Mechanism and Regulation of Prokaryotic Transcription
June 25-30, 2017
Saxtons River, VT
Co-Organizers:
Deborah Hinton
NIDDK, National Institutes of Health
Bethesda, MD
Elizabeth Campbell
The Rockefeller University
New York, NY
Eduardo Groisman
Yale School of Medicine
New Haven, CT
Sunday,
June 25, 2017
4:00PM – 9:00PM
Conference Registration
6:00PM – 7:00PM
FASEB Opening Reception
7:00PM – 8:00PM
Dinner
8:15PM – 8:45PM
Keynote Speaker: Sankar Adhya, National Cancer Institute,
Bethesda, MD, USA. “Bacterial Nucleoid Condensation”
8:45PM – 9:15PM
Keynote Speaker: Joan Conaway, Stowers Institute for
Medical Research, Kansas City, MO, USA. “Regulators of
RNA polymerase II transcription”
9:15PM – 9:50PM
Lightning Round of Posters to be presented on Monday
and Tuesday (Odd-numbered abstracts)
Monday,
June 26, 2017
7:30AM – 9:00AM
Breakfast
Session 1:
9:00AM – 12:00PM
RNA Polymerase Structural Biology
Chair, Richard Ebright, Waksman Institute, Rutgers
University, Piscataway, NJ, USA.
9:00AM – 9:15AM
Welcome from FASEB and Organizers
9:15AM - 9:40AM
Seth Darst: The Rockefeller University, New York, NY, USA.
“Structural Biology of Bacterial Transcription: Electron
Microscopy to X-ray Crystallography and Back Again”
9:40AM –10:05AM
Richard Ebright: Waksman Institute, Rutgers University,
Piscataway, NJ, USA. "Structural biology and structural
biophysics of transcription”
10:05AM – 10:20AM
Vadim Molodtsov: The Pennsylvania State University,
University Park, PA, USA. “X-ray crystal structures of
Escherichia coli RNA polymerase in complex with the
secondary channel binding transcription factors reveal the
mechanisms of transcription repression by ppGpp-dependent
transcription factor DksA and ppGpp-independent
transcription factor TraR” Poster Abstract 1
10:20AM - 10:35AM
Michael Lawson: University of California, Berkeley, CA,
USA. “ Mechanism for the regulated control of transcription
termination by a universal adapter protein” Poster Abstract
11
10:35AM – 10:55AM
FASEB Sponsored Coffee Break
10:55AM – 11:20AM
Stefan Knauer: Universität Bayreuth, Bayreuth, DE.
“Deciphering bacterial transcription by NMR”
11:20AM – 11:45AM
Finn Werner: University College London, UK. “Mechanisms
of Archaeal Transcription - the cleavage factor paralogue
TFS4 is a potent RNA polymerase inhibitor”
11:45AM – 12:00PM
Haruhiko Ehara: RIKEN, Center for Life Science
Technologies, JA. “ Structural elucidation of eukaryotic RNA
polymerase II “holo”-elongation complex” Poster Abstract 19
12:00PM – 1:30PM
Lunch
1:30PM – 2:30PM
Meet the Experts:
Finn Werner, University College London
Dick Brennan, Duke University School of Medicine
Irina Artsimovitch, Ohio State University
Sankar Adhya, National Cancer Institute
Joan Conaway, Stowers Institute for Medical Research
Wilma Ross, University of Wisconsin-Madison
Free Afternoon
4:00PM – 6:00PM
Poster Session 1 (Odd-numbered abstracts)
6:00PM – 7:00PM
Dinner
Session 2:
7:00PM – 9:50PM
Initiation and Promoter Escape
Chair, Wilma Ross, University of Wisconsin, Madison, WI,
USA.
7:00PM - 7:25PM
Wilma Ross: University of Wisconsin, Madison, WI, USA.
“Regulation of transcription initiation by ppGpp and RNAP
secondary channel-binding proteins”
7:25PM – 7:50PM
Achillefs Kapanidis: University of Oxford, UK. “Pausing in
initial transcription: mechanism, kinetics, and sequence
dependence”
7:50PM – 8:15PM
Tomasz Heyduk: Saint Louis University School of Medicine,
St. Louis, MO, USA. “DNA template sequence control of
promoter escape”
8:15PM – 8:30PM
Coffee Break
8:30PM – 8:55PM
Dmitry Temiakov: Rowan University School of Osteopathic
Medicine, Stratford, NJ, USA. “Mechanisms of transcription
initiation and elongation in human mitochondria”
8:55PM – 9:10PM
Hauke Hillen: Max-Planck-Institute, Goettingen, DE
“Structural basis of mitochondrial transcription initiation”
Poster Abstract 5
9:10PM – 9:35PM
Katsu Murakami: The Pennsylvania State University,
University Park, PA, USA. “X-ray crystal structure of the
reiterative transcription complex reveals a new RNA
extension pathway”
9:35PM – 9:50PM
Sergei Borukhov: Rowan University, Stratford, NJ, USA.
“Promoter trapping of E. coli RNA polymerase under
hyperosmotic stress and the role of transcript cleavage
factors GreA and GreB” Poster Abstract 18
Tuesday,
June 27, 2017
7:30AM – 9:00AM
Breakfast
Session 3
9:00AM – 12:00PM
Elongation and Termination
Chair, Paul Babitzke: The Pennsylvania State University,
University Park, PA, USA.
9:00AM - 9:25AM
Paul Babitzke: The Pennsylvania State University, University
Park, PA, USA. "NusG-stimulated pausing and the control of
gene expression”
9:25AM –9:50AM
Bob Landick: University of Wisconsin, Madison, WI, USA.
“Pausing regulates RNA polymerase during transcription of
bacterial chromosomes”
9:50AM – 10:05AM
Georgiy Belogurov: University of Turku, FI. “Two-step
translocation mechanism of multisubunit RNA polymerase”
Poster Abstract 13
10:05AM – 10:20AM
Tatiana Mishanina: University of Wisconsin–Madison, WI
USA. “ The trigger loop of RNA polymerase is a positional,
not acid-base, catalyst: A unifying model of transcription and
proofreading” Poster Abstract 9
10:20AM – 10:45AM
FASEB Sponsored Coffee Break and Group Photo
10:45AM – 11:10AM
Irina Artsimovitch: Ohio State University, Columbus, OH,
USA. “Flipping states: a few key residues decide the winning
conformation”
11:10AM – 11:35AM
Markus Wahl: Freie Universität Berlin, Berlin, DE. “Structural
basis of processive transcription antitermination”
11:35AM – 12:00PM
Nickolay Zenkin: Newcastle University, Newcastle upon
Tyne, UK. “RNA-hairpin-dependent termination by eukaryotic
RNA polymerase I”
12:00PM – 1:30PM
Lunch
1:30PM – 3:30PM
Career-Oriented Workshop
Group Discussion with Workshop Panel:
Scarlet Shell, Worcester Polytechnic Institute
Dina Grohmann, Universität Regensburg
Sean Crosson, University of Chicago
Chuck Turnbough, University of Alabama at Birmingham
Debbie Hinton, National Institutes of Health
4:00PM – 6:00PM
Poster Session 1 (Odd-numbered abstracts)
6:00PM – 7:00PM
Dinner
Session 4:
Specificity Factors and Regulation
7:00PM – 9:45PM
Chair, Dina Grohmann: Universität Regensburg,
Regensburg, DE.
7:00PM - 7:25PM
Dina Grohmann: Universität Regensburg, Regensburg, DE.
“Conformational changes during transcription initiation,
unplugged”
7:25PM – 7:50PM
Thomas O’Halloran: Northwestern University, Evanston, IL,
USA. “Switching Gene Expression through DNA Distortion:
Structure and Mechanism of E. coli Activators and
Repressors that Control Cellular Metal Economies”
7:50PM – 8:05PM
Justin Kinney: Cold Spring Harbor Laboratory, NY, USA.
“General strategies for quantitatively measuring in vivo
interactions between transcription factors and RNA
polymerase” Poster Abstract 21
8:05PM – 8:25PM
Coffee Break
8:25PM – 8:50PM
Deborah Hinton: NIDDK, National Institutes of Health,
Bethesda, MD, USA. “Unusual promoter/RNA Polymerase
architectures in bacteria and phage”
8:50PM – 9:15PM
Ramesh Wigneshweraraj: Imperial College London, London,
UK. “Full shut-off of the Escherichia coli RNA polymerase
during T7 phage infection requires two small proteins”
9:15PM – 9:45PM
Lightning Round of Posters to be presented on
Wednesday and Thursday (Even-numbered abstracts)
Wednesday,
June 28, 2017
7:30AM – 9:00AM
Breakfast
Session 5
9:00AM – 12:10PM
Alternative Mechanisms of Transcription Regulation Pathogens and other Organisms
Chair, Elizabeth Campbell: The Rockefeller University, New
York, NY, USA.
9:00AM – 9:25AM
Elizabeth Campbell: The Rockefeller University, New York,
NY, USA. “Structural and Functional Studies of mycobacteria
RNAP”
9:25AM – 9:50AM
Scarlet Shell: Worcester Polytechnic Institute, Worcester,
MA, USA. “Regulation of mRNA stability during
mycobacterial stress response”
9:50AM – 10:05AM
Yu Zhang: Chinese Academy of Sciences, Shanghai, CN.
“Structural basis for transcription initiation by
extracytoplasmic function (ECF) σ factors” Poster Abstract
36
10:05AM – 10:20AM
Kemardo Henry: University of Wisconsin-Madison, WI, USA.
“The role of CarD in promoter function in Rhodobacter
sphaeroides” Poster Abstract 52
10:20AM – 10:35AM
FASEB Sponsored Coffee Break
10:35AM – 11:00AM
Steve Busby: University of Birmingham, Birmingham, UK.
“Regulation of transcription by E. coli NarL protein and its
friends”
11:00AM – 11:25AM
Paolo Landini: Università degli Studi di Milano, Milan, IT.
“Effects of c-di-GMP/ppGpp inhibition on gene expression
and virulence-related traits in Gram negative bacteria”
11:25AM – 11:40AM
Jonathan Goodson: University of Maryland, College Park,
MD, USA. “ LoaP is a broadly conserved antiterminator
protein that regulates antibiotic gene clusters.” Poster
Abstract 70
11:40AM – 11:55AM
Kathryn Ramsey: Harvard Medical School, Boston, MA,
USA. “Repression of an anti-virulence factor by a response
regulator promotes Francisella tularensis intramacrophage
growth” Poster Abstract 40
11:55AM – 12:10PM
Urmimala Basu: Rutgers University, Piscataway, NJ, USA.
“The C-terminal region of the yeast mitochondrial
transcription factor Mtf1 regulates the efficiency and
precision of transcription initiation” Poster Abstract 30
12:15PM – 1:30PM
Lunch
Free Afternoon
4:00PM – 6:00PM
Poster Session 2 (Even-numbered abstracts)
6:00PM – 7:00PM
Dinner
Session 6:
7:00PM – 9:40PM
Transcriptional Networks
Chair, Tricia Kiley: University of Wisconsin School of
Medicine and Public Health, Madison, WI, USA.
7:00PM - 7:25PM
Tricia Kiley: University of Wisconsin School of Medicine and
Public Health, Madison, WI, USA. “The role of IscR in control
of oxygen-regulated gene expression”
7:25PM – 7:50PM
Richard Brennan: Duke University School of Medicine,
Durham, NC, USA. "Towards understanding the molecular
mechanism of transcription regulation of the Francisella
Pathogenicity Island"
7:50PM – 8:05PM
Daniela Ledezma-Tejeida: Universidad Nacional Autónoma
de México, Cuernavaca, MOR, MX. “ Genome-wide mapping
of transcriptional regulation and metabolism describes
information-processing units in Escherichia coli K12” Poster
Abstract 42
8:05PM – 8:20PM
Ioly Kotta-Loizou: Imperial College London, London, UK.
“Expression regulation and function of the Rtc RNA repair
system in Escherichia coli” Poster Abstract 48
8:20PM – 8:35PM
Coffee Break
8:35PM – 9:00PM
Sean Crosson: University of Chicago, Chicago, IL, USA.
“The small RNA GsrN is a central regulator of stress
adaptation in Caulobacter”
9:00PM – 9:25PM
Bianca Sclavi: CNRS, ENS, Cachan, FR. “The role of global
regulators and genome position in the change of
transcription activity upon adaptation to different growth
rates”
9:25 PM – 9:40PM
Elena Sineva: The Pennsylvania State University, University
Park, PA, USA. “ Towards an understanding of the role of
omega in regulation of EσE-dependent transcription” Poster
Abstract 32
Thursday,
June 29, 2017
7:30AM – 9:00AM
Breakfast
Session 7
9:00AM – 11:35AM
Systems and Unexpected Connections
Chair, Eduardo Groisman: Yale School of Medicine, New
Haven, CN, USA.
9:00AM – 9:25AM
Thomas Santangelo: Colorado State University, Fort Collins,
CO, USA. “A global perspective of archaeal transcription”
9:25AM – 9:40AM
Fabian Blombach: University College London, UK. “ Stressinduced reconfiguration of the basal transcription machinery
in archaea” Poster Abstract 54
9:40AM – 9:55AM
Horia Todor: University of California, San Francisco, CA,
USA. “Rewiring the specificity of extracytoplasmic function
sigma factors” Poster Abstract 24
9:55AM – 10:10AM
Gabriele Baniulyte: Wadsworth Center, NY State
Department of Health, Albany, NY, USA. “Nus factors have a
widespread regulatory function in bacteria” Poster Abstract
68
10:10AM -10:30AM
FASEB Sponsored Coffee Break
10:30AM –10:55AM
Jeff Gelles: Brandeis University, Waltham, MA, USA.
“Alternative transcription cycle for bacterial RNA polymerase”
10:55AM--11:10AM
David Dulin: University of Oxford, UK. “ A network of pauses
traps the bacterial RNA polymerase and its nascent
transcript on the promoter” Poster Abstract 20
11:10AM – 11:25AM
Gene-Wei Li: Massachusetts Institute of Technology,
Cambridge, MA, USA. “ Ancient operons have divergent
transcript architecture but conserved protein expression
stoichiometry” Poster Abstract 16
11:25AM-11:40AM
Arkady Mustaev: Rutgers Biomedical and Health Sciences.
NJ, USA. “Predicting the past: Iron Age of life?” Poster
Abstract 66
11:40AM -- 12:10PM
Business Meeting
12:10PM – 1:30PM
Lunch
12:10PM – 6:00PM
Optional Organized Group Activity
4:00PM – 6:00PM
Poster Session 2 (Even-numbered abstracts)
6:00PM – 7:30PM
Dinner
Session 8:
7:30PM – 9:40PM
RNA-based Control
Chair, Bryce Nickels: Waksman Institute, Rutgers University,
Piscataway, NJ, USA.
7:30PM - 7:55PM
Bryce Nickels: Waksman Institute, Rutgers University,
Piscataway, NJ, USA. “Mechanistic studies of transcription
initiation”
7:55PM – 8:20PM
Cari Vanderpool: University of Illinois, Champaign-Urbana,
IL, USA. “Expanding mechanisms of small RNA-mediated
gene regulation”
8:20PM – 8:35PM
Eric Strobel: Northwestern University, Chicago, IL, USA. “
Cotranscriptional folding of a ZTP riboswitch at nucleotide
resolution” Poster Abstract 28
8:35PM – 8:50PM
Coffee Break
8:50PM – 9:15PM
Eduardo Groisman: Yale School of Medicine, New Haven, CT,
USA. “Signal-specific outputs from a transcriptional regulator”
9:15PM – 9:40PM
Konstantin Brodolin: Université de Montpellier,
France. “'Single-molecule and structural analysis of the M.
tuberculosis RNA polymerase”
Friday,
June 30, 2017
7:30AM – 8:30AM
Breakfast
Session 9
8:30AM – 10:50AM
Cell Topology, Chromosomal Dynamics, and
Transcription
Chair, Jade Wang, University of Wisconsin, Madison, WI,
USA.
8:30AM – 8:55AM
Jade Wang: University of Wisconsin, Madison, WI, USA.
“Replication-Transcription Conflict in Bacillus subtilis”
8:55AM – 9:10AM
Max Gottesman: Columbia University Medical Center, New
York, NY, USA. “ DksA is essential for constitutive stable
DNA replication (cSDR) in E. coli” Poster Abstract 31
9:10AM – 9:25AM
Ranjan Sen: Center for DNA Fingerprinting and Diagnostics,
Hyderabad, IN. “Rho-dependent transcription termination in
bacteria is a component of Transcription-coupled DNA repair
process” Poster Abstract 38
9:25AM – 9:45AM
FASEB Sponsored Coffee Break
9:45AM – 10:00AM
Venu Kamarthapu: New York University School of Medicine,
NY, USA. “Structural model of UvrD-mediated transcriptioncoupled DNA repair” Poster Abstract 62
10:00AM – 10:25AM
Terence Strick: Institut Jacques Monod/Université Paris
Diderot/CNRS Paris, FR. “Obstacles on the path to promoter
escape"
10:25 AM – 10:50AM
Closing Comments, Organizers
Lunch - - Lunch Boxes available for bus passengers.
11:30AM
Bus due to arrive at Logon Airport by 3:00PM
END OF CONFERENCE
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