Biology subjects

Lee, B.-G.

Publications and source records attributed to Lee, B.-G..

7 recordsLinked to original sources

bioRxiv2024

Native Korean wild mice (Mus musculus): molecular phylogeny and morphometrics

Taxonomic status of house mice in the Korean Peninsula remains poorly understood. Here, we analyze genetic and morphological characteristics of mice from Korea and evaluate their phylogenetic relationships to the well-known primary subspecies. Using a comprehensive set of publicly available genetic data (mtDNA cytb gene), Korean mice including our specimens from islands, mountains, and agricultural fields were identified to Mus mus musculus. External morphology, such as tail ratios of our specimens, resembled previously assigned subspecies (e.g., M. m. molossinus, M. m. utsuryonis, and M. m. yamashinai), suggesting a single subspecific group within M. m. musculus. Korean mice displayed a distinctive landmark configuration around the snout, with a relatively short and slender premaxillary tooth-patch width (PMXW) and a larger maxillary tooth-row length (MXTL) compared to laboratory strains derived from M. m. domesticus. Our investigation provides insights into the phylogenetic relationships and taxonomic status of Korean mice relative to the primary lineages of M. musculus subspecies. Understanding the evolutionary history of Korean M. m. musculus sheds new light on how their spatiotemporal dynamics led to diversification, with the Korean Peninsula serving as an ecological bridge between East Eurasia and neighboring regions.

zoology↗

bioRxiv2023

What Alphafold tells us about cohesin's retention and release from chromosomes

Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1s association with two large hook shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latters replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1s N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the twenty years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1s NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapls C-terminal domain (CTD). AF also reveals how Scc1s dissociation from Smc3 arises from a distortion of Smc3s CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.

biochemistry↗

bioRxiv2021

Clamping of DNA shuts the condensin neck gate

Condensin is a Structural Maintenance of Chromosomes (SMC) complex needed for the compaction of DNA into chromatids during mitosis. Lengthwise DNA compaction by condensin is facilitated by ATPase-driven loop extrusion, a process that is believed to be the fundamental activity of most, if not all SMC complexes. In order to obtain molecular insights, we obtained cryo-EM structures of yeast condensin in the presence of a slowly-hydrolysable ATP analogue and linear, as well as circular DNAs. The DNAs were shown to be "clamped" between the engaged heterodimeric SMC ATPase heads and the Ycs4 subunit, in a manner similar to previously reported DNA-bound SMC complex structures. Ycgl, the other non-SMC subunit was only flexibly bound to the complex, while also binding DNA tightly, and often remaining at a distance from the head module. In the clamped state, the DNA is encircled, or topologically entrapped, by the kleisin Brnl and the two engaged head domains of Smc2 and Smc4, and this tripartite ring is closed at all interfaces, including at the neck of Smc2. We show that the neck gate opens upon head engagement in the absence of DNA, but it remains shut when DNA is present. Our work demonstrates that condensin and other SMC complexes go through similar conformations of the head modules during their ATPase cycle. In contrast, the behaviour of the Ycgl subunit in the condensin complex might indicate differences in the implementation of the extrusion reactions and our findings will constrain further mechanistic models of loop extrusion by SMC complexes. SIGNIFICANCE STATEMENTDNA needs to be compacted dramatically to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolysed. The DNA is clamped within a compartment that has been reported previously in other SMC complexes, including Rad50, cohesin and MukBEF. With the caveat of important differences that we also uncovered, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolysing ATP and translocating DNA.

molecular biology↗

bioRxiv2021

Opening the side exit pores of ClpP by lowering the pH of proteolytic chamber coupled with substrate hydrolysis

The ClpP serine peptidase is a tetradecameric degradation machine involved in many physiological processes. It becomes a competent ATP-dependent protease with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause dysregulation and activation of ClpP without ATPases, and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed the structural details, conformational changes, and activation mechanism. Although product release by the side exit pores has been proposed, the detailed driving force for product release remains elusive. Here, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures revealed various conformational states at different pH conditions. To understand the conformational change for product release, we investigated the relationship between substrate hydrolysis and the pH lowering process. Our data, together with previous findings, provide insight into the molecular mechanism of product release by ClpP self-compartmentalizing protease.

biochemistry↗

bioRxiv2020

Scc2 and Scc3 promote distinct modes of topological association between cohesin and DNA

In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are "clamped" in a sub-compartment created by Scc2s association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.

biochemistry↗

bioRxiv2018

A folded conformation of MukBEF and Cohesin

Structural maintenance of chromosomes (SMC)-kleisin complexes organize chromosomal DNAs in all domains of life, where they have key roles in chromosome segregation, DNA repair and regulation of gene expression. They function through topological entrapment and active translocation of DNA, but the underlying conformational changes are largely unclear. Using structural biology, mass spectrometry and cross-linking, we investigated the architecture of two evolutionarily distant SMC-kleisin complexes: proteobacterial MukBEF and eukaryotic cohesin. We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation. Bending at the elbow brings into proximity the hinge dimerization domain and the head/kleisin module, situated at opposite ends of the arms. Our findings favor SMC activity models that include a large conformational change in the arms, such as a relative movement between DNA contact sites during DNA loading and translocation.

molecular biology↗

bioRxiv2017

Multiple interactions between Scc1 and Scc2 activate cohesin’s DNA dependent ATPase and replace Pds5 during loading

In addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesins ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesins initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.

cell biology↗