Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M.; Ito, Masakazu; Mondo, Stephen J.; Reilly, Morgann C.; Cheng, Ya-Fang; Bauer, Stefan; Grigoriev, Igor V.; Gladden, John M.; Simmons, Blake A.; Brem, Rachel B.; Arkin, Adam P.; Skerker, Jeffrey M.

doi:10.7554/eLife.32110

Title: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Journal Article · Fri Mar 09 00:00:00 EST 2018 · eLife

DOI:https://doi.org/10.7554/eLife.32110· OSTI ID:1466439

^[1]; Pinel, Dominic ^[2]; Geiselman, Gina M. ^[2]; Ito, Masakazu ^[2];

^[3]; Reilly, Morgann C. ^[4]; Cheng, Ya-Fang ^[2]; Bauer, Stefan ^[2]; Grigoriev, Igor V. ^[5];

^[6]; Simmons, Blake A. ^[7]; Brem, Rachel B. ^[8];

^[9];

^[10]

The Buck Institute for Research on Aging, Novato, United States
Energy Biosciences Institute, Berkeley, United States
United States Department of Energy Joint Genome Institute, Walnut Creek, United States
Joint BioEnergy Institute, Emeryville, United States, Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
United States Department of Energy Joint Genome Institute, Walnut Creek, United States, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
Joint BioEnergy Institute, Emeryville, United States
Joint BioEnergy Institute, Emeryville, United States, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
The Buck Institute for Research on Aging, Novato, United States, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
Energy Biosciences Institute, Berkeley, United States, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States, Department of Bioengineering, University of California, Berkeley, Berkeley, United States
Energy Biosciences Institute, Berkeley, United States, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States, Department of Bioengineering, University of California, Berkeley, Berkeley, United States

The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. Lastly, these results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.

View Journal Article

Cite

Export

Save

Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: Office of Biological and Environmental Research, DE-SC-0012527; Office of Biological and Environmental Research, DE-AC02-05CH11231; AC05-76RL01830; AC02-05CH11231

OSTI ID:: 1466439

Alternate ID(s):: OSTI ID: 1437152; OSTI ID: 1459403; OSTI ID: 1466441

Journal Information:: eLife, Journal Name: eLife Vol. 7; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 52 works

Citation information provided by
Web of Science

References (198)

A Lipid Droplet-Associated GFP Reporter-Based Screen Identifies New Fat Storage Regulators in C. elegans Liu, Zhenglong; Li, Xia; Ge, Qinlan Journal of Genetics and Genomics, Vol. 41, Issue 5 https://doi.org/10.1016/j.jgg.2014.03.002	journal	May 2014
The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism Kleinboelting, Nils; Huep, Gunnar; Appelhagen, Ingo Molecular Plant, Vol. 8, Issue 11 https://doi.org/10.1016/j.molp.2015.08.011	journal	November 2015
Mitochondrial long chain fatty acid β-oxidation in man and mouse Chegary, Malika; Brinke, Heleen te; Ruiter, Jos P. N. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1791, Issue 8 https://doi.org/10.1016/j.bbalip.2009.05.006	journal	August 2009
Agrobacterium tumefaciens-mediated transformation of the soybean pathogen Phomopsis longicolla Li, Shuxian; Ridenour, John B.; Kim, Hun Journal of Microbiological Methods, Vol. 92, Issue 3 https://doi.org/10.1016/j.mimet.2012.12.015	journal	March 2013
PomBase: a comprehensive online resource for fission yeast Wood, V.; Harris, M. A.; McDowall, M. D. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr853	journal	October 2011
Identification of Conidiogenesis-Associated Genes in Colletotrichum gloeosporioides by Agrobacterium tumefaciens-Mediated Transformation Wu, Jianyuan; Ji, Zhirui; Wang, Na Current Microbiology, Vol. 73, Issue 6 https://doi.org/10.1007/s00284-016-1131-8	journal	September 2016
Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica Beopoulos, A.; Verbeke, J.; Bordes, F. Applied Microbiology and Biotechnology, Vol. 98, Issue 1 https://doi.org/10.1007/s00253-013-5295-x	journal	October 2013
Regulation of the Regulators: Post-Translational Modifications, Subcellular, and Spatiotemporal Distribution of Plant 14-3-3 Proteins Wilson, Rashaun S.; Swatek, Kirby N.; Thelen, Jay J. Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00611	journal	May 2016
Agrobacterium tumefaciens Integrates Transfer DNA into Single Chromosomal Sites of Dimorphic Fungi and Yields Homokaryotic Progeny from Multinucleate Yeast Sullivan, Thomas D.; Rooney, Peggy J.; Klein, Bruce S. Eukaryotic Cell, Vol. 1, Issue 6 https://doi.org/10.1128/EC.1.6.895-905.2002	journal	December 2002
Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora Molecular & Cellular Proteomics, Vol. 12, Issue 5 https://doi.org/10.1074/mcp.M112.020230	journal	January 2013
Transposon sequencing: methods and expanding applications Kwon, Young Min; Ricke, Steven C.; Mandal, Rabindra K. Applied Microbiology and Biotechnology, Vol. 100, Issue 1 https://doi.org/10.1007/s00253-015-7037-8	journal	October 2015
Kinetic Regulation of the Mitochondrial Glycerol-3-phosphate Dehydrogenase by the External NADH Dehydrogenase in Saccharomyces cerevisiae Påhlman, Inga-lill; Larsson, Christer; Averét, Nicole Journal of Biological Chemistry, Vol. 277, Issue 31 https://doi.org/10.1074/jbc.M204079200	journal	May 2002
A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae Huang, B.; Lu, J.; Bystrom, A. S. RNA, Vol. 14, Issue 10 https://doi.org/10.1261/rna.1184108	journal	August 2008
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action Hillenmeyer, Maureen E.; Ericson, Elke; Davis, Ronald W. Genome Biology, Vol. 11, Issue 3 https://doi.org/10.1186/gb-2010-11-3-r30	journal	January 2010
Fatty Acid Trafficking in Starved Cells: Regulation by Lipid Droplet Lipolysis, Autophagy, and Mitochondrial Fusion Dynamics Rambold, Angelika S.; Cohen, Sarah; Lippincott-Schwartz, Jennifer Developmental Cell, Vol. 32, Issue 6 https://doi.org/10.1016/j.devcel.2015.01.029	journal	March 2015
Agrobacterium-mediated transformation of Guignardia citricarpa: An efficient tool to gene transfer and random mutagenesis Rodrigues, Maria Beatriz Calderan; Fávaro, Léia Cecília de Lima; Pallu, Ana Paula de Souza Fungal Biology, Vol. 117, Issue 7-8 https://doi.org/10.1016/j.funbio.2013.06.005	journal	July 2013
Phosphate-limitation mediated lipid production by Rhodosporidium toruloides Wu, Siguo; Hu, Cuimin; Jin, Guojie Bioresource Technology, Vol. 101, Issue 15 https://doi.org/10.1016/j.biortech.2010.02.111	journal	August 2010
Functional genomic screen reveals genes involved in lipid-droplet formation and utilization Guo, Yi; Walther, Tobias C.; Rao, Meghana Nature, Vol. 453, Issue 7195 https://doi.org/10.1038/nature06928	journal	April 2008
A role for lipid droplets in inter-membrane lipid traffic Zehmer, John K.; Huang, Youguo; Peng, Gong PROTEOMICS, Vol. 9, Issue 4 https://doi.org/10.1002/pmic.200800584	journal	February 2009
Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution Swigoňová, Zuzana; Mohsen, Al-Walid; Vockley, Jerry Journal of Molecular Evolution, Vol. 69, Issue 2 https://doi.org/10.1007/s00239-009-9263-0	journal	July 2009
Comprehensive identification of conditionally essential genes in mycobacteria Sassetti, C. M.; Boyd, D. H.; Rubin, E. J. Proceedings of the National Academy of Sciences, Vol. 98, Issue 22 https://doi.org/10.1073/pnas.231275498	journal	October 2001
Not Just Fat: The Structure and Function of the Lipid Droplet Fujimoto, T.; Parton, R. G. Cold Spring Harbor Perspectives in Biology, Vol. 3, Issue 3 https://doi.org/10.1101/cshperspect.a004838	journal	January 2011
Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica Vasdekis, Andreas E.; Silverman, Andrew M.; Stephanopoulos, Gregory PLOS ONE, Vol. 12, Issue 1 https://doi.org/10.1371/journal.pone.0168889	journal	January 2017
Peroxisomal Acyl-CoA oxidase 4 activity differs between Arabidopsis accessions Khan, Bibi Rafeiza; Adham, A. Raquel; Zolman, Bethany K. Plant Molecular Biology, Vol. 78, Issue 1-2 https://doi.org/10.1007/s11103-011-9843-4	journal	November 2011
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources Arnaud, M. B.; Cerqueira, G. C.; Inglis, D. O. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr875	journal	November 2011
In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiae Mitochondria Overkamp, K. M.; Bakker, B. M.; Kotter, P. Journal of Bacteriology, Vol. 182, Issue 10 https://doi.org/10.1128/JB.182.10.2823-2830.2000	journal	May 2000
Lipid particles/droplets of the yeast Saccharomyces cerevisiae revisited: Lipidome meets Proteome Grillitsch, Karlheinz; Connerth, Melanie; Köfeler, Harald Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1811, Issue 12 https://doi.org/10.1016/j.bbalip.2011.07.015	journal	December 2011
FSP27 contributes to efficient energy storage in murine white adipocytes by promoting the formation of unilocular lipid droplets Nishino, Naonobu; Tamori, Yoshikazu; Tateya, Sanshiro Journal of Clinical Investigation https://doi.org/10.1172/JCI34090	journal	July 2008
Concomitant Production of Lipids and Carotenoids in Rhodosporidium toruloides under Osmotic Stress Using Response Surface Methodology Singh, Gunjan; Jawed, Arshad; Paul, Debarati Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01686	journal	October 2016
Cloning and disruption of a gene required for growth on acetate but not on ethanol: The acetyl-coenzyme a synthetase gene ofSaccharmoyces cerevisiae De Virgilio, Claudio; Bürckert, Niels; Barth, Gerold Yeast, Vol. 8, Issue 12, p. 1043-1051 https://doi.org/10.1002/yea.320081207	journal	December 1992
Phylogenetic diversity of stress signaling pathways in fungi Nikolaou, Elissavet; Agriafioti, Ino; Stumpf, Michael BMC Evolutionary Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2148-9-44	journal	January 2009
14-3-3 Proteins Are Essential for RAS/MAPK Cascade Signaling during Pseudohyphal Development in S. cerevisiae Roberts, Radclyffe L.; Mösch, Hans-Ulrich; Fink, Gerald R. Cell, Vol. 89, Issue 7 https://doi.org/10.1016/S0092-8674(00)80293-7	journal	June 1997
The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology Szymanski, K. M.; Binns, D.; Bartz, R. Proceedings of the National Academy of Sciences, Vol. 104, Issue 52 https://doi.org/10.1073/pnas.0704154104	journal	December 2007
The MAP1-LC3 conjugation system is involved in lipid droplet formation Shibata, Masahiro; Yoshimura, Kentaro; Furuya, Norihiko Biochemical and Biophysical Research Communications, Vol. 382, Issue 2 https://doi.org/10.1016/j.bbrc.2009.03.039	journal	May 2009
Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level Vasdekis, A. E.; Silverman, A. M.; Stephanopoulos, G. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep17689	journal	December 2015
Human disorders of peroxisome metabolism and biogenesis Waterham, Hans R.; Ferdinandusse, Sacha; Wanders, Ronald J. A. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1863, Issue 5 https://doi.org/10.1016/j.bbamcr.2015.11.015	journal	May 2016
UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology Pulschen, André A.; Rodrigues, Fabio; Duarte, Rubens T. D. MicrobiologyOpen, Vol. 4, Issue 4 https://doi.org/10.1002/mbo3.262	journal	July 2015
Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae: Saccharomyces cerevisiae NADH kinases Shi, Feng; Kawai, Shigeyuki; Mori, Shigetarou FEBS Journal, Vol. 272, Issue 13 https://doi.org/10.1111/j.1742-4658.2005.04749.x	journal	June 2005
The cAMP/protein kinase A signaling pathway in pathogenic basidiomycete fungi: Connections with iron homeostasis Choi, Jaehyuk; Jung, Won Hee; Kronstad, James W. Journal of Microbiology, Vol. 53, Issue 9 https://doi.org/10.1007/s12275-015-5247-5	journal	August 2015
Functional profiling of the Saccharomyces cerevisiae genome Giaever, Guri; Chu, Angela M.; Ni, Li Nature, Vol. 418, Issue 6896 https://doi.org/10.1038/nature00935	journal	July 2002
Lipid droplets maintain lipid homeostasis during anaphase for efficient cell separation in budding yeast Yang, Po-Lin; Hsu, Tzu-Han; Wang, Chao-Wen Molecular Biology of the Cell, Vol. 27, Issue 15 https://doi.org/10.1091/mbc.E16-02-0106	journal	August 2016
Emergence and Spread of New Races of Wheat Stem Rust Fungus: Continued Threat to Food Security and Prospects of Genetic Control Singh, Ravi P.; Hodson, David P.; Jin, Yue Phytopathology, Vol. 105, Issue 7 https://doi.org/10.1094/PHYTO-01-15-0030-FI	journal	July 2015
Effects of biomass hydrolysis by-products on oleaginous yeast Rhodosporidium toruloides Hu, Cuimin; Zhao, Xin; Zhao, Jin Bioresource Technology, Vol. 100, Issue 20 https://doi.org/10.1016/j.biortech.2009.04.041	journal	October 2009
Lipid Droplet Protein LID-1 Mediates ATGL-1-Dependent Lipolysis during Fasting in Caenorhabditis elegans Lee, J. H.; Kong, J.; Jang, J. Y. Molecular and Cellular Biology, Vol. 34, Issue 22 https://doi.org/10.1128/MCB.00722-14	journal	September 2014
A simple technique for the preparation and storage of sucrose gradients Luthe, Dawn S. Analytical Biochemistry, Vol. 135, Issue 1 https://doi.org/10.1016/0003-2697(83)90755-8	journal	November 1983
14-3-3 proteins: potential roles in vesicular transport and Ras signaling in Saccharomyces cerevisiae. Gelperin, D.; Weigle, J.; Nelson, K. Proceedings of the National Academy of Sciences, Vol. 92, Issue 25 https://doi.org/10.1073/pnas.92.25.11539	journal	December 1995
Seipin regulates ER –lipid droplet contacts and cargo delivery Salo, Veijo T.; Belevich, Ilya; Li, Shiqian The EMBO Journal, Vol. 35, Issue 24 https://doi.org/10.15252/embj.201695170	journal	October 2016
Regulation of lipid droplet dynamics in Saccharomyces cerevisiae depends on the Rab7-like Ypt7p, HOPS complex and V1-ATPase Bouchez, I.; Pouteaux, M.; Canonge, M. Biology Open, Vol. 4, Issue 7 https://doi.org/10.1242/bio.20148615	journal	May 2015
Identification of Genes Affecting Lipid Content Using Transposon Mutagenesis in Saccharomyces cerevisiae Kamisaka, Yasushi; Noda, Naomi; Tomita, Nao Bioscience, Biotechnology, and Biochemistry, Vol. 70, Issue 3 https://doi.org/10.1271/bbb.70.646	journal	January 2006
A critical assessment of Agrobacterium tumefaciens-mediated transformation as a tool for pathogenicity gene discovery in the phytopathogenic fungus Leptosphaeria maculans Blaise, Françoise; Rémy, Estelle; Meyer, Michel Fungal Genetics and Biology, Vol. 44, Issue 2 https://doi.org/10.1016/j.fgb.2006.07.006	journal	February 2007
“Density equilibrium” method for the quantitative and rapid in situ determination of lipid, hydrocarbon, or biopolymer content in microorganisms Eroglu, Ela; Melis, Anastasios Biotechnology and Bioengineering, Vol. 102, Issue 5 https://doi.org/10.1002/bit.22182	journal	April 2009
Highly efficient transformation system for Malassezia furfur and Malassezia pachydermatis using Agrobacterium tumefaciens-mediated transformation Celis, A. M.; Vos, A. M.; Triana, S. Journal of Microbiological Methods, Vol. 134 https://doi.org/10.1016/j.mimet.2017.01.001	journal	March 2017
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica Kerkhoven, Eduard J.; Pomraning, Kyle R.; Baker, Scott E. npj Systems Biology and Applications, Vol. 2, Issue 1 https://doi.org/10.1038/npjsba.2016.5	journal	March 2016
Identification of 23 complementation groups required for post-translational events in the yeast secretory pathway Novick, Peter; Field, Charles; Schekman, Randy Cell, Vol. 21, Issue 1 https://doi.org/10.1016/0092-8674(80)90128-2	journal	August 1980
Involvement of Rad52 in T-DNA circle formation during A grobacterium tumefaciens -mediated transformation of S accharomyces cerevisiae : Involvement of Rad52 in T-DNA circle formation Rolloos, Martijn; Dohmen, Marius H. C.; Hooykaas, Paul J. J. Molecular Microbiology, Vol. 91, Issue 6 https://doi.org/10.1111/mmi.12531	journal	February 2014
Lipid droplet autophagy in the yeast Saccharomyces cerevisiae van Zutphen, Tim; Todde, Virginia; de Boer, Rinse Molecular Biology of the Cell, Vol. 25, Issue 2 https://doi.org/10.1091/mbc.E13-08-0448	journal	January 2014
High-throughput fluorescence-activated cell sorting for lipid hyperaccumulating Chlamydomonas reinhardtii mutants Xie, Bo; Stessman, Dan; Hart, Jason H. Plant Biotechnology Journal, Vol. 12, Issue 7 https://doi.org/10.1111/pbi.12190	journal	April 2014
Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library: T-DNA flanking sequence tags in rice Zhang, Jian; Guo, Dong; Chang, Yuxiao The Plant Journal, Vol. 49, Issue 5 https://doi.org/10.1111/j.1365-313X.2006.03001.x	journal	February 2007
Genetic and dietary regulation of lipid droplet expansion in Caenorhabditis elegans Zhang, S. O.; Box, A. C.; Xu, N. Proceedings of the National Academy of Sciences, Vol. 107, Issue 10 https://doi.org/10.1073/pnas.0912308107	journal	February 2010
Lipid production in batch and fed-batch cultures of Rhodosporidium toruloidesfrom 5 and 6 carbon carbohydrates Wiebe, Marilyn G.; Koivuranta, Kari; Penttilä, Merja BMC Biotechnology, Vol. 12, Issue 1 https://doi.org/10.1186/1472-6750-12-26	journal	May 2012
Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae Choi, Jaehyuk; Park, Jongsun; Jeon, Junhyun Molecular Microbiology, Vol. 66, Issue 2 https://doi.org/10.1111/j.1365-2958.2007.05918.x	journal	October 2007
tRNA thiolation links translation to stress responses in Saccharomyces cerevisiae Damon, Jadyn R.; Pincus, David; Ploegh, Hidde L. Molecular Biology of the Cell, Vol. 26, Issue 2 https://doi.org/10.1091/mbc.E14-06-1145	journal	January 2015
Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism Smith, Jennifer J.; Sydorskyy, Yaroslav; Marelli, Marcello Molecular Systems Biology, Vol. 2, Issue 1 https://doi.org/10.1038/msb4100051	journal	January 2006
Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation Zhang, Shuyan; Ito, Masakazu; Skerker, Jeffrey M. Applied Microbiology and Biotechnology, Vol. 100, Issue 21 https://doi.org/10.1007/s00253-016-7815-y	journal	September 2016
Metabolomic Profiling of Rhodosporidium toruloides Grown on Glycerol for Carotenoid Production during Different Growth Phases Lee, Jaslyn Jie Lin; Chen, Liwei; Shi, Jiahua Journal of Agricultural and Food Chemistry, Vol. 62, Issue 41 https://doi.org/10.1021/jf502987q	journal	October 2014
Seipin is required for converting nascent to mature lipid droplets Wang, Huajin; Becuwe, Michel; Housden, Benjamin E. eLife, Vol. 5 https://doi.org/10.7554/eLife.16582	journal	August 2016
A Role for Phosphatidic Acid in the Formation of “Supersized” Lipid Droplets Fei, Weihua; Shui, Guanghou; Zhang, Yuxi PLoS Genetics, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pgen.1002201	journal	July 2011
Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome–Mitochondria Interactions through the ERMES Complex Mattiazzi Ušaj, M.; Brložnik, M.; Kaferle, P. Journal of Molecular Biology, Vol. 427, Issue 11 https://doi.org/10.1016/j.jmb.2015.03.004	journal	June 2015
Signaling pathways for stress responses and adaptation in Aspergillus species: stress biology in the post-genomic era Hagiwara, Daisuke; Sakamoto, Kazutoshi; Abe, Keietsu Bioscience, Biotechnology, and Biochemistry, Vol. 80, Issue 9 https://doi.org/10.1080/09168451.2016.1162085	journal	February 2016
Insertional mutagenesis in yeasts using T-DNA fromAgrobacterium tumefaciens Bundock, Paul; van Attikum, Haico; den Dulk-Ras, Amke Yeast, Vol. 19, Issue 6 https://doi.org/10.1002/yea.858	journal	January 2002
Culture strategies for lipid production using acetic acid as sole carbon source by Rhodosporidium toruloides Huang, Xiang-Feng; Liu, Jia-Nan; Lu, Li-Jun Bioresource Technology, Vol. 206 https://doi.org/10.1016/j.biortech.2016.01.073	journal	April 2016
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The yeast p24 complex regulates GPI-anchored protein transport and quality control by monitoring anchor remodeling Castillon, Guillaume A.; Aguilera-Romero, Auxiliadora; Manzano-Lopez, Javier Molecular Biology of the Cell, Vol. 22, Issue 16 https://doi.org/10.1091/mbc.E11-04-0294	journal	August 2011
P58 ^IPK , a Novel Endoplasmic Reticulum Stress-inducible Protein and Potential Negative Regulator of eIF2α Signaling van Huizen, Rika; Martindale, Jennifer L.; Gorospe, Myriam Journal of Biological Chemistry, Vol. 278, Issue 18 https://doi.org/10.1074/jbc.M212074200	journal	February 2003
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J. mBio, Vol. 6, Issue 3, Article No. e00306-15 https://doi.org/10.1128/mBio.00306-15	journal	May 2015
Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes Le Breton, Yoann; Belew, Ashton T.; Valdes, Kayla M. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep09838	journal	May 2015
The Lipid-Droplet Proteome Reveals that Droplets Are a Protein-Storage Depot Cermelli, Silvia; Guo, Yi; Gross, Steven P. Current Biology, Vol. 16, Issue 18 https://doi.org/10.1016/j.cub.2006.07.062	journal	September 2006
Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum Wanders, Ronald J. A.; Waterham, Hans R.; Ferdinandusse, Sacha Frontiers in Cell and Developmental Biology, Vol. 3 https://doi.org/10.3389/fcell.2015.00083	journal	January 2016
Yeast diversity in hypersaline habitats Butinar, L.; Santos, S.; Spencer-Martins, I. FEMS Microbiology Letters, Vol. 244, Issue 2 https://doi.org/10.1016/j.femsle.2005.01.043	journal	March 2005
Microbial lipid production by Rhodosporidium toruloides under sulfate-limited conditions Wu, Siguo; Zhao, Xin; Shen, Hongwei Bioresource Technology, Vol. 102, Issue 2 https://doi.org/10.1016/j.biortech.2010.09.033	journal	January 2011
Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes Sliva, Anna; Kuang, Zheng; Meluh, Pamela B. G3: Genes\|Genomes\|Genetics, Vol. 6, Issue 4 https://doi.org/10.1534/g3.115.026757	journal	February 2016
tRNA transfers to the limelight Hopper, A. K. Genes & Development, Vol. 17, Issue 2 https://doi.org/10.1101/gad.1049103	journal	January 2003
Agrobacterium-Mediated Plant Transformation: the Biology behind the "Gene-Jockeying" Tool Gelvin, S. B. Microbiology and Molecular Biology Reviews, Vol. 67, Issue 1, p. 16-37 https://doi.org/10.1128/MMBR.67.1.16-37.2003	journal	March 2003
TRAPP ing Rab18 in lipid droplets Zappa, Francesca; Venditti, Rossella; De Matteis, Maria Antonietta The EMBO Journal, Vol. 36, Issue 4 https://doi.org/10.15252/embj.201696287	journal	December 2016
Autophagy-independent function of Atg8 in lipid droplet dynamics in yeast Maeda, Yuichiro; Oku, Masahide; Sakai, Yasuyoshi Journal of Biochemistry https://doi.org/10.1093/jb/mvw078	journal	December 2016
The Role of Nuclear Cap Binding Protein Cbc1p of Yeast in mRNA Termination and Degradation Das, B.; Guo, Z.; Russo, P. Molecular and Cellular Biology, Vol. 20, Issue 8 https://doi.org/10.1128/MCB.20.8.2827-2838.2000	journal	April 2000
Factors underlying the variability of lipid droplet fluorescence in MA-10 leydig tumor cells Gocze, Peter M.; Freeman, Dale A. Cytometry, Vol. 17, Issue 2 https://doi.org/10.1002/cyto.990170207	journal	October 1994
The lipid droplet—a well-connected organelle Gao, Qiang; Goodman, Joel M. Frontiers in Cell and Developmental Biology, Vol. 3 https://doi.org/10.3389/fcell.2015.00049	journal	August 2015
The Biochemistry and Physiology of Mitochondrial Fatty Acid β-Oxidation and Its Genetic Disorders Houten, Sander M.; Violante, Sara; Ventura, Fatima V. Annual Review of Physiology, Vol. 78, Issue 1 https://doi.org/10.1146/annurev-physiol-021115-105045	journal	February 2016
Measurement of mass, density, and volume during the cell cycle of yeast Bryan, A. K.; Goranov, A.; Amon, A. Proceedings of the National Academy of Sciences, Vol. 107, Issue 3 https://doi.org/10.1073/pnas.0901851107	journal	December 2009
New insights into the peroxisomal protein inventory: Acyl-CoA oxidases and -dehydrogenases are an ancient feature of peroxisomes Camões, Fátima; Islinger, Markus; Guimarães, Sofia C. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 1 https://doi.org/10.1016/j.bbamcr.2014.10.005	journal	January 2015
Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling Zinshteyn, Boris; Gilbert, Wendy V. PLoS Genetics, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pgen.1003675	journal	August 2013
Agrobacterium tumefaciens-mediated transformation of Aspergillus aculeatus for insertional mutagenesis Kunitake, Emi; Tani, Shuji; Sumitani, Jun-ichi AMB Express, Vol. 1, Issue 1 https://doi.org/10.1186/2191-0855-1-46	journal	January 2011
Lipid droplets and their component triglycerides and steryl esters regulate autophagosome biogenesis Shpilka, Tomer; Welter, Evelyn; Borovsky, Noam The EMBO Journal, Vol. 34, Issue 16 https://doi.org/10.15252/embj.201490315	journal	July 2015
Development of an Agrobacterium-mediated transformation system for the cold-adapted fungi Pseudogymnoascus destructans and P. pannorum Zhang, Tao; Ren, Ping; Chaturvedi, Vishnu Fungal Genetics and Biology, Vol. 81 https://doi.org/10.1016/j.fgb.2015.05.009	journal	August 2015
Agrobacterium tumefaciens-mediated transformation of Lasiodiplodia theobromae, the causal agent of gummosis in cashew nut plants Muniz, C. R.; da Silva, G. F.; Souza Jr, M. T. Genetics and Molecular Research, Vol. 13, Issue AOP https://doi.org/10.4238/2014.February.21.8	journal	January 2014
NADP(H) Phosphatase Activities of Archaeal Inositol Monophosphatase and Eubacterial 3'-Phosphoadenosine 5'-Phosphate Phosphatase Fukuda, C.; Kawai, S.; Murata, K. Applied and Environmental Microbiology, Vol. 73, Issue 17 https://doi.org/10.1128/AEM.02703-06	journal	July 2007
Indirect and suboptimal control of gene expression is widespread in bacteria Price, Morgan N.; Deutschbauer, Adam M.; Skerker, Jeffrey M. Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2013.16	journal	January 2013
Genome-wide identification of bacterial plant colonization genes Cole, Benjamin J.; Feltcher, Meghan E.; Waters, Robert J. PLOS Biology, Vol. 15, Issue 9 https://doi.org/10.1371/journal.pbio.2002860	journal	September 2017
Essential Gene Discovery in the Basidiomycete Cryptococcus neoformans for Antifungal Drug Target Prioritization Ianiri, Giuseppe; Idnurm, Alexander mBio, Vol. 6, Issue 2 https://doi.org/10.1128/mBio.02334-14	journal	March 2015
AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation Seo, Arnold Y.; Lau, Pick-Wei; Feliciano, Daniel eLife, Vol. 6 https://doi.org/10.7554/eLife.21690	journal	April 2017
Overcoming recalcitrant transformation and gene manipulation in Pucciniomycotina yeasts Abbott, Erika P.; Ianiri, Giuseppe; Castoria, Raffaello Applied Microbiology and Biotechnology, Vol. 97, Issue 1 https://doi.org/10.1007/s00253-012-4561-7	journal	November 2012
Phosphoregulatory protein 14-3-3 facilitates SAC1 transport from the endoplasmic reticulum Bajaj Pahuja, Kanika; Wang, Jinzhi; Blagoveshchenskaya, Anastasia Proceedings of the National Academy of Sciences, Vol. 112, Issue 25 https://doi.org/10.1073/pnas.1509119112	journal	June 2015
The role of malic enzyme in the regulation of lipid accumulation in filamentous fungi Wynn, J. P.; Hamid, A. b. A.; Ratledge, C. Microbiology, Vol. 145, Issue 8 https://doi.org/10.1099/13500872-145-8-1911	journal	August 1999
A Functional, Genome-wide Evaluation of Liposensitive Yeast Identifies the “ ARE2 Required for Viability” ( ARV1 ) Gene Product as a Major Component of Eukaryotic Fatty Acid Resistance Ruggles, Kelly V.; Garbarino, Jeanne; Liu, Ying Journal of Biological Chemistry, Vol. 289, Issue 7 https://doi.org/10.1074/jbc.M113.515197	journal	November 2013
A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides Zhu, Zhiwei; Zhang, Sufang; Liu, Hongwei Nature Communications, Vol. 3, Issue 1 https://doi.org/10.1038/ncomms2112	journal	January 2012
SEIPIN Regulates Lipid Droplet Expansion and Adipocyte Development by Modulating the Activity of Glycerol-3-phosphate Acyltransferase Pagac, Martin; Cooper, Daniel E.; Qi, Yanfei Cell Reports, Vol. 17, Issue 6 https://doi.org/10.1016/j.celrep.2016.10.037	journal	November 2016
Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica Pomraning, Kyle R.; Bredeweg, Erin L.; Baker, Scott E. mSphere, Vol. 2, Issue 1 https://doi.org/10.1128/mSphere.00038-17	journal	February 2017
Phylogenetic classification of yeasts and related taxa within Pucciniomycotina Wang, Q. -M.; Yurkov, A. M.; Göker, M. Studies in Mycology, Vol. 81 https://doi.org/10.1016/j.simyco.2015.12.002	journal	June 2015
The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins Angerer, Heike Biochemical Society Transactions, Vol. 41, Issue 5 https://doi.org/10.1042/BST20130116	journal	September 2013
A One Pot, One Step, Precision Cloning Method with High Throughput Capability Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre PLoS ONE, Vol. 3, Issue 11, Article No. e3647 https://doi.org/10.1371/journal.pone.0003647	journal	November 2008
A fluorescence-activated cell sorting-based strategy for rapid isolation of high-lipid Chlamydomonas mutants Terashima, Mia; Freeman, Elizabeth S.; Jinkerson, Robert E. The Plant Journal, Vol. 81, Issue 1 https://doi.org/10.1111/tpj.12682	journal	October 2014
Integration of Agrobacterium tumefaciens T-DNA in the Saccharomyces cerevisiae genome by illegitimate recombination Bundock, P.; Hooykaas, P. J. J. Proceedings of the National Academy of Sciences, Vol. 93, Issue 26, p. 15272-15275 https://doi.org/10.1073/pnas.93.26.15272	journal	December 1996
Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica Silverman, Andrew M.; Qiao, Kangjian; Xu, Peng Applied Microbiology and Biotechnology, Vol. 100, Issue 8 https://doi.org/10.1007/s00253-016-7376-0	journal	February 2016
Leaf Rust of Cultivated Barley: Pathology and Control Park, Robert F.; Golegaonkar, Prashant G.; Derevnina, Lida Annual Review of Phytopathology, Vol. 53, Issue 1 https://doi.org/10.1146/annurev-phyto-080614-120324	journal	August 2015
Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation Zhang, Y.; Adams, I. P.; Ratledge, C. Microbiology, Vol. 153, Issue 7 https://doi.org/10.1099/mic.0.2006/002683-0	journal	July 2007
COPI Complex Is a Regulator of Lipid Homeostasis Beller, Mathias; Sztalryd, Carole; Southall, Noel PLoS Biology, Vol. 6, Issue 11 https://doi.org/10.1371/journal.pbio.0060292	journal	November 2008
Annotating non-coding regions of the genome Alexander, Roger P.; Fang, Gang; Rozowsky, Joel Nature Reviews Genetics, Vol. 11, Issue 8 https://doi.org/10.1038/nrg2814	journal	July 2010
From The Cover: Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining Ninomiya, Y.; Suzuki, K.; Ishii, C. Proceedings of the National Academy of Sciences, Vol. 101, Issue 33 https://doi.org/10.1073/pnas.0402780101	journal	August 2004
Agrobacterium tumefaciens-mediated genetic transformation of the Taxol-producing endophytic fungus Ozonium sp EFY21 Liu, L.; Wei, Y. M.; Zhou, X. W. Genetics and Molecular Research, Vol. 12, Issue 3 https://doi.org/10.4238/2013.August.12.7	journal	January 2013
The T-DNA integration pattern in Arabidopsis transformants is highly determined by the transformed target cell De Buck, Sylvie; Podevin, Nancy; Nolf, Jonah The Plant Journal, Vol. 60, Issue 1 https://doi.org/10.1111/j.1365-313X.2009.03942.x	journal	October 2009
LC3, a microtubule-associated protein1A/B light chain3, is involved in cytoplasmic lipid droplet formation Shibata, Masahiro; Yoshimura, Kentaro; Tamura, Hirosumi Biochemical and Biophysical Research Communications, Vol. 393, Issue 2 https://doi.org/10.1016/j.bbrc.2010.01.121	journal	March 2010
The Saccharomyces cerevisiae ICL2 Gene Encodes a Mitochondrial 2-Methylisocitrate Lyase Involved in Propionyl-Coenzyme A Metabolism Luttik, M. A. H.; Kotter, P.; Salomons, F. A. Journal of Bacteriology, Vol. 182, Issue 24 https://doi.org/10.1128/JB.182.24.7007-7013.2000	journal	December 2000
Transformation of the cucurbit powdery mildew pathogen Podosphaera xanthii by Agrobacterium tumefaciens Martínez‐Cruz, Jesús; Romero, Diego; Vicente, Antonio New Phytologist, Vol. 213, Issue 4 https://doi.org/10.1111/nph.14297	journal	November 2016
Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source Athenstaedt, Karin; Jolivet, Pascale; Boulard, Céline PROTEOMICS, Vol. 6, Issue 5, p. 1450-1459 https://doi.org/10.1002/pmic.200500339	journal	March 2006
Autophagy regulates lipid metabolism Singh, Rajat; Kaushik, Susmita; Wang, Yongjun Nature, Vol. 458, Issue 7242 https://doi.org/10.1038/nature07976	journal	April 2009
A New Fluorescence-Based Method Identifies Protein Phosphatases Regulating Lipid Droplet Metabolism Bozaquel-Morais, Bruno L.; Madeira, Juliana B.; Maya-Monteiro, Clarissa M. PLoS ONE, Vol. 5, Issue 10 https://doi.org/10.1371/journal.pone.0013692	journal	October 2010
An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica Liu, Leqian; Pan, Anny; Spofford, Caitlin Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.02.003	journal	May 2015
Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica Qiao, Kangjian; Imam Abidi, Syed Hussain; Liu, Hongjuan Metabolic Engineering, Vol. 29, p. 56-65 https://doi.org/10.1016/j.ymben.2015.02.005	journal	May 2015
Lipid Droplets Finally Get a Little R-E-S-P-E-C-T Farese, Robert V.; Walther, Tobias C. Cell, Vol. 139, Issue 5 https://doi.org/10.1016/j.cell.2009.11.005	journal	November 2009
The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica Wasylenko, Thomas M.; Ahn, Woo Suk; Stephanopoulos, Gregory Metabolic Engineering, Vol. 30 https://doi.org/10.1016/j.ymben.2015.02.007	journal	July 2015
Crossroads of PI3K and Rac pathways Campa, Carlo C.; Ciraolo, Elisa; Ghigo, Alessandra Small GTPases, Vol. 6, Issue 2 https://doi.org/10.4161/21541248.2014.989789	journal	April 2015
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants Langridge, G. C.; Phan, M. -D.; Turner, D. J. Genome Research, Vol. 19, Issue 12 https://doi.org/10.1101/gr.097097.109	journal	October 2009
Production of Lactones and Peroxisomal Beta-Oxidation in Yeasts Endrizzi, Anne; Pagot, Yves; Clainche, Annick Le Critical Reviews in Biotechnology, Vol. 16, Issue 4 https://doi.org/10.3109/07388559609147424	journal	January 1996
Cryptococcus: from environmental saprophyte to global pathogen May, Robin C.; Stone, Neil R. H.; Wiesner, Darin L. Nature Reviews Microbiology, Vol. 14, Issue 2 https://doi.org/10.1038/nrmicro.2015.6	journal	December 2015
Validating regulatory predictions from diverse bacteria with mutant fitness data Sagawa, Shiori; Price, Morgan N.; Deutschbauer, Adam M. PLOS ONE, Vol. 12, Issue 5 https://doi.org/10.1371/journal.pone.0178258	journal	May 2017
Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network Tu, Z.; Argmann, C.; Wong, K. K. Genome Research, Vol. 19, Issue 6 https://doi.org/10.1101/gr.087890.108	journal	March 2009
Engineering Rhodosporidium toruloides for the production of very long-chain monounsaturated fatty acid-rich oils Fillet, Sandy; Ronchel, Carmen; Callejo, Carla Applied Microbiology and Biotechnology, Vol. 101, Issue 19 https://doi.org/10.1007/s00253-017-8461-8	journal	August 2017
T-DNA integration patterns in co-transformed plant cells suggest that T-DNA repeats originate from co-integration of separate T-DNAs Neve, Myriam; Buck, Sylvie; Jacobs, Anni The Plant Journal, Vol. 11, Issue 1 https://doi.org/10.1046/j.1365-313X.1997.11010015.x	journal	January 1997
Inositol Deacylation of Glycosylphosphatidylinositol-anchored Proteins Is Mediated by Mammalian PGAP1 and Yeast Bst1p Tanaka, Satoshi; Maeda, Yusuke; Tashima, Yuko Journal of Biological Chemistry, Vol. 279, Issue 14 https://doi.org/10.1074/jbc.M313755200	journal	January 2004
A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors Colot, H. V.; Park, G.; Turner, G. E. Proceedings of the National Academy of Sciences, Vol. 103, Issue 27 https://doi.org/10.1073/pnas.0601456103	journal	June 2006
Involvement of the G3P shuttle and β-oxidation pathway in the control of TAG synthesis and lipid accumulation in Yarrowia lipolytica Dulermo, Thierry; Nicaud, Jean-Marc Metabolic Engineering, Vol. 13, Issue 5, p. 482-491 https://doi.org/10.1016/j.ymben.2011.05.002	journal	September 2011
Synthesis of Triacylglycerols by the Acyl-Coenzyme A:Diacyl-Glycerol Acyltransferase Dga1p in Lipid Particles of the Yeast Saccharomyces cerevisiae Sorger, D.; Daum, G. Journal of Bacteriology, Vol. 184, Issue 2 https://doi.org/10.1128/JB.184.2.519-524.2002	journal	January 2002
G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences Faul, Franz; Erdfelder, Edgar; Lang, Albert-Georg Behavior Research Methods, Vol. 39, Issue 2 https://doi.org/10.3758/BF03193146	journal	May 2007
Fiji: an open-source platform for biological-image analysis Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2019	journal	June 2012
Fatty alcohols production by oleaginous yeast Fillet, Sandy; Gibert, Jordi; Suárez, Beatriz Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 11 https://doi.org/10.1007/s10295-015-1674-x	journal	August 2015
Novel gene functions required for melanization of the human pathogen Cryptococcus neoformans : Genes for melanization of Walton, Felicia J.; Idnurm, Alexander; Heitman, Joseph Molecular Microbiology, Vol. 57, Issue 5 https://doi.org/10.1111/j.1365-2958.2005.04779.x	journal	July 2005
Engineered high content of ricinoleic acid in fission yeast Schizosaccharomyces pombe Holic, Roman; Yazawa, Hisashi; Kumagai, Hiromichi Applied Microbiology and Biotechnology, Vol. 95, Issue 1 https://doi.org/10.1007/s00253-012-3959-6	journal	February 2012
Agrobacterium-mediated transformation as a tool for functional genomics in fungi Michielse, Caroline B.; Hooykaas, Paul J. J.; van den Hondel, Cees A. M. J. J. Current Genetics, Vol. 48, Issue 1 https://doi.org/10.1007/s00294-005-0578-0	journal	May 2005
High-value oils from plants Dyer, John M.; Stymne, Sten; Green, Allan G. The Plant Journal, Vol. 54, Issue 4 https://doi.org/10.1111/j.1365-313X.2008.03430.x	journal	May 2008
Inositol Deacylation by Bst1p Is Required for the Quality Control of Glycosylphosphatidylinositol-anchored Proteins Fujita, Morihisa; Yoko-o, Takehiko; Jigami, Yoshifumi Molecular Biology of the Cell, Vol. 17, Issue 2 https://doi.org/10.1091/mbc.E05-05-0443	journal	February 2006
Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen-limited Chlamydomonas Krismer, Jasmin; Tamminen, Manu; Fontana, Simone The ISME Journal, Vol. 11, Issue 4 https://doi.org/10.1038/ismej.2016.167	journal	December 2016
Lipid Droplets and Cellular Lipid Metabolism Walther, Tobias C.; Farese, Robert V. Annual Review of Biochemistry, Vol. 81, Issue 1 https://doi.org/10.1146/annurev-biochem-061009-102430	journal	July 2012
Role of Rab GTPases in Membrane Traffic and Cell Physiology Hutagalung, Alex H.; Novick, Peter J. Physiological Reviews, Vol. 91, Issue 1 https://doi.org/10.1152/physrev.00059.2009	journal	January 2011
Balancing the fat: lipid droplets and human disease Krahmer, Natalie; Farese, Robert V.; Walther, Tobias C. EMBO Molecular Medicine, Vol. 5, Issue 7 https://doi.org/10.1002/emmm.201100671	journal	June 2013
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1069	journal	November 2013
An evaluation of new and established methods to determine T-DNA copy number and homozygosity in transgenic plants.: Estimating T-DNA copy number in transgenic plants Głowacka, Katarzyna; Kromdijk, Johannes; Leonelli, Lauriebeth Plant, Cell & Environment, Vol. 39, Issue 4 https://doi.org/10.1111/pce.12693	journal	January 2016
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
Fld1p, a functional homologue of human seipin, regulates the size of lipid droplets in yeast Fei, Weihua; Shui, Guanghou; Gaeta, Bruno The Journal of Cell Biology, Vol. 180, Issue 3 https://doi.org/10.1083/jcb.200711136	journal	February 2008
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung Gawronski, J. D.; Wong, S. M. S.; Giannoukos, G. Proceedings of the National Academy of Sciences, Vol. 106, Issue 38 https://doi.org/10.1073/pnas.0906627106	journal	September 2009
Metabolic network analysis and experimental study of lipid production in Rhodosporidium toruloides grown on single and mixed substrates Bommareddy, Rajesh Reddy; Sabra, Wael; Maheshwari, Garima Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0217-5	journal	March 2015
Engineering Rhodosporidium toruloides with a membrane transporter facilitates production and separation of carotenoids and lipids in a bi-phasic culture Lee, Jaslyn J. L.; Chen, Liwei; Cao, Bin Applied Microbiology and Biotechnology, Vol. 100, Issue 2 https://doi.org/10.1007/s00253-015-7102-3	journal	November 2015
PAT proteins, an ancient family of lipid droplet proteins that regulate cellular lipid stores Bickel, Perry E.; Tansey, John T.; Welte, Michael A. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1791, Issue 6 https://doi.org/10.1016/j.bbalip.2009.04.002	journal	June 2009
Efficient transformation of Agrobacterium tumefaciens by electroporation Mersereau, Mark; Pazour, Gregory J.; Das, Anath Gene, Vol. 90, Issue 1 https://doi.org/10.1016/0378-1119(90)90452-W	journal	May 1990
Characterization of the Drosophila Lipid Droplet Subproteome Beller, Mathias; Riedel, Dietmar; Jänsch, Lothar Molecular & Cellular Proteomics, Vol. 5, Issue 6 https://doi.org/10.1074/mcp.M600011-MCP200	journal	March 2006
Open source clustering software de Hoon, M. J. L.; Imoto, S.; Nolan, J. Bioinformatics, Vol. 20, Issue 9 https://doi.org/10.1093/bioinformatics/bth078	journal	February 2004
Sulfur Amino Acids Regulate Translational Capacity and Metabolic Homeostasis through Modulation of tRNA Thiolation Laxman, Sunil; Sutter, Benjamin M.; Wu, Xi Cell, Vol. 154, Issue 2 https://doi.org/10.1016/j.cell.2013.06.043	journal	July 2013
14-3-3 Proteins Interact with a Hybrid Prenyl-Phosphorylation Motif to Inhibit G Proteins Riou, Philippe; Kjær, Svend; Garg, Ritu Cell, Vol. 153, Issue 5 https://doi.org/10.1016/j.cell.2013.05.003	journal	May 2013
Unraveling the roles of PLIN5: linking cell biology to physiology Mason, Rachael R.; Watt, Matthew J. Trends in Endocrinology & Metabolism, Vol. 26, Issue 3 https://doi.org/10.1016/j.tem.2015.01.005	journal	March 2015
Biotechnological production of carotenoids by yeasts: an overview Mata-Gómez, Luis; Montañez, Julio; Méndez-Zavala, Alejandro Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/1475-2859-13-12	journal	January 2014
The diversity of fungal genome Mohanta, Tapan Kumar; Bae, Hanhong Biological Procedures Online, Vol. 17, Issue 1 https://doi.org/10.1186/s12575-015-0020-z	journal	April 2015
tRNA’s Wobble Decoding of the Genome: 40 Years of Modification Agris, Paul F.; Vendeix, Franck A. P.; Graham, William D. Journal of Molecular Biology, Vol. 366, Issue 1 https://doi.org/10.1016/j.jmb.2006.11.046	journal	February 2007
Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii Hassan, Karl A.; Cain, Amy K.; Huang, TaoTao mBio, Vol. 7, Issue 5 https://doi.org/10.1128/mBio.01200-16	journal	September 2016
Dynamics of the Lipid Droplet Proteome of the Oleaginous Yeast Rhodosporidium toruloides Zhu, Zhiwei; Ding, Yunfeng; Gong, Zhiwei Eukaryotic Cell, Vol. 14, Issue 3 https://doi.org/10.1128/EC.00141-14	journal	January 2015
Isolation of oleaginous yeast ( Rhodosporidium toruloides ) mutants tolerant of sugarcane bagasse hydrolysate Kitahara, Yuki; Yin, Tie; Zhao, Xuebing Bioscience, Biotechnology, and Biochemistry, Vol. 78, Issue 2 https://doi.org/10.1080/09168451.2014.882746	journal	February 2014
Functional mapping of yeast genomes by saturated transposition Michel, Agnès H.; Hatakeyama, Riko; Kimmig, Philipp eLife, Vol. 6 https://doi.org/10.7554/eLife.23570	journal	May 2017
Two T-DNA's co-transformed intoBrassica napus by a doubleAgrobacterium tumefaciens infection are mainly integrated at the same locus De Block, Marc; Debrouwer, Dirk Theoretical and Applied Genetics, Vol. 82, Issue 3 https://doi.org/10.1007/BF02190610	journal	September 1991
Cell-to-Cell Heterogeneity in Lipid Droplets Suggests a Mechanism to Reduce Lipotoxicity Herms, Albert; Bosch, Marta; Ariotti, Nicholas Current Biology, Vol. 23, Issue 15 https://doi.org/10.1016/j.cub.2013.06.032	journal	August 2013
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Li, L. Genome Research, Vol. 13, Issue 9 https://doi.org/10.1101/gr.1224503	journal	September 2003
Autophagy regulates adipose mass and differentiation in mice Singh, Rajat; Xiang, Youqing; Wang, Yongjun Journal of Clinical Investigation https://doi.org/10.1172/JCI39228	journal	October 2009
Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells Pettitt, Stephen J.; Krastev, Dragomir B.; Pemberton, Helen N. Scientific Data, Vol. 4, Issue 1 https://doi.org/10.1038/sdata.2017.20	journal	March 2017
Expanding Roles for Lipid Droplets Welte, Michael A. Current Biology, Vol. 25, Issue 11 https://doi.org/10.1016/j.cub.2015.04.004	journal	June 2015
Enhanced lipid production by Rhodosporidium toruloides using different fed-batch feeding strategies with lignocellulosic hydrolysate as the sole carbon source Fei, Qiang; O’Brien, Marykate; Nelson, Robert Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0542-x	journal	June 2016
Autophagy Regulates Cholesterol Efflux from Macrophage Foam Cells via Lysosomal Acid Lipase Ouimet, Mireille; Franklin, Vivian; Mak, Esther Cell Metabolism, Vol. 13, Issue 6 https://doi.org/10.1016/j.cmet.2011.03.023	journal	June 2011
Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes Ashrafi, Kaveh; Chang, Francesca Y.; Watts, Jennifer L. Nature, Vol. 421, Issue 6920 https://doi.org/10.1038/nature01279	journal	January 2003
Engineering Rhodosporidium toruloides for increased lipid production : Engineering Zhang, Shuyan; Skerker, Jeffrey M.; Rutter, Charles D. Biotechnology and Bioengineering, Vol. 113, Issue 5 https://doi.org/10.1002/bit.25864	journal	November 2015
Recurrent background mutations in WHI2 impair proteostasis and degradation of misfolded cytosolic proteins in Saccharomyces cerevisiae Comyn, Sophie A.; Flibotte, Stéphane; Mayor, Thibault Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-04525-8	journal	June 2017
High confidence proteomic analysis of yeast LDs identifies additional droplet proteins and reveals connections to dolichol synthesis and sterol acetylation Currie, Erin; Guo, Xiuling; Christiano, Romain Journal of Lipid Research, Vol. 55, Issue 7 https://doi.org/10.1194/jlr.M050229	journal	May 2014
Autophagy and Lipid Metabolism Coordinately Modulate Life Span in Germline-less C. elegans Lapierre, Louis R.; Gelino, Sara; Meléndez, Alicia Current Biology, Vol. 21, Issue 18 https://doi.org/10.1016/j.cub.2011.07.042	journal	September 2011
Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803 Tyo, Keith E. J.; Jin, Yong-Su; Espinoza, Freddy A. Biotechnology Progress, Vol. 25, Issue 5 https://doi.org/10.1002/btpr.228	journal	July 2009
An efficient Agrobacterium-mediated transformation method for the edible mushroom Hypsizygus marmoreus Zhang, Jin jing; Shi, Liang; Chen, Hui Microbiological Research, Vol. 169, Issue 9-10 https://doi.org/10.1016/j.micres.2014.01.004	journal	September 2014
Neutral Lipid Stores and Lipase PNPLA5 Contribute to Autophagosome Biogenesis Dupont, Nicolas; Chauhan, Santosh; Arko-Mensah, John Current Biology, Vol. 24, Issue 6 https://doi.org/10.1016/j.cub.2014.02.008	journal	March 2014
Contributions of Carnitine Acetyltransferases to Intracellular Acetyl Unit Transport in Candida albicans Strijbis, Karin; van Roermund, Carlo W.; van den Burg, Janny Journal of Biological Chemistry, Vol. 285, Issue 32 https://doi.org/10.1074/jbc.M109.094250	journal	June 2010
Fatty acid composition of leaf lipids determined after combined digestion and fatty acid methyl ester formation from fresh tissue Browse, John; McCourt, Peter J.; Somerville, Christopher R. Analytical Biochemistry, Vol. 152, Issue 1 https://doi.org/10.1016/0003-2697(86)90132-6	journal	January 1986
Saccharomyces Genome Database: the genomics resource of budding yeast Cherry, J. M.; Hong, E. L.; Amundsen, C. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1029	journal	November 2011
High-density cultivation of oleaginous yeast Rhodosporidium toruloides Y4 in fed-batch culture Li, Yonghong; Zhao, Zongbao (Kent); Bai, Fengwu Enzyme and Microbial Technology, Vol. 41, Issue 3 https://doi.org/10.1016/j.enzmictec.2007.02.008	journal	August 2007
Yeasts colonizing the leaves of fruit trees SlÁviková, Elena; Vadkertiová, Renata; Vránová, Dana Annals of Microbiology, Vol. 59, Issue 3 https://doi.org/10.1007/BF03175125	journal	September 2009
Lipid Droplets and Peroxisomes: Key Players in Cellular Lipid Homeostasis or A Matter of Fat--Store 'em Up or Burn 'em Down Kohlwein, S. D.; Veenhuis, M.; van der Klei, I. J. Genetics, Vol. 193, Issue 1, p. 1-50 https://doi.org/10.1534/genetics.112.143362	journal	December 2012

Cited By (5)

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production Tiukova, Ievgeniia A.; Brandenburg, Jule; Blomqvist, Johanna Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1478-8	journal	June 2019
Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880 Jagtap, Sujit Sadashiv; Bedekar, Ashwini Ashok; Liu, Jing-Jing Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1586-5	journal	October 2019
Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover McLoughlin, Fionn; Augustine, Robert C.; Marshall, Richard S. Nature Plants, Vol. 4, Issue 12 https://doi.org/10.1038/s41477-018-0299-2	journal	November 2018
RNA interference in the oleaginous yeast Rhodosporidium toruloides Liu, Xiangjian; Zhang, Yue; Liu, Hongdi FEMS Yeast Research, Vol. 19, Issue 3 https://doi.org/10.1093/femsyr/foz031	journal	April 2019
Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans -acting effects influencing species-dependent essential genes Sanchez, Monica R.; Payen, Celia; Cheong, Frances Genome Research, Vol. 29, Issue 3 https://doi.org/10.1101/gr.232330.117	journal	January 2019

Similar Records

Development of the Oleaginous Yeast Rhodosporidium Toruloides as a New Model Organism for a Systems-Level Analysis of Lipid Productivity

Technical Report · Wed Nov 29 00:00:00 EST 2017 · OSTI ID:1466439

Brem, Rachel; Coradetti, Samuel; Skerker, Jeffrey; +3 more

Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts

Journal Article · Thu Aug 03 00:00:00 EDT 2023 · Microbial Cell Factories · OSTI ID:1466439

Coradetti, Samuel T.; Adamczyk, Paul A.; Liu, Di; +9 more

Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880

Journal Article · Fri Oct 18 00:00:00 EDT 2019 · Biotechnology for Biofuels · OSTI ID:1466439

Jagtap, Sujit Sadashiv; Bedekar, Ashwini Ashok; Liu, Jing-Jing; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Citation Formats

References (198)

Cited By (5)

Similar Records

Related Subjects