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Crystal structure of xenotropic murine leukaemia virus-related virus (XMRV) ribonuclease H
Kim, Ju ,Hee,Kang, Sunghyun,Jung, Suk-Kyeong,Yu, Keum ,Ran,Chung, Sang ,J.,Chung, Bong ,Hyun,Erikson, Raymond ,L.,Kim, Bo ,Yeon,Kim, Seung ,Jun Portland Press Ltd. 2012 Bioscience reports Vol.32 No.5
<P>RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase). The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop. Structural superposition and subsequent mutagenesis experiments suggest that the basic protrusion motif plays a role in direct binding to the major groove in RNA/DNA hybrid, as well as in establishing the co-ordination among modules in RT necessary for proper function.</P>
Khan, Imran,Lee, Kyeong-Lim,Fakruzzaman, Md.,Song, Seok-Hwan,Ihsan-ul-Haq,Mirza, Bushra,Yan, Chang ,Guo,Kong, Il-Keun Portland Press Ltd. 2016 Bioscience reports Vol.36 No.2
<P>Coagulansin-A (withanolide) is the steroidal lactone obtained from <I>Withania coagulans</I> which belong to Solanaceae family. The present study investigated the effects of coagulansin-A on bovine oocyte maturation and embryo development <I>in vitro</I>. All these oocytes were aspirated from the ovaries obtained from Korean Hanwoo cows at a local abattoir. To determine whether coagulansin-A has beneficial effects on bovine oocyte maturation <I>in vitro</I>, 355 oocytes per group (control and treated) in seven replicates were subjected with different concentrations (1, 2.5, 5, 7.5 and 10 μM) of coagulansin-A. The coagulansin-A was added in the <I>in vitro</I> maturation (IVM) media followed by <I>in vitro</I> fertilization (IVF) and then <I>in vitro</I> culture (IVC). Only treatment with 5 μM coagulansin-A remarkably (<I>P</I><0.05) improved embryos development (Day 8 blastocyst) having 27.30 and 40.01% for control and coagulansin-A treated groups respectively. Treatment with 5 μM coagulansin-A significantly induced activation of heat shock protein 70 (HSP70) (<I>P</I><0.05). Immunofluorescence analysis revealed that 5 μM coagulansin-A treatment also significantly inhibited oxidative stress and inflammation during bovine embryo development <I>in vitro</I> by decreasing 8-oxoguanosine (8-OxoG) (<I>P</I><0.05) and nuclear factor-κB (NF-κB) (<I>P</I><0.05)<I>.</I> The expressions of HSP70 and NF-κB were also conformed through real-time PCR (RT-PCR). Additionally, the terminal deoxynucleotidyl transferase dUTP nick-end labelling (TUNEL) assay confirmed that coagulansin-A treatment significantly improved the embryo quality and reduced bovine embryo DNA damage (<I>P</I><0.05). The present study provides new information regarding the mechanisms by which coagulansin-A promotes bovine embryo development <I>in vitro</I>.</P>
Sequence preference and structural heterogeneity of BZ junctions
Kim, Doyoun,Hur, Jeonghwan,Han, Ji ,Hoon,Ha, Sung ,Chul,Shin, Donghyuk,Lee, Sangho,Park, Soyoung,Sugiyama, Hiroshi,Kim, Kyeong ,Kyu Oxford University Press 2018 Nucleic acids research Vol.46 No.19
<P><B>Abstract</B></P><P>BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.</P>
Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding
Soh, Young-Min,Bü,rmann, Frank,Shin, Ho-Chul,Oda, Takashi,Jin, Kyeong ,Sik,Toseland, Christopher ,P.,Kim, Cheolhee,Lee, Hansol,Kim, Soo ,Jin,Kong, Min-Seok,Durand-Diebold, Marie-Laure Cell Press 2015 Molecular cell Vol.57 No.2
<▼1><P><B>Summary</B></P><P>SMC condensin complexes are central modulators of chromosome superstructure in all branches of life. Their SMC subunits form a long intramolecular coiled coil, which connects a constitutive “hinge” dimerization domain with an ATP-regulated “head” dimerization module. Here, we address the structural arrangement of the long coiled coils in SMC complexes. We unequivocally show that prokaryotic Smc-ScpAB, eukaryotic condensin, and possibly also cohesin form rod-like structures, with their coiled coils being closely juxtaposed and accurately anchored to the hinge. Upon ATP-induced binding of DNA to the hinge, however, Smc switches to a more open configuration. Our data suggest that a long-distance structural transition is transmitted from the Smc head domains to regulate Smc-ScpAB’s association with DNA. These findings uncover a conserved architectural theme in SMC complexes, provide a mechanistic basis for Smc’s dynamic engagement with chromosomes, and offer a molecular explanation for defects in Cornelia de Lange syndrome.</P></▼1><▼2><P><B>Highlights</B></P><P>•<P>Prokaryotic Smc-ScpAB complexes form rod-like structures</P>•<P>Binding of ATP and DNA induces a rod-to-ring transition in prokaryotic condensin</P>•<P>The condensin hinge is rigidly anchored to its coiled coil</P>•<P>The rod-like conformation is a conserved feature of SMC protein dimers</P></P></▼2><▼3><P>Soh et al. show that the rod-like conformation is a conserved architectural scheme of SMC complexes. Upon ATP-induced binding to DNA, the juxtaposed coiled coils of prokaryotic Smc-ScpAB adopt an open conformation to expose a DNA binding site at the inner surface of the hinge domain.</P></▼3>