Sandy Johnson, PHD
Professor
Microbiology and Immunology
School of Medicine

Websites

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• Johnson Lab at UCSF (johnsonlab.ucsf.edu)

Grants and Projects

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• Cell Biology, Genetics, and Biochemistry Training Grant, NIH, 1979-2021
• The transcriptional circuitry controlling biofilm development in Candida albicans, NIH, 2009-2020
• Mechanism of Yeast Transcriptional Regulators, NIH, 1986-2019
• Regulatory Circuits and Virulence in Candida albicans, NIH, 2001-2016
• Comprehensive Biology: Exploiting the Yeast Genome, NIH, 1996-2016
• Chromosome loss in the fungal pathogen C. albicans, NIH, 2004-2010
• Molecular Biology of Eukaryotic Cells and Viruses, NIH, 1976-2006
• Transcriptional Regulation in Growth,diff,development, NIH, 2000-2001
• Chromosome Position Effects on Gene Expression in Yeast, NIH, 1995-2000
• Dna-protein Interactions in Dna-replication Control, NIH, 1976-1996
• Meiotic Pairing of Chromosomes in Yeast, NIH, 1991-1994

Publications (105)

Top publication keywords:
Transcription, GeneticAscomycotaCandida albicansEvolution, MolecularCandidiasisFungiTranscription FactorsFungal ProteinsSaccharomyces cerevisiae ProteinsSaccharomyces cerevisiaeGene Expression Regulation, FungalGene Regulatory NetworksGenes, Mating Type, FungalBiofilmsGenes, Fungal

• Shared metabolism between a bacterial and fungal species that reside in the human gut.
  Proceedings of the National Academy of Sciences of the United States of America 2025 Gause H, Johnson AD
• Variation in transcription regulator expression underlies differences in white-opaque switching between the SC5314 reference strain and the majority of Candida albicans clinical isolates.
  Genetics 2023 Lohse MB, Ziv N, Johnson AD
• Broad susceptibility of Candida auris strains to 8-hydroxyquinolines and mechanisms of resistance.
  mBio 2023 Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD
• Ancient transcriptional regulators can easily evolve new pair-wise cooperativity.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Fowler KR, Leon F, Johnson AD
• Evolution of a new form of haploid-specific gene regulation appearing in a limited clade of ascomycete yeast species.
  Genetics 2023 Del Frate F, Garber ME, Johnson AD

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• Cell-type memory in a single-cell eukaryote requires the continuous presence of a specific transcription regulator.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Lee CD, Ziv N, Johnson AD
• Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance.
  bioRxiv : the preprint server for biology 2023 Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD
• Farnesol and phosphorylation of the transcriptional regulator Efg1 affect Candida albicans white-opaque switching rates.
  PloS one 2023 Brenes LR, Johnson AD, Lohse MB
• Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.
  Microbiome 2021 West PT, Peters SL, Olm MR, Yu FB, Gause H, Lou YC, Firek BA, Baker R, Johnson AD, Morowitz MJ, Hettich RL, Banfield JF
• Evolution of the complex transcription network controlling biofilm formation in Candida species.
  eLife 2021 Mancera E, Nocedal I, Hammel S, Gulati M, Mitchell KF, Andes DR, Nobile CJ, Butler G, Johnson AD
• Lineage-specific selection and the evolution of virulence in the Candida clade.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Singh-Babak SD, Babak T, Fraser HB, Johnson AD
• A Screen for Small Molecules to Target Candida albicans Biofilms.
  Journal of fungi (Basel, Switzerland) 2020 Lohse MB, Ennis CL, Hartooni N, Johnson AD, Nobile CJ
• An Opaque Cell-Specific Expression Program of Secreted Proteases and Transporters Allows Cell-Type Cooperation in Candida albicans.
  Genetics 2020 Lohse MB, Brenes LR, Ziv N, Winter MB, Craik CS, Johnson AD
• A Set of Diverse Genes Influence the Frequency of White-Opaque Switching in Candida albicans.
  G3 (Bethesda, Md.) 2020 Brenes LR, Lohse MB, Hartooni N, Johnson AD
• Combination of Antifungal Drugs and Protease Inhibitors Prevent Candida albicans Biofilm Formation and Disrupt Mature Biofilms.
  Frontiers in microbiology 2020 Lohse MB, Gulati M, Craik CS, Johnson AD, Nobile CJ
• A Selective Serotonin Reuptake Inhibitor, a Proton Pump Inhibitor, and Two Calcium Channel Blockers Inhibit Candida albicans Biofilms.
  Microorganisms 2020 Nobile CJ, Ennis CL, Hartooni N, Johnson AD, Lohse MB
• Corrigendum: Genetic Modification of Closely Related Candida Species.
  Frontiers in microbiology 2020 Mancera E, Frazer C, Porman AM, Ruiz-Castro S, Johnson AD, Bennett RJ
• Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit.
  Science (New York, N.Y.) 2020 Britton CS, Sorrells TR, Johnson AD
• A population shift between two heritable cell types of the pathogen Candida albicans is based both on switching and selective proliferation.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Dalal CK, Zuleta IA, Lohse MB, Zordan RE, El-Samad H, Johnson AD
• Candida albicans white and opaque cells exhibit distinct spectra of organ colonization in mouse models of infection.
  PloS one 2019 Takagi J, Singh-Babak SD, Lohse MB, Dalal CK, Johnson AD
• Genetic Modification of Closely Related Candida Species.
  Frontiers in microbiology 2019 Mancera E, Frazer C, Porman AM, Ruiz-Castro S, Johnson AD, Bennett RJ
• Intrinsic cooperativity potentiates parallel cis-regulatory evolution.
  eLife 2018 Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle JT, Weil PA, Johnson AD
• The rewiring of transcription circuits in evolution.
  Current opinion in genetics & development 2017 Johnson AD
• Development and regulation of single- and multi-species Candida albicans biofilms.
  Nature reviews. Microbiology 2017 Lohse MB, Gulati M, Johnson AD, Nobile CJ
• Sensitivity of White and Opaque Candida albicans Cells to Antifungal Drugs.
  Antimicrobial agents and chemotherapy 2017 Craik VB, Johnson AD, Lohse MB
• How transcription circuits explore alternative architectures while maintaining overall circuit output.
  Genes & development 2017 Dalal CK, Johnson AD
• Assessment and Optimizations of Candida albicans In Vitro Biofilm Assays.
  Antimicrobial agents and chemotherapy 2017 Lohse MB, Gulati M, Valle Arevalo A, Fishburn A, Johnson AD, Nobile CJ
• Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator.
  eLife 2017 Nocedal I, Mancera E, Johnson AD
• Sex differences in vascular dysfunction and cardiovascular outcomes: The cardiac, endothelial function, and arterial stiffness in ESRD (CERES) study.
  Hemodialysis international. International Symposium on Home Hemodialysis 2017 Guajardo I, Ayer A, Johnson AD, Ganz P, Mills C, Donovan C, Scherzer R, Shah SJ, Peralta CA, Dubin RF
• Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells.
  mBio 2016 Ene IV, Lohse MB, Vladu AV, Morschhäuser J, Johnson AD, Bennett RJ
• Global Identification of Biofilm-Specific Proteolysis in Candida albicans.
  mBio 2016 Winter MB, Salcedo EC, Lohse MB, Hartooni N, Gulati M, Sanchez H, Takagi J, Hube B, Andes DR, Johnson AD, Craik CS, Nobile CJ
• Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression.
  eLife 2016 Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD
• Systematic Genetic Screen for Transcriptional Regulators of the Candida albicans White-Opaque Switch.
  Genetics 2016 Lohse MB, Ene IV, Craik VB, Hernday AD, Mancera E, Morschhäuser J, Bennett RJ, Johnson AD
• Ssn6 Defines a New Level of Regulation of White-Opaque Switching in Candida albicans and Is Required For the Stochasticity of the Switch.
  mBio 2016 Hernday AD, Lohse MB, Nobile CJ, Noiman L, Laksana CN, Johnson AD
• Identification and Characterization of Wor4, a New Transcriptional Regulator of White-Opaque Switching.
  G3 (Bethesda, Md.) 2016 Lohse MB, Johnson AD
• How Transcription Networks Evolve and Produce Biological Novelty.
  Cold Spring Harbor symposia on quantitative biology 2015 Nocedal I, Johnson AD
• N-Acetylglucosamine-Induced Cell Death in Candida albicans and Its Implications for Adaptive Mechanisms of Nutrient Sensing in Yeasts.
  mBio 2015 Du H, Guan G, Li X, Gulati M, Tao L, Cao C, Johnson AD, Nobile CJ, Huang G
• Intersecting transcription networks constrain gene regulatory evolution.
  Nature 2015 Sorrells TR, Booth LN, Tuch BB, Johnson AD
• Making sense of transcription networks.
  Cell 2015 Sorrells TR, Johnson AD
• Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome.
  Proceedings of the National Academy of Sciences of the United States of America 2015 O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ
• An expanded regulatory network temporally controls Candida albicans biofilm formation.
  Molecular microbiology 2015 Fox EP, Bui CK, Nett JE, Hartooni N, Mui MC, Andes DR, Nobile CJ, Johnson AD
• Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis.
  G3 (Bethesda, Md.) 2015 Mancera E, Porman AM, Cuomo CA, Bennett RJ, Johnson AD
• Candida albicans Biofilms and Human Disease.
  Annual review of microbiology 2015 Nobile CJ, Johnson AD
• Mucins suppress virulence traits of Candida albicans.
  mBio 2014 Kavanaugh NL, Zhang AQ, Nobile CJ, Johnson AD, Ribbeck K
• Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity.
  eLife 2014 Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ
• Anaerobic bacteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures.
  Current biology : CB 2014 Fox EP, Cowley ES, Nobile CJ, Hartooni N, Newman DK, Johnson AD
• Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Lohse MB, Rosenberg OS, Cox JS, Stroud RM, Finer-Moore JS, Johnson AD
• A histone deacetylase complex mediates biofilm dispersal and drug resistance in Candida albicans.
  mBio 2014 Nobile CJ, Fox EP, Hartooni N, Mitchell KF, Hnisz D, Andes DR, Kuchler K, Johnson AD
• How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes.
  Genes & development 2014 Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD
• Regulatory circuits that enable proliferation of the fungus Candida albicans in a mammalian host.
  PLoS pathogens 2013 Pérez JC, Johnson AD
• Following gene duplication, paralog interference constrains transcriptional circuit evolution.
  Science (New York, N.Y.) 2013 Baker CR, Hanson-Smith V, Johnson AD
• Structure of the transcriptional network controlling white-opaque switching in Candida albicans.
  Molecular microbiology 2013 Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD
• Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD
• Genetic control of conventional and pheromone-stimulated biofilm formation in Candida albicans.
  PLoS pathogens 2013 Lin CH, Kabrawala S, Fox EP, Nobile CJ, Johnson AD, Bennett RJ
• White-opaque switching in natural MTLa/α isolates of Candida albicans: evolutionary implications for roles in host adaptation, pathogenesis, and sex.
  PLoS biology 2013 Xie J, Tao L, Nobile CJ, Tong Y, Guan G, Sun Y, Cao C, Hernday AD, Johnson AD, Zhang L, Bai FY, Huang G
• Candida albicans commensalism and pathogenicity are intertwined traits directed by a tightly knit transcriptional regulatory circuit.
  PLoS biology 2013 Pérez JC, Kumamoto CA, Johnson AD
• Candida albicans white and opaque cells undergo distinct programs of filamentous growth.
  PLoS pathogens 2013 Si H, Hernday AD, Hirakawa MP, Johnson AD, Bennett RJ
• Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification.
  Cell 2012 Baker CR, Booth LN, Sorrells TR, Johnson AD
• A recently evolved transcriptional network controls biofilm development in Candida albicans.
  Cell 2012 Nobile CJ, Fox EP, Nett JE, Sorrells TR, Mitrovich QM, Hernday AD, Tuch BB, Andes DR, Johnson AD
• A conserved transcriptional regulator governs fungal morphology in widely diverged species.
  Genetics 2011 Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD
• Extensive DNA-binding specificity divergence of a conserved transcription regulator.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Baker CR, Tuch BB, Johnson AD
• Intercalation of a new tier of transcription regulation into an ancient circuit.
  Nature 2010 Booth LN, Tuch BB, Johnson AD
• Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss.
  Science (New York, N.Y.) 2010 Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD
• Evolution of transcription networks--lessons from yeasts.
  Current biology : CB 2010 Li H, Johnson AD
• Temporal anatomy of an epigenetic switch in cell programming: the white-opaque transition of C. albicans.
  Molecular microbiology 2010 Lohse MB, Johnson AD
• The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation.
  PLoS genetics 2010 Tuch BB, Mitrovich QM, Homann OR, Hernday AD, Monighetti CK, De La Vega FM, Johnson AD
• Distinct class of DNA-binding domains is exemplified by a master regulator of phenotypic switching in Candida albicans.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Lohse MB, Zordan RE, Cain CW, Johnson AD
• Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity.
  Nature genetics 2010 Noble SM, French S, Kohn LA, Chen V, Johnson AD
• MochiView: versatile software for genome browsing and DNA motif analysis.
  BMC biology 2010 Homann OR, Johnson AD
• Genetics and molecular biology in Candida albicans.
  Methods in enzymology 2010 Hernday AD, Noble SM, Mitrovich QM, Johnson AD
• A phenotypic profile of the Candida albicans regulatory network.
  PLoS genetics 2009 Homann OR, Dea J, Noble SM, Johnson AD
• White-opaque switching in Candida albicans.
  Current opinion in microbiology 2009 Lohse MB, Johnson AD
• An RNA transport system in Candida albicans regulates hyphal morphology and invasive growth.
  PLoS genetics 2009 Elson SL, Noble SM, Solis NV, Filler SG, Johnson AD
• Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.
  Science (New York, N.Y.) 2009 Holt LJ, Tuch BB, Villén J, Johnson AD, Gygi SP, Morgan DO
• Biofilm matrix regulation by Candida albicans Zap1.
  PLoS biology 2009 Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault JS, Nantel A, Andes DR, Johnson AD, Mitchell AP
• Phagocytosis of Candida albicans by RNAi-treated Drosophila S2 cells.
  Methods in molecular biology (Clifton, N.J.) 2009 Stroschein-Stevenson SL, Foley E, O'Farrell PH, Johnson AD
• The parasexual cycle in Candida albicans provides an alternative pathway to meiosis for the formation of recombinant strains.
  PLoS biology 2008 Forche A, Alby K, Schaefer D, Johnson AD, Berman J, Bennett RJ
• Evolution of eukaryotic transcription circuits.
  Science (New York, N.Y.) 2008 Tuch BB, Li H, Johnson AD
• The evolution of combinatorial gene regulation in fungi.
  PLoS biology 2008 Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD
• Differential phagocytosis of white versus opaque Candida albicans by Drosophila and mouse phagocytes.
  PloS one 2008 Lohse MB, Johnson AD
• Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans.
  PLoS biology 2007 Zordan RE, Miller MG, Galgoczy DJ, Tuch BB, Johnson AD
• Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans.
  Genome research 2007 Mitrovich QM, Tuch BB, Guthrie C, Johnson AD
• Genetics of Candida albicans, a diploid human fungal pathogen.
  Annual review of genetics 2007 Noble SM, Johnson AD
• The role of nutrient regulation and the Gpa2 protein in the mating pheromone response of C. albicans.
  Molecular microbiology 2006 Bennett RJ, Johnson AD
• Evolution of alternative transcriptional circuits with identical logic.
  Nature 2006 Tsong AE, Tuch BB, Li H, Johnson AD
• Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop.
  Proceedings of the National Academy of Sciences of the United States of America 2006 Zordan RE, Galgoczy DJ, Johnson AD
• Identification of Drosophila gene products required for phagocytosis of Candida albicans.
  PLoS biology 2005 Stroschein-Stevenson SL, Foley E, O'Farrell PH, Johnson AD
• Transcriptional response of Candida albicans to nitric oxide and the role of the YHB1 gene in nitrosative stress and virulence.
  Molecular biology of the cell 2005 Hromatka BS, Noble SM, Johnson AD
• A human-curated annotation of the Candida albicans genome.
  PLoS genetics 2005 Braun BR, van Het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, …
• Induction of the Candida albicans filamentous growth program by relief of transcriptional repression: a genome-wide analysis.
  Molecular biology of the cell 2005 Kadosh D, Johnson AD
• Genome-wide analysis of the functions of a conserved surface on the corepressor Tup1.
  Molecular biology of the cell 2005 Green SR, Johnson AD
• Nuclear fusion occurs during mating in Candida albicans and is dependent on the KAR3 gene.
  Molecular microbiology 2005 Bennett RJ, Miller MG, Chua PR, Maxon ME, Johnson AD
• Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen Candida albicans.
  Eukaryotic cell 2005 Noble SM, Johnson AD
• Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae.
  Proceedings of the National Academy of Sciences of the United States of America 2004 Galgoczy DJ, Cassidy-Stone A, Llinás M, O'Rourke SM, Herskowitz I, DeRisi JL, Johnson AD
• Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae.
  Molecular biology of the cell 2004 Green SR, Johnson AD
• Evolution of a combinatorial transcriptional circuit: a case study in yeasts.
  Cell 2003 Tsong AE, Miller MG, Raisner RM, Johnson AD
• Identification and characterization of a Candida albicans mating pheromone.
  Molecular and cellular biology 2003 Bennett RJ, Uhl MA, Miller MG, Johnson AD
• The biology of mating in Candida albicans.
  Nature reviews. Microbiology 2003 Johnson A
• Haploinsufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen C.albicans.
  The EMBO journal 2003 Uhl MA, Biery M, Craig N, Johnson AD
• Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains.
  The EMBO journal 2003 Bennett RJ, Johnson AD
• Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes.
  The EMBO journal 2003 Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM
• Ash1 protein, an asymmetrically localized transcriptional regulator, controls filamentous growth and virulence of Candida albicans.
  Molecular and cellular biology 2002 Inglis DO, Johnson AD
• In Candida albicans, white-opaque switchers are homozygous for mating type.
  Genetics 2002 Lockhart SR, Pujol C, Daniels KJ, Miller MG, Johnson AD, Pfaller MA, Soll DR
• White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating.
  Cell 2002 Miller MG, Johnson AD
• Development of Streptococcus thermophilus lacZ as a reporter gene for Candida albicans.
  Microbiology (Reading, England) 2001 Uhl MA, Johnson AD