Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

Abstract

Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC (Structural Maintenance of Chromosomes) protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery responsible for DNA loop extrusion, like eukaryotic condensin or cohesin complexes, which act as chromosome organizers. Attention is now turning to how the prototype of the complex is loaded on the entry site and translocated on chromosomal DNA, explaining its overall conformational changes at atomic levels. Here, we review and highlight recent findings concerning the prokaryotic SMC complex and discuss possible mechanisms from the viewpoint of protein architecture.

Evidence for binary Smc complexes lacking kite subunits in archaea

“…The result of the HMM search was basically identical to that of the BLAST search, uncovering no additional credible homologues (Table 2). Of note, in the orders Methanococcales, Thermoplasmatales and Thermococcales, where scpB is found, this gene is remotely located from scpA in all of the member species, in contrast to the juxtaposition of scpA and scpB in most bacterial genomes, as noted previously (Kamada & Barillà , 2018). In a total of 61 out of 160 archaeal species containing both scpA and scpB, scpB is remotely located from scpA in the genome, and this is observed in three out of nine euryarchaeotal orders [ Fig.…”

“…One is the Smc-ScpAB complex, which is composed of an Smc homodimer and two non-SMC subunits, ScpA and ScpB, that form a tight binary complex (usually referred to as ScpAB). This condensin-like complex is also found in archaea (Soppa et al, 2002;Mascarenhas et al, 2002;Barillà , 2016;Kamada & Barillà , 2018). The other two are MukBEF and MksBEF, which are composed of the SMC subunit MukB (or MksB) and two non-SMC proteins called MukE and MukF (or MksE and MksF) that also form a binary complex (Niki et al, 1991;Yamanaka et al, 1996;Yamazoe et al, 1999;Petrushenko et al, 2011).…”

Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement

“…4). Cohesin is an essential regulator of most aspects of chromosome biology, including chromo some segregation, maintenance of genome stability, regulation of gene expression, chromatin structure and genome organization [19][20][21][22] . Although the exact pathomechanisms in CdLS are currently not fully understood, the direct role of cohesin as a regulator of gene expression is estimated to be of crucial importance for cohesin function.…”

Delineation of phenotypes and genotypes related to cohesin structural protein RAD21

“…S1). The cohesin complex is a major modulator of chromosome structure, is involved in regulating chromosome segregation during mitosis, DNA repair and chromatin condensation, and plays an important role in gene transcription during interphase and cellular homeostasis (Kamada and Barilla 2018;Mullenders et al 2015;Watrin et al 2016). RAD21 has been implicated in additional processes including mediation of epigenetic silencing and induction of apoptosis (Fisher et al 2017;Pati et al 2002).…”