Evgeny Nudler

Summary

Affiliation: New York University School of Medicine
Country: USA

Publications

  1. ncbi request reprint Therapeutic effect of exogenous hsp70 in mouse models of Alzheimer's disease
    Natalia V Bobkova
    Institute of Cell Biophysics, RAS, Pushchino, Moscow Region, Russia
    J Alzheimers Dis 38:425-35. 2014
  2. pmc RNA polymerase backtracking in gene regulation and genome instability
    Evgeny Nudler
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Cell 149:1438-45. 2012
  3. pmc RNA polymerase active center: the molecular engine of transcription
    Evgeny Nudler
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Annu Rev Biochem 78:335-61. 2009
  4. ncbi request reprint UvrD facilitates DNA repair by pulling RNA polymerase backwards
    Vitaly Epshtein
    1 Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA 2
    Nature 505:372-7. 2014
  5. pmc Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics
    Ivan Gusarov
    Department of Biochemistry, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
    Science 325:1380-4. 2009
  6. pmc Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    Sergey Proshkin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 328:504-8. 2010
  7. pmc An allosteric mechanism of Rho-dependent transcription termination
    Vitaly Epshtein
    Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
    Nature 463:245-9. 2010
  8. doi request reprint H2S: a universal defense against antibiotics in bacteria
    Konstantin Shatalin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 334:986-90. 2011
  9. ncbi request reprint A ratchet mechanism of transcription elongation and its control
    Gil Bar-Nahum
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Cell 120:183-93. 2005
  10. ncbi request reprint An allosteric path to transcription termination
    Vitaly Epshtein
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 28:991-1001. 2007

Research Grants

  1. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 1999
  2. Transcription Elongation Control in E. coli
    Evgeny Nudler; Fiscal Year: 2006
  3. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2006
  4. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2007
  5. Transcription Elongation Control in E. coli
    Evgeny Nudler; Fiscal Year: 2007
  6. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2007
  7. Transcription Termination and its Regulation in E. coli
    Evgeny Nudler; Fiscal Year: 2009
  8. Transcription Termination and its Regulation in E. coli
    Evgeny Nudler; Fiscal Year: 2010
  9. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2005
  10. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2006

Collaborators

  • Oleg Laptenko
  • Alexander Serganov
  • Laurent Gautier
  • Irina Artsimovitch
  • Zhi-Qiang Wang
  • Vitaly Epshtein
  • Ivan Gusarov
  • Vladimir Svetlov
  • Ilya Shamovsky
  • Alexander Mironov
  • Konstantin Shatalin
  • Katelyn McGary
  • Sergey Proshkin
  • Dipak Dutta
  • Christopher J Cardinale
  • Natalia V Bobkova
  • Eugene S Kandel
  • Max E Gottesman
  • Marina Starodubtseva
  • Stephen J Lippard
  • A Rachid Rahmouni
  • Andrei E Ruckenstein
  • Gil Bar-Nahum
  • Sergei Borukhov
  • Andrey A Smirnov
  • Venu Kamarthapu
  • Natalia Medvinskaya
  • Michail S Kukharsky
  • Beatrix Ueberheide
  • Valerii Yashin
  • Inna Nesterova
  • David G Garbuz
  • Michael Evgen'ev
  • Vadim Karpov
  • Irina Alexandrova
  • Alexander Samokhin
  • Natalia N Ninkina
  • Olga Smolentseva
  • Svetlana Eremina
  • Elena Shatalina
  • Joseph Wade
  • Lewis M Brown
  • Robert S Washburn
  • Lindsey McQuade
  • Vasisht R Tadigotla
  • Yelena Shatalina
  • Dennis J Stuehr
  • Ekaterina Avetissova
  • Lindsey E McQuade
  • David Gershon
  • Maxim Ivannikov
  • Ruslan Rafikov
  • Arkady Mustaev
  • Alexander S Mironov
  • Francine Toulmé

Detail Information

Publications37

  1. ncbi request reprint Therapeutic effect of exogenous hsp70 in mouse models of Alzheimer's disease
    Natalia V Bobkova
    Institute of Cell Biophysics, RAS, Pushchino, Moscow Region, Russia
    J Alzheimers Dis 38:425-35. 2014
    ....
  2. pmc RNA polymerase backtracking in gene regulation and genome instability
    Evgeny Nudler
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Cell 149:1438-45. 2012
    ....
  3. pmc RNA polymerase active center: the molecular engine of transcription
    Evgeny Nudler
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Annu Rev Biochem 78:335-61. 2009
    ..Recent advances in the structural and biochemical characterization of RNAP explain the active center at the atomic level and enable new approaches to understanding the entire transcription mechanism, its exceptional fidelity and control...
  4. ncbi request reprint UvrD facilitates DNA repair by pulling RNA polymerase backwards
    Vitaly Epshtein
    1 Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA 2
    Nature 505:372-7. 2014
    ..Because backtracking is a shared feature of all cellular RNA polymerases, we propose that this mechanism enables RNA polymerases to function as global DNA damage scanners in bacteria and eukaryotes. ..
  5. pmc Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics
    Ivan Gusarov
    Department of Biochemistry, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
    Science 325:1380-4. 2009
    ..Our results suggest that the inhibition of NOS activity may increase the effectiveness of antimicrobial therapy...
  6. pmc Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    Sergey Proshkin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 328:504-8. 2010
    ..Such a cooperative mechanism ensures that the transcriptional yield is always adjusted to translational needs at different genes and under various growth conditions...
  7. pmc An allosteric mechanism of Rho-dependent transcription termination
    Vitaly Epshtein
    Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
    Nature 463:245-9. 2010
    ....
  8. doi request reprint H2S: a universal defense against antibiotics in bacteria
    Konstantin Shatalin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 334:986-90. 2011
    ..The mechanism of gas-mediated antibiotic resistance relies on mitigation of oxidative stress imposed by antibiotics...
  9. ncbi request reprint A ratchet mechanism of transcription elongation and its control
    Gil Bar-Nahum
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Cell 120:183-93. 2005
    ..This balance is critical for cell viability since it determines the rate, processivity, and fidelity of transcription...
  10. ncbi request reprint An allosteric path to transcription termination
    Vitaly Epshtein
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 28:991-1001. 2007
    ..Our results envision the elongation complex as a flexible structure, not a rigid body, and establish basic principles of the termination pathway that are likely to be universal in prokaryotic and eukaryotic systems...
  11. pmc Isolation and characterization of the heat shock RNA 1
    Ilya Shamovsky
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Methods Mol Biol 540:265-79. 2009
    ..We have shown that a large, noncoding RNA, HSR1, and the translation elongation factor eEF1A form a complex with HSF during HS and are required for its activation...
  12. pmc Transcriptional approaches to riboswitch studies
    Alexander Mironov
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Methods Mol Biol 540:39-51. 2009
    ..The system can be utilized to facilitate biochemical studies of riboswitches in general, i.e., to simplify analysis of riboswitches that are not necessarily involved in transcriptional control...
  13. pmc Linking RNA polymerase backtracking to genome instability in E. coli
    Dipak Dutta
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Cell 146:533-43. 2011
    ..Our results establish RNAP backtracking as the intrinsic hazard to chromosomal integrity and implicate active ribosomes and other anti-backtracking mechanisms in genome maintenance...
  14. pmc Transcription through the roadblocks: the role of RNA polymerase cooperation
    Vitaly Epshtein
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    EMBO J 22:4719-27. 2003
    ..These results support a cooperation model of transcription whereby RNAP molecules behave as 'partners' helping one another to traverse intrinsic and extrinsic obstacles...
  15. pmc Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli
    Christopher J Cardinale
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Science 320:935-8. 2008
    ..Deletion of the cryptic rac prophage in wild-type E. coli increases bicyclomycin resistance and permits deletion of nusG. Thus, Rho termination, supported by NusA and NusG, is required to suppress the toxic activity of foreign genes...
  16. ncbi request reprint Bacterial nitric oxide extends the lifespan of C. elegans
    Ivan Gusarov
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Cell 152:818-30. 2013
    ..Our work provides an example of interspecies signaling by a small molecule and illustrates the lifelong value of commensal bacteria to their host...
  17. ncbi request reprint Gene control by large noncoding RNAs
    Ilya Shamovsky
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Sci STKE 2006:pe40. 2006
    ..Evf-2 is the first example of lncRNA directly involved in organogenesis in vertebrates...
  18. pmc Bacterial nitric-oxide synthases operate without a dedicated redox partner
    Ivan Gusarov
    Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
    J Biol Chem 283:13140-7. 2008
    ....
  19. doi request reprint A decade of riboswitches
    Alexander Serganov
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Cell 152:17-24. 2013
    ....
  20. doi request reprint S-nitrosylation signaling in Escherichia coli
    Ivan Gusarov
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Sci Signal 5:pe26. 2012
    ..We discuss a structural model that may explain the remarkable stability and specificity of OxyR S-nitrosylation...
  21. doi request reprint Modular RNA heats up
    Ilya Shamovsky
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 29:415-7. 2008
    ..2008) demonstrate that Alu RNA from a human SINE represses RNA polymerase II transcription during heat shock. This noncoding RNA is the first example of a "protein-like" transcription factor with a distinct modular architecture...
  22. pmc RNA polymerase and the ribosome: the close relationship
    Katelyn McGary
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Curr Opin Microbiol 16:112-7. 2013
    ..The direct link between the moving ribosome and RNAP provides a basis for maintaining genomic integrity while enabling efficient transcription and timely translation of various genes within the bacterial cell...
  23. ncbi request reprint Analysis of the intrinsic transcription termination mechanism and its control
    Evgeny Nudler
    Department of Biochemistry, New York University Medical Center, New York, New York 10016, USA
    Methods Enzymol 371:369-82. 2003
  24. ncbi request reprint Characterization of protein-nucleic acid interactions that are required for transcription processivity
    Evgeny Nudler
    Department of Biochemistry, New York University Medical Center, New York, New York 10016, USA
    Methods Enzymol 371:179-90. 2003
  25. pmc Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages
    Konstantin Shatalin
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Proc Natl Acad Sci U S A 105:1009-13. 2008
    ..Thus, bNOS represents an attractive antimicrobial target for treatment of anthrax and other infectious diseases...
  26. ncbi request reprint Flipping riboswitches
    Evgeny Nudler
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Cell 126:19-22. 2006
    ..The publication of five high-resolution crystal structures provides a comprehensive view of how riboswitches sense their ligands and points to new challenges in this emerging field...
  27. pmc Basic mechanism of transcription by RNA polymerase II
    Vladimir Svetlov
    Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
    Biochim Biophys Acta 1829:20-8. 2013
    ..This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation...
  28. pmc Response to Klyuyev and Vassylyev: on the mechanism of tagetitoxin inhibition of transcription
    Vladimir Svetlov
    Department of Biochemistry, New York University School of Medicine, New York, NY, USA
    Transcription 3:51-5. 2012
    ....
  29. ncbi request reprint Methods of walking with the RNA polymerase
    Evgeny Nudler
    Department of Biochemistry, New York University Medical Center, New York, New York 10016, USA
    Methods Enzymol 371:160-9. 2003
  30. ncbi request reprint RNA-mediated response to heat shock in mammalian cells
    Ilya Shamovsky
    Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
    Nature 440:556-60. 2006
    ..The central role of HSR1 during heat shock implies that targeting this RNA could serve as a new therapeutic model for cancer, inflammation and other conditions associated with HSF1 deregulation...
  31. ncbi request reprint Cooperation between RNA polymerase molecules in transcription elongation
    Vitaly Epshtein
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Science 300:801-5. 2003
    ..Such cooperation between RNAP molecules links the rate of elongation to the rate of initiation and explains why elongation is still fast and processive in vivo even without anti-arrest factors...
  32. pmc Macromolecular micromovements: how RNA polymerase translocates
    Vladimir Svetlov
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Curr Opin Struct Biol 19:701-7. 2009
    ..Here we review some of the more recently acquired insights into the structural flexibility and morphic fluctuations of RNA polymerases and their mechanistic implications...
  33. ncbi request reprint The riboswitch control of bacterial metabolism
    Evgeny Nudler
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Trends Biochem Sci 29:11-7. 2004
    ..Here, we summarize the recent progress in the identification and characterization of riboswitches and discuss their evolution and distribution...
  34. pmc Unfolding the bridge between transcription and translation
    Vladimir Svetlov
    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
    Cell 150:243-5. 2012
    ....
  35. pmc NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria
    Ivan Gusarov
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Proc Natl Acad Sci U S A 102:13855-60. 2005
    ..Our data also reveal a critical role for bacterial NO-synthase in adaptation to oxidative stress associated with fast metabolic changes, and suggest a possible role for NO in defending pathogens against immune oxidative attack...
  36. pmc The riboswitch-mediated control of sulfur metabolism in bacteria
    Vitaly Epshtein
    Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
    Proc Natl Acad Sci U S A 100:5052-6. 2003
    ..The S-box leader RNA thus expands the family of newly discovered riboswitches, i.e., natural regulatory RNA aptamers that seem to sense small molecules ranging from amino acid derivatives to vitamins...
  37. ncbi request reprint Template switching by RNA polymerase II in vivo. Evidence and implications from a retroviral system
    Eugene S Kandel
    Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA
    Mol Cell 10:1495-502. 2002
    ..These observations argue that RNAP II can utilize double-strand breaks and gaps in DNA to generate "recombinant" transcripts in vivo and suggest a mechanism for mutation and recombination of retroviruses...

Research Grants22

  1. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 1999
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  2. Transcription Elongation Control in E. coli
    Evgeny Nudler; Fiscal Year: 2006
    ..It is further proposed to examine whether GreA/GreB transcript cleavage factors contribute to transcription fidelity in vivo. ..
  3. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2006
    ..Chemically modified stable HSR antisense oligos will be obtained for transfection of thermotolerant breast cancer cultural cells and nude mice tumors for making them more susceptible to apoptosis and existing therapies. ..
  4. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2007
    ..Experiments are proposed to examine the role of newly discovered "riboswitches", i.e. natural regulatory RNA aptamers that directly sense small molecules, in regulation of purine operons in B.subtilis. ..
  5. Transcription Elongation Control in E. coli
    Evgeny Nudler; Fiscal Year: 2007
    ..It is further proposed to examine whether GreA/GreB transcript cleavage factors contribute to transcription fidelity in vivo. ..
  6. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2007
    ..Chemically modified stable HSR antisense oligos will be obtained for transfection of thermotolerant breast cancer cultural cells and nude mice tumors for making them more susceptible to apoptosis and existing therapies. ..
  7. Transcription Termination and its Regulation in E. coli
    Evgeny Nudler; Fiscal Year: 2009
    ..and other important biologically active compounds. Finally, the proposed experiments will also provide insight to the basic mechanisms of eukaryotic transcription termination. ..
  8. Transcription Termination and its Regulation in E. coli
    Evgeny Nudler; Fiscal Year: 2010
    ..and other important biologically active compounds. Finally, the proposed experiments will also provide insight to the basic mechanisms of eukaryotic transcription termination. ..
  9. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2005
    ..Experiments are proposed to examine the role of newly discovered "riboswitches", i.e. natural regulatory RNA aptamers that directly sense small molecules, in regulation of purine operons in B.subtilis. ..
  10. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2006
    ..Experiments are proposed to examine the role of newly discovered "riboswitches", i.e. natural regulatory RNA aptamers that directly sense small molecules, in regulation of purine operons in B.subtilis. ..
  11. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 2000
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  12. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 2001
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  13. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 2002
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  14. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 2003
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  15. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2004
    ..Experiments are proposed to examine the role of newly discovered "riboswitches", i.e. natural regulatory RNA aptamers that directly sense small molecules, in regulation of purine operons in B.subtilis. ..
  16. MECHANISMS OF INTRINSIC TRANSCRIPTION
    Evgeny Nudler; Fiscal Year: 2003
    ..Differences between two structures will allow a detection of the major conformational changes associated with termination. ..
  17. Transcription Termination and Its Control in Bacteria
    Evgeny Nudler; Fiscal Year: 2005
    ..Experiments are proposed to examine the role of newly discovered "riboswitches", i.e. natural regulatory RNA aptamers that directly sense small molecules, in regulation of purine operons in B.subtilis. ..
  18. The Mechanism of Heat Shock Activation
    Evgeny Nudler; Fiscal Year: 2005
    ..Chemically modified stable HSR antisense oligos will be obtained for transfection of thermotolerant breast cancer cultural cells and nude mice tumors for making them more susceptible to apoptosis and existing therapies. ..
  19. Transcription Elongation Control in E. coli
    Evgeny Nudler; Fiscal Year: 2005
    ..It is further proposed to examine whether GreA/GreB transcript cleavage factors contribute to transcription fidelity in vivo. ..
  20. Sensor Mechanisms of HSF Activation
    Evgeny Nudler; Fiscal Year: 2010
    ....