes of certain archaeal lineages even lack scpB while they contain smc and scpA .…”

“…30,31 Recent in vitro experiments failed to detect a physical interaction between ScpA and ScpB from some archaea including Pyrococcus yayanosii, Thermococcus onnurineus, Methanosalsum zhilinae and Methanothrix soehngenii , despite the fact that their bacterial homologs form a stable subcomplex. 30,32,33 Genomes of certain archaeal lineages even lack scpB while they contain smc and scpA . 30 These findings led to the proposal that the archaeal homolog of Smc-ScpAB may function as a binary complex composed of only Smc and ScpA.…”

“…30,32,33 Genomes of certain archaeal lineages even lack scpB while they contain smc and scpA . 30 These findings led to the proposal that the archaeal homolog of Smc-ScpAB may function as a binary complex composed of only Smc and ScpA. However, this possibility has never been tested in vivo .…”