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Dive into the research topics where David Degen is active.

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Featured researches published by David Degen.


eLife | 2014

Transcription inhibition by the depsipeptide antibiotic salinamide A

David Degen; Yu Feng; Yu Zhang; Katherine Y Ebright; Yon W. Ebright; Matthew Gigliotti; Hanif Vahedian-Movahed; Sukhendu Mandal; Meliza Talaue; Nancy D. Connell; Eddy Arnold; William Fenical; Richard H. Ebright

We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center ‘bridge-helix cap’ comprising the ‘bridge-helix N-terminal hinge’, ‘F-loop’, and ‘link region’. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge. DOI: http://dx.doi.org/10.7554/eLife.02451.001


eLife | 2014

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Yu Zhang; David Degen; Mary X Ho; Elena Sineva; Katherine Y Ebright; Yon W. Ebright; Vladimir Mekler; Hanif Vahedian-Movahed; Yu Feng; Ruiheng Yin; Steve Tuske; Herbert Irschik; Rolf Jansen; Sonia I. Maffioli; Stefano Donadio; Eddy Arnold; Richard H. Ebright

Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI: http://dx.doi.org/10.7554/eLife.02450.001


The Journal of Antibiotics | 2015

Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp

Hossam M Hassan; David Degen; Kyoung Hwa Jang; Richard H. Ebright; William Fenical

Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp.


Antimicrobial Agents and Chemotherapy | 2012

Frequency, Spectrum, and Nonzero Fitness Costs of Resistance to Myxopyronin in Staphylococcus aureus

Aashish Srivastava; David Degen; Yon W. Ebright; Richard H. Ebright

ABSTRACT The antibiotic myxopyronin (Myx) functions by inhibiting bacterial RNA polymerase (RNAP). The binding site on RNAP for Myx—the RNAP “switch region SW1/SW2 subregion”—is different from the binding site on RNAP for the RNAP inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (Rif). Here, we report the frequency, spectrum, and fitness costs of Myx resistance in Staphylococcus aureus. The resistance rate for Myx is 4 × 10−8 to 7 × 10−8 per generation, which is equal within error to the resistance rate for Rif (3 × 10−8 to 10 × 10−8 per generation). Substitutions conferring Myx resistance were obtained in the RNAP β subunit [six substitutions: V1080(1275)I, V1080(1275)L, E1084(1279)K, D1101(1296)E, S1127(1322)L, and S1127(1322)P] and the RNAP β′ subunit [five substitutions: K334(345)N, T925(917)K, T925(917)R, G1172(1354)C, and G1172(1354)D] (residues numbered as in Staphylococcus aureus RNAP and, in parentheses, as in Escherichia coli RNAP). Sites of substitutions conferring Myx resistance map to the RNAP switch region SW1/SW2 subregion and do not overlap the binding site on RNAP for Rif, and, correspondingly, Myx-resistant mutants exhibit no cross-resistance to Rif. All substitutions conferring Myx resistance exhibit significant fitness costs (4 to 15% per generation). In contrast, at least three substitutions conferring Rif resistance exhibit no fitness costs (≤0% per generation). The observation that all Myx-resistant mutants have significant fitness costs whereas at least three Rif-resistant mutants have no fitness costs, together with the previously established inverse correlation between fitness cost and clinical prevalence, suggests that Myx resistance is likely to have lower clinical prevalence than Rif resistance.


bioRxiv | 2018

Structural basis of ECF-sigma-factor-dependent transcription initiation.

Wei Lin; Sukhendu Mandal; David Degen; Minsung Cho; Yu Feng; Kalyan Das; Richard H. Ebright

Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of the six conserved functional modules present in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor--although unrelated in sequence--follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.


Current Opinion in Microbiology | 2011

New target for inhibition of bacterial RNA polymerase: 'switch region'.

Aashish Srivastava; Meliza Talaue; Shuang Liu; David Degen; Richard Y. Ebright; Elena Sineva; Anirban Chakraborty; Sergey Y. Druzhinin; Sujoy Chatterjee; Jayanta Mukhopadhyay; Yon W. Ebright; Alex Zozula; Juan Shen; Sonali Sengupta; Rui Rong Niedfeldt; Cai Xin; Takushi Kaneko; Herbert Irschik; Rolf Jansen; Stefano Donadio; Nancy D. Connell; Richard H. Ebright


Molecular Cell | 2017

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.

Wei Lin; Soma Mandal; David Degen; Yu Liu; Yon W. Ebright; Shengjian Li; Yu Feng; Yunpeng Zhang; Sukhendu Mandal; Yilin Jiang; Shuang Liu; Matthew Gigliotti; Meliza Talaue; Nancy D. Connell; Kalyan Das; Eddy Arnold; Richard H. Ebright


Cell | 2017

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase

Sonia I. Maffioli; Yu Zhang; David Degen; Thomas Carzaniga; Giancarlo Del Gatto; Stefania Serina; Paolo Monciardini; Carlo Mazzetti; Paola Guglierame; Gianpaolo Candiani; Alina Iulia Chiriac; Giuseppe Facchetti; Petra Kaltofen; Hans-Georg Sahl; Gianni Dehò; Stefano Donadio; Richard H. Ebright


Structure | 2015

Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.

Yu Feng; David Degen; Xinyue Wang; Matthew Gigliotti; Shuang Liu; Yu Zhang; Deepankar Das; Trevor Michalchuk; Yon W. Ebright; Meliza Talaue; Nancy D. Connell; Richard H. Ebright


Chemistry: A European Journal | 2014

Synthesis and Evaluation of Novel Analogues of Ripostatins

Wufeng Tang; Shuang Liu; David Degen; Richard H. Ebright; Evgeny V. Prusov

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Aashish Srivastava

Howard Hughes Medical Institute

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