STRUCTURAL STUDIES OF ENDOPLASMIC RETICULUM-MITOCHONDRIA ENCOUNTER STRUCTURE (ERMES) COMPLEX

Department of Biological SciencesThe endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report three crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mdm12, Mmm1, and the Mdm12-Mmm1 complex at 3.1 ??, 2.8 ??, and 3.8 ?? resolution, respectively. The Mdm12 forms a dimeric SMP structure through domain swapping of the ??1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12-Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-??-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12-Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro.ope

Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.

Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae. Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-angstrom extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Delta 19-33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways

The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination.

EXD2 (3'-5' exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3'-5' exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central α5-α7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.Cell Logistics Research Center [2016R1A5A1007318]; Basic Research Program, National Research Foundation of Korea [NRF-2019R1A2C3008463]; Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea [HI18C1395]; Institute for Basic Science [IBS-R022-D1]. Funding for open access charge: Cell Logistics Research Center, National Research Foundation of Korea [2016R1A5A1007318]

Organic–Inorganic Hybrid Ternary Bulk Heterojunction of Nanostructured Perovskite–Low Bandgap Polymer–PCBM for Improved Efficiency of Organic Solar Cells

A new organic–inorganic ternary bulk heterojunction (TBHJ) hybrid configuration comprised of nanostructured (CH₃)₃NHPbI₃ (MAPbI₃) perovskite–low bandgap PCPDTBT–PCBM was investigated. Well-organized TBHJ films were readily prepared by sequential spin-casting of sparsely covered MAPbI₃ nano dots and PCPDTBT–PCBM bulk heterojunction (BHJ) composites on ITO/PEDOT:PSS substrates. The TBHJ hybrid device configuration comprising diiooctane (DIO) treated MAPbI₃ perovskite nano dots and a PCPDTBT–PCBM BHJ composite processed with DIO additive exhibited excellent performances. The DIO additive played a key role in developing perovskite structures of MAPbI₃ nano dots and induced the (110) directional crystallinity growth of longitudinal constructive morphologies such as nano rods. The improved photocurrent and fill factor compared to those of conventional BHJ devices led to an increase in efficiency of ∼28%. This improved photovoltaic performance originated from the higher quantum efficiencies contributed by the charge transfer from nanostructured MAPbI₃ perovskite to PCBM. These TBHJs composed of nanostructured MAPbI₃ perovskite, PCPDTBT, and PCBM also facilitated the exciton dissociation in the multi-BHJ system between MAPbI₃ perovskite, PCPDTBT, and PCBM

MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering

The standard analysis pipeline for single-cell RNA-seq data consists of sequential steps initiated by clustering the cells. An innate limitation of this pipeline is that an imperfect clustering result can irreversibly affect the succeeding steps. For example, there can be cell types not well distinguished by clustering because they largely share the global structure, such as the anterior primitive streak and mid primitive streak cells. If one searches differentially expressed genes (DEGs) solely based on clustering, marker genes for distinguishing these types will be missed. Moreover, clustering depends on many parameters and can often be subjective to manual decisions. To overcome these limitations, we propose MarcoPolo, a method that identifies informative DEGs independently of prior clustering. MarcoPolo sorts out genes by evaluating if the distributions are bimodal, if similar expression patterns are observed in other genes, and if the expressing cells are proximal in a low-dimensional space. Using real datasets with FACS-purified cell labels, we demonstrate that MarcoPolo recovers marker genes better than competing methods. Notably, MarcoPolo finds key genes that can distinguish cell types that are not distinguishable by the standard clustering. MarcoPolo is built in a convenient software package that provides analysis results in an HTML file.Y

Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex

The endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex is composed of Mdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. Here, we report the crystal structure of S. cerevisiae Mdm12. The Mdm12 forms a dimeric SMP structure through domain swapping of the ??1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Strikingly, both full-length Mdm12 and Mdm12 truncated to exclude the disordered region (residues 74-114) display the same organization in the asymmetric unit, although they crystallize as a tetramer and hexamer, respectively. Taken together, these studies provide a novel understanding of the overall organization of SMP domains in the ERMES complex, indicating that Mdm12 interacts with Mdm34 through head-to-head contact, and with Mmm1 through tail-to-tail contact of SMP domains.clos

Structure and function of Organelle Contact Sites

Organelle contactsites are specialized intracellular zones called membrane contact sites (MCS),in which two distinct suborganelles are closely apposed in eukaryotic cells. MCSsplay pivotal roles in cellular processes such as cooperative lipid biosynthesis,ion homeostasis, and interorganellar trafficking of molecules in eukaryoticcells. The MCSs are physically formed through dynamic and direct interactionsbetween proteins that are located in two distinct subcompartments. In thistalk, I will introduce structural and functional studies for two representativeMCSs, nucleus-vacuole contact site and endoplasmic reticulum (ER)-mitochondriacontact site. The nucleus–vacuole junction (NVJ) is the first identifiedinterorganellar MCS in the budding yeast Saccharomycescerevisiae, and its formation depends on the nuclear membrane protein Nvj1pand vacuolar membrane protein Vac8p. Here, I will show the crystal structure ofVac8p–Nvj1p complex. The endoplasmic reticulum–mitochondria encounter structure(ERMES) is a protein complex that plays a tethering role in physicallyconnecting ER and mitochondria membranes. The ERMES complex is composed ofMdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. I willshow the crystal structure of S.cerevisiae Mdm12. Based on these structures, I will address the molecularmechanisms by which the protein complexes are organized, mediate the formationof membrane contact sites, and perform their versatile functions at thecircumscribed area

Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites

The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mmm1 and the Mdm12-Mmm1 complex at 2.8 angstrom and 3.8 angstrom resolution, respectively. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12-Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-angstrom-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12-Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro