Johan Paulsson
Harvard University, 1350 Massachusetts Ave, Cambridge, Ma 02138
Abstract: Project 4 Optical monitoring of post-translational modification of proteins in vivo (Thorn)(#27) We developed tools to study protein modification and interactions using fluorescence resonance energy transfer (FRET) microscopy. The main effort was to detect protein-protein interactions in wVo12 and use these data to predict the structure of large protein complexes. We developed methods to produce precise and reproducible FRET data from yeast, and used them to derive a low-resolution structure for the septin complex (which is required for cell division from yeast to mammals). With Michael Laub (project 7) we found interactions between two-component signaling proteins, the predominant participants in post-translational regulation in bacteria, and collaborated with Daugherty and his colleagues to develop high throughput, quantitative, FRETbased methods to identify protein interactions13. Kurt Thorn, the PI, was a Bauer Fellow and is now Director of the Nikon Imaging Center at UCSF. New project 4 Tandem repeats in genes hyper-variable modules for adaptation? (Verstrepen) (#28-30) We tested the hypothesis35 that in budding yeast, tandemly repeated sequences are hyper-variable genetic modules, whose variability helps organisms adapt to changing environments. Most sequenced genomes contain tandem repeats; some of these occur in coding sequences, where recombination can alter the number of peptide repeats in translated proteins. We have, 1) developed an algorithm36 (http//hulsweb1.cgr.harvard.edu/SERV/) to find and annotate repeats, predict whether they vary in number, associate them with other information (expression level, overlap with transcription factor binding sites, nucleosome sites etc.), and deposit this data in a publicly accessible database (http//hulsweb1.cgr.harvard.edu/TandemRepeat/) that allows rapid and automated comparison to existing databases; 2) generated yeast strains with different numbers of repeats in the promoters and open reading frames of selected genes, and studied the phenotypic consequences of this variation (ongoing); 3) studied tandem repeats in Arabidopsis thaliana and Oryza sativa (with C. Queitsch, new project 7). We have used two sequenced genomes to find all ORFs containing variable numbers of repeats, selected 150 genes, characterized their variation across twelve A. thaliana isolates from different locations, and found more than 70 genes that show variation in repeat number between different isolates. Kevin Verstrepen became a Bauer Fellow in 2005 and joined the CMB in 2006
Keywords: Arabidopsis thaliana; Bacteria; Binding Sites; Cell division; Code; Coding System; Combining Site; Complex; Cress, Mouse-ear; DNA Recombination; DNA recombination (naturally occurring); Data; Data Banks; Data Bases; Databank, Electronic; Databanks; Database, Electronic; Databases; Deposit; Deposition; Endomycetales; Environment; FRET; Fluorescence Resonance Energy Transfer; Genes; Genetic; Genetic Recombination; Image; Location; Mammalia; Mammals; Mammals, General; Methods; Microscopy; Monitor; Mouse-ear Cress; Nucleosomes; ORFs; Open Reading Frames; Optics; Organism; Oryza sativa; Participant; Peptides; Post-Translational Modifications; Post-Translational Protein Processing; Post-Translational Regulation; Posttranslational Modifications; Posttranslational Regulation; Promoter; Promoters (Genetics); Promotor; Promotor (Genetics); Protein Coding Region; Protein Modification; Protein Modification, Post-Translational; Protein Processing, Post-Translational; Protein Processing, Posttranslational; Protein/Amino Acid Biochemistry, Post-Translational Modification; Proteins; Reactive Site; Recombination; Recombination, Genetic; Resolution; Saccharomycetales; Signaling Protein; Site; Structure; Tandem Repeat Sequences; Tandem Repeats; Testing; Translating; Translatings; Variant; Variation; Yeast, Budding; Yeasts; clinical data repository; clinical data warehouse; data repository; gene product; genome sequencing; imaging; in vivo; language translation; living system; protein complex; protein protein interaction; relational database; tool; transcription factor
Budget start date: 1-SEP-2010
Budget end date: 31-AUG-2011
5P50GM068763-08_0004 (2010): $124739
Sponsored Links Excellgen http://Excellgen.com
Johan Paulsson, Assistant Professor
Harvard University, 1350 Massachusetts Ave, Cambridge, Ma 02138
Abstract: Project 4 Optical monitoring of post-translational modification of proteins in vivo (Thorn)(#27) We developed tools to study protein modification and interactions using fluorescence resonance energy transfer (FRET) microscopy. The main effort was to detect protein-protein interactions in wVo12 and use these data to predict the structure of large protein complexes. We developed methods to produce precise and reproducible FRET data from yeast, and used them to derive a low-resolution structure for the septin complex (which is required for cell division from yeast to mammals). With Michael Laub (project 7) we found interactions between two-component signaling proteins, the predominant participants in post-translational regulation in bacteria, and collaborated with Daugherty and his colleagues to develop high throughput, quantitative, FRETbased methods to identify protein interactions13. Kurt Thorn, the PI, was a Bauer Fellow and is now Director of the Nikon Imaging Center at UCSF. New project 4 Tandem repeats in genes hyper-variable modules for adaptation? (Verstrepen) (#28-30) We tested the hypothesis35 that in budding yeast, tandemly repeated sequences are hyper-variable genetic modules, whose variability helps organisms adapt to changing environments. Most sequenced genomes contain tandem repeats; some of these occur in coding sequences, where recombination can alter the number of peptide repeats in translated proteins. We have, 1) developed an algorithm36 (http//hulsweb1.cgr.harvard.edu/SERV/) to find and annotate repeats, predict whether they vary in number, associate them with other information (expression level, overlap with transcription factor binding sites, nucleosome sites etc.), and deposit this data in a publicly accessible database (http//hulsweb1.cgr.harvard.edu/TandemRepeat/) that allows rapid and automated comparison to existing databases; 2) generated yeast strains with different numbers of repeats in the promoters and open reading frames of selected genes, and studied the phenotypic consequences of this variation (ongoing); 3) studied tandem repeats in Arabidopsis thaliana and Oryza sativa (with C. Queitsch, new project 7). We have used two sequenced genomes to find all ORFs containing variable numbers of repeats, selected 150 genes, characterized their variation across twelve A. thaliana isolates from different locations, and found more than 70 genes that show variation in repeat number between different isolates. Kevin Verstrepen became a Bauer Fellow in 2005 and joined the CMB in 2006
Keywords: Arabidopsis thaliana; Bacteria; Binding Sites; Biodiversity; Biological Diversity; Cell division; Code; Coding System; Combining Site; Complex; Cress, Mouse-ear; DNA Recombination; DNA recombination (naturally occurring); Data; Data Banks; Data Bases; Databank, Electronic; Databanks; Database, Electronic; Databases; Deposit; Deposition; Endomycetales; Environment; FRET; Fluorescence Resonance Energy Transfer; Generations; Genes; Genetic; Genetic Recombination; Image; Location; Mammalia; Mammals; Mammals, General; Methods; Microscopy; Monitor; Mouse-ear Cress; Nucleosomes; ORFs; Open Reading Frames; Optics; Organism; Oryza sativa; Participant; Peptides; Post-Translational Modifications; Post-Translational Protein Processing; Post-Translational Regulation; Posttranslational Modifications; Posttranslational Regulation; Promoter; Promoters (Genetics); Promotor; Promotor (Genetics); Protein Coding Region; Protein Modification; Protein Modification, Post-Translational; Protein Processing, Post-Translational; Protein Processing, Posttranslational; Protein/Amino Acid Biochemistry, Post-Translational Modification; Proteins; Reactive Site; Recombination; Recombination, Genetic; Resolution; Saccharomycetales; Signaling Protein; Site; Structure; Tandem Repeat Sequences; Tandem Repeats; Testing; Translating; Translatings; Variant; Variation; Yeast, Budding; Yeasts; clinical data repository; clinical data warehouse; data repository; gene product; genome sequencing; imaging; in vivo; language translation; living system; protein complex; protein protein interaction; relational database; tool; transcription factor
Budget start date: 1-SEP-2009
Budget end date: 31-AUG-2010
PFA/PA: RFA-GM-08-004
5P50GM068763-07_0004 (2009): $126000
Grants awarded to Johan Paulsson
Johan Paulsson
Harvard University (medical School)
Project start date: 2008-04-01
Project end date: 2013-02-28
LIMITS AND TRADE-OFFS OF FEEDBACK CONTROL
Johan Paulsson, Assistant Professor
Harvard University (medical School), Medical School Campus, Boston, Ma 02115
Grant 5R01GM081563-03 from National Institute Of General Medical Sciences
Keywords: Address; Assay; Autoregulation; Bacteria; Bacteria sigma factor KatF protein; Bioassay; Biochemical; Biologic Assays; Biological; Biological Assay; Biological Function; Biological Models; Biological Process; Biology; Body Temperature; Cells; Complex; Control Groups; Disadvantaged; Disease; Disorder; Drug resistance; E coli; Engineering; Engineerings; Escherichia coli; Event; Extinction; Extinction (Psychology); FLR; Failure (biologic function); Feedback; Frustration; Gene Expression; Generalized Growth; Goals; Growth; Half-Life; Half-Lifes; Health; Homeostasis; Human; Human, General; Individual; KatF protein, Bacteria; Kinetic; Kinetics; Laws; Literature; Man (Taxonomy); Man, Modern; Measurement; Measures; Memory; Methods; Microscopic; Model System; Modeling; Models, Biologic; Molecular; Noise; Phase; Physics; Physiological Homeostasis; Plasmids; Probability Theory; Process; Promoter; Promoters (Genetics); Promotor; Promotor (Genetics); Property; Property, LOINC Axis 2; Proteins; RpoS; Sigma Element; Sigma Factor; Sigma Initiation Factor; Sigma Subunit; Source; Stress; System; System, LOINC Axis 4; Testing; Time; Tissue Growth; Variant; Variation; Virulence; Work; base; behavioral extinction; biological adaptation to stress; biological systems; design; designing; disease/disorder; drug resistant; experiment; experimental research; experimental study; failure; gene product; improved; inhibitor; inhibitor/antagonist; novel; ontogeny; reaction; crisis; research study; resistance to Drug; resistant to Drug; response; rpoS protein, Bacteria; sigma factor 38 protein, Bacteria; sigma factor KatF protein, Bacteria; sigma factor S protein, Bacteria; sigma(38) protein, Bacteria; sigma(S) protein, Bacteria; simulation; stress response; stress; reaction; theories; tool
Project start date: 2008-04-01
Project end date: 2013-02-28
Budget start date: 1-MAR-2010
Budget end date: 28-FEB-2011
PFA/PA: PA-07-070
5R01GM081563-03 (2010): $335610