Reverse genetics identifies proteins regulating lipid droplet biogenesis via amphipathic helices

[1]  Shugo Nakamura,et al.  Multiple genes evolved for fungal septal pore plugging identified via large-scale localization and functional screenings , 2022, bioRxiv.

[2]  J. Teng,et al.  EI24 promotes cell adaption to ER stress by coordinating IRE1 signaling and calcium homeostasis , 2022, EMBO reports.

[3]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[4]  S. Dzurendová,et al.  Mucoromycota fungi as powerful cell factories for modern biorefinery , 2021, Applied microbiology and biotechnology.

[5]  Y. Ohsaki,et al.  Nuclear lipid droplets form in the inner nuclear membrane in a seipin-independent manner , 2020, The Journal of cell biology.

[6]  L. Wakim,et al.  Intracellular lipid droplet accumulation occurs early following viral infection and is required for an efficient interferon response , 2020, Nature Communications.

[7]  G. Moreno-Hagelsieb,et al.  Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2 , 2020, BMC genomics.

[8]  M. Sweet,et al.  Mammalian lipid droplets are innate immune hubs integrating cell metabolism and host defense , 2020, Science.

[9]  J. Swanson,et al.  Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting. , 2020, Developmental cell.

[10]  P. Juvvadi,et al.  Aspergillus fumigatus Cyp51A and Cyp51B Proteins Are Compensatory in Function and Localize Differentially in Response to Antifungals and Cell Wall Inhibitors , 2020, Antimicrobial Agents and Chemotherapy.

[11]  Jacob L. Steenwyk,et al.  Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota , 2020, Science Advances.

[12]  R. Schneiter,et al.  Seipin and Nem1 establish discrete ER subdomains to initiate yeast lipid droplet biogenesis , 2020, bioRxiv.

[13]  A. Thiam,et al.  Neutral lipids regulate amphipathic helix affinity for model lipid droplets , 2020, The Journal of cell biology.

[14]  Shugo Nakamura,et al.  A novel Pezizomycotina‐specific protein with gelsolin domains regulates contractile actin ring assembly and constriction in perforated septum formation , 2020, Molecular microbiology.

[15]  B. Trost,et al.  Lipid droplets can promote drug accumulation and activation , 2019, Nature Chemical Biology.

[16]  N. Turner,et al.  ORP5 localizes to ER–lipid droplet contacts and regulates the level of PI(4)P on lipid droplets , 2019, The Journal of cell biology.

[17]  T. Gabaldón,et al.  Fungal evolution: major ecological adaptations and evolutionary transitions , 2019, Biological reviews of the Cambridge Philosophical Society.

[18]  L. Nagy,et al.  Comparative genomics reveals the origin of fungal hyphae and multicellularity , 2019, Nature Communications.

[19]  J. Olzmann,et al.  Dynamics and functions of lipid droplets , 2018, Nature Reviews Molecular Cell Biology.

[20]  A. Salamov,et al.  Leveraging single-cell genomics to expand the fungal tree of life , 2018, Nature Microbiology.

[21]  L. Cowen,et al.  Antifungal drug resistance: evolution, mechanisms and impact. , 2018, Current opinion in microbiology.

[22]  Joshua E. Elias,et al.  Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors , 2018, Proceedings of the National Academy of Sciences.

[23]  W. Prinz,et al.  Lipid droplet and peroxisome biogenesis occur at the same ER subdomains , 2018, Nature Communications.

[24]  Anete Romanauska,et al.  The Inner Nuclear Membrane Is a Metabolically Active Territory that Generates Nuclear Lipid Droplets , 2018, Cell.

[25]  B. Antonny,et al.  A giant amphipathic helix from a perilipin that is adapted for coating lipid droplets , 2018, Nature Communications.

[26]  N. Afseth,et al.  High-throughput screening of Mucoromycota fungi for production of low- and high-value lipids , 2018, Biotechnology for Biofuels.

[27]  G. Hummer,et al.  The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1 , 2018, bioRxiv.

[28]  Robert V Farese,et al.  Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets. , 2018, Developmental cell.

[29]  Robert V Farese,et al.  Lipid Droplet Biogenesis. , 2017, Annual review of cell and developmental biology.

[30]  Tu Anh Nguyen,et al.  Innovation and constraint leading to complex multicellularity in the Ascomycota , 2017, Nature Communications.

[31]  M. Simon,et al.  BODIPY 493/503 Staining of Neutral Lipid Droplets for Microscopy and Quantification by Flow Cytometry. , 2016, Bio-protocol.

[32]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[33]  V. Saudek,et al.  Conserved Amphipathic Helices Mediate Lipid Droplet Targeting of Perilipins 1–3 , 2016, The Journal of Biological Chemistry.

[34]  Judith Klein-Seetharaman,et al.  The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix , 2015, eLife.

[35]  W. Prinz,et al.  A conserved family of proteins facilitates nascent lipid droplet budding from the ER , 2022 .

[36]  Robert V Farese,et al.  Protein Crowding Is a Determinant of Lipid Droplet Protein Composition. , 2015, Developmental cell.

[37]  M. Welte Expanding Roles for Lipid Droplets , 2015, Current Biology.

[38]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[39]  T. Reynolds,et al.  Candida albicans OPI1 Regulates Filamentous Growth and Virulence in Vaginal Infections, but Not Inositol Biosynthesis , 2015, PloS one.

[40]  Antonis Rokas,et al.  The Evolution of Fungal Metabolic Pathways , 2014, PLoS genetics.

[41]  G. Moreno-Hagelsieb,et al.  Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss? , 2014, PloS one.

[42]  Robert V Farese,et al.  High confidence proteomic analysis of yeast LDs identifies additional droplet proteins and reveals connections to dolichol synthesis and sterol acetylation[S] , 2014, Journal of Lipid Research.

[43]  S. Kohlwein,et al.  Lipid droplet autophagy in the yeast Saccharomyces cerevisiae , 2014, Molecular biology of the cell.

[44]  Shaojie Li,et al.  Transcription Factor CCG-8 as a New Regulator in the Adaptation to Antifungal Azole Stress , 2013, Antimicrobial Agents and Chemotherapy.

[45]  Ane Markina-Iñarrairaegui,et al.  The Aspergillus nidulans Peripheral ER: Disorganization by ER Stress and Persistence during Mitosis , 2013, PloS one.

[46]  Bruno Antonny,et al.  Curvature, lipid packing, and electrostatics of membrane organelles: defining cellular territories in determining specificity. , 2012, Developmental cell.

[47]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[48]  R. Cornell,et al.  The amphipathic helix of an enzyme that regulates phosphatidylcholine synthesis remodels membranes into highly curved nanotubules. , 2012, Biochimica et biophysica acta.

[49]  R. Schneiter,et al.  Lipid droplets are functionally connected to the endoplasmic reticulum in Saccharomyces cerevisiae , 2011, Journal of Cell Science.

[50]  K. Kitamoto,et al.  Targeted gene disruption in Koji mold Aspergillus oryzae. , 2011, Methods in molecular biology.

[51]  P. Cresswell,et al.  The antiviral protein, viperin, localizes to lipid droplets via its N-terminal amphipathic α-helix , 2009, Proceedings of the National Academy of Sciences.

[52]  Brigitte Cambon,et al.  Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 , 2009, Proceedings of the National Academy of Sciences.

[53]  M. Tomita,et al.  Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs , 2009, Proceedings of the National Academy of Sciences.

[54]  R. Fukuda,et al.  Yas3p, an Opi1 Family Transcription Factor, Regulates Cytochrome P450 Expression in Response to n-Alkanes in Yarrowia lipolytica* , 2009, Journal of Biological Chemistry.

[55]  S. Osmani,et al.  The three fungal transmembrane nuclear pore complex proteins of Aspergillus nidulans are dispensable in the presence of an intact An-Nup84-120 complex. , 2008, Molecular biology of the cell.

[56]  Dominique Douguet,et al.  HELIQUEST: a web server to screen sequences with specific alpha-helical properties , 2008, Bioinform..

[57]  Robert V Farese,et al.  Functional genomic screen reveals genes involved in lipid-droplet formation and utilization , 2008, Nature.

[58]  R. Parton,et al.  Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast , 2008, The Journal of cell biology.

[59]  Richard G. W. Anderson,et al.  The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology , 2007, Proceedings of the National Academy of Sciences.

[60]  D. Ussery,et al.  Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina , 2007, BMC Genomics.

[61]  Elysa B. Goldberg,et al.  Adipocyte differentiation‐related protein reduces lipid droplet association of adipose triglyceride lipase and slows triacylglycerol turnover , 2007, Journal of lipid research.

[62]  D. Small,et al.  Apolipoprotein B is conformationally flexible but anchored at a triolein/water interface: a possible model for lipoprotein surfaces. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[63]  W. Nierman,et al.  Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole , 2006, Current Genetics.

[64]  A. Repenning,et al.  Constitutive expression of yeast phospholipid biosynthetic genes by variants of Ino2 activator defective for interaction with Opi1 repressor , 2005, Molecular microbiology.

[65]  Christopher J. R. Loewen,et al.  Phospholipid Metabolism Regulated by a Transcription Factor Sensing Phosphatidic Acid , 2004, Science.

[66]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[67]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[68]  L. Pedersen,et al.  Structure and function of sulfotransferases. , 2001, Archives of biochemistry and biophysics.

[69]  A. Kimmel,et al.  Perilipin A Increases Triacylglycerol Storage by Decreasing the Rate of Triacylglycerol Hydrolysis* , 2000, The Journal of Biological Chemistry.

[70]  J Schultz,et al.  SMART, a simple modular architecture research tool: identification of signaling domains. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Hamer,et al.  hyp loci control cell pattern formation in the vegetative mycelium of Aspergillus nidulans. , 1998, Genetics.

[72]  R. Fischer,et al.  Nuclear traffic in fungal hyphae: in vivo study of nuclear migration and positioning in Aspergillus nidulans , 1997, Molecular microbiology.

[73]  L Regan,et al.  Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude. , 1997, Folding & design.

[74]  J. Cashman,et al.  A nomenclature for the mammalian flavin-containing monooxygenase gene family based on amino acid sequence identities. , 1994, Archives of biochemistry and biophysics.

[75]  S. Fowler,et al.  Nile red: a selective fluorescent stain for intracellular lipid droplets , 1985, The Journal of cell biology.

[76]  David Eisenberg,et al.  The helical hydrophobic moment: a measure of the amphiphilicity of a helix , 1982, Nature.

[77]  A. Stoppani,et al.  Pyruvate metabolism in Saccharomyces cerevisiae. , 1951, Nature.