Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism

Peek, James; Lilic, Mirjana; Montiel, Daniel; Milshteyn, Aleksandr; Woodworth, Ian; Biggins, John B.; Ternei, Melinda A.; Calle, Paula Y.; Danziger, Michael; Warrier, Thulasi; Saito, Kohta; Braffman, Nathaniel; Fay, Allison; Glickman, Michael S.; Darst, Seth A.; Campbell, Elizabeth A.; Brady, Sean F.

doi:10.1038/s41467-018-06587-2

Title: Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism

Journal Article · 07 October 2018 · Nature Communications

DOI: https://doi.org/10.1038/s41467-018-06587-2 · OSTI ID:1570722

Peek, James ^[1]; Lilic, Mirjana ^[2]; Montiel, Daniel ^[2]; Milshteyn, Aleksandr ^[2]; Woodworth, Ian ^[2]; Biggins, John B. ^[2]; Ternei, Melinda A. ^[2]; Calle, Paula Y. ^[2]; Danziger, Michael ^[2]; Warrier, Thulasi ^[3]; Saito, Kohta ^[3]; Braffman, Nathaniel ^[2]; Fay, Allison ^[4];

^[4]; Darst, Seth A. ^[2]; Campbell, Elizabeth A. ^[2];

^[2]

Rockefeller Univ., New York, NY (United States); DOE/OSTI
Rockefeller Univ., New York, NY (United States)
Weill Cornell Medicine, New York, NY (United States)
Sloan-Kettering Inst., New York, NY (United States)

Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (Rif^R). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant Rif^R mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of Rif^R RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: NIH; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-06CH11357; SC0012704

OSTI ID:: 1570722

Report Number(s):: BNL-220025-2020-JACI

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 9; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (127)

Natural-Product Sugar Biosynthesis and Enzymatic Glycodiversification Thibodeaux, Christopher J.; Melançon, Charles E.; Liu, Hung-wen Angewandte Chemie International Edition, Vol. 47, Issue 51 https://doi.org/10.1002/anie.200801204	journal	December 2008
The Structural Diversity of Acidic Lipopeptide Antibiotics Strieker, Matthias; Marahiel, Mohamed A. ChemBioChem, Vol. 10, Issue 4 https://doi.org/10.1002/cbic.200800546	journal	January 2009
Glycopeptide and Lipoglycopeptide Antibiotics Kahne, Dan; Leimkuhler, Catherine; Lu, Wei ChemInform, Vol. 36, Issue 24 https://doi.org/10.1002/chin.200524268	journal	June 2005
Bisintercalator Natural Products with Potential Therapeutic Applications: Isolation, Structure Determination, Synthetic and Biological Studies Dawson, Simon; Malkinson, John P.; Paumier, David ChemInform, Vol. 38, Issue 22 https://doi.org/10.1002/chin.200722263	journal	May 2007
Selective Isolation and Ansamycin-Targeted Screenings of Commensal Actinomycetes from the “Maytansinoids-Producing” Arboreal Trewia nudiflora Zhu, Na; Zhao, Peiji; Shen, Yuemao Current Microbiology, Vol. 58, Issue 1 https://doi.org/10.1007/s00284-008-9284-8	journal	October 2008
Drilling accurate nanopores for biosensors by energetic multi-wall carbon nanotubes: a molecular dynamics investigation Li, Changsheng; Wang, Zilin; Ma, Lei Journal of Molecular Modeling, Vol. 28, Issue 10 https://doi.org/10.1007/s00894-022-05276-8	journal	September 2022
Studies of the binding of Escherichia coli RNA polymerase to DNA Hinkle, David C.; Mangel, Walter F.; Chamberlin, Michael J. Journal of Molecular Biology, Vol. 70, Issue 2 https://doi.org/10.1016/0022-2836(72)90534-7	journal	September 1972
Rifamycins: an insight into biological activity based on structural investigations Brufani, M.; Cerrini, S.; Fedeli, W. Journal of Molecular Biology, Vol. 87, Issue 3 https://doi.org/10.1016/0022-2836(74)90094-1	journal	August 1974
Allosteric Modulation of the RNA Polymerase Catalytic Reaction Is an Essential Component of Transcription Control by Rifamycins Artsimovitch, Irina; Vassylyeva, Marina N.; Svetlov, Dmitri Cell, Vol. 122, Issue 3 https://doi.org/10.1016/j.cell.2005.07.014	journal	August 2005
Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F. Chemistry & Biology, Vol. 21, Issue 9 https://doi.org/10.1016/j.chembiol.2014.08.006	journal	September 2014
Drug resistance-conferring mutations in Mycobacterium tuberculosis from pulmonary tuberculosis patients in Southwest Ethiopia Tadesse, Mulualem; Aragaw, Dossegnaw; Dimah, Belayneh International Journal of Mycobacteriology, Vol. 5, Issue 2 https://doi.org/10.1016/j.ijmyco.2016.02.009	journal	June 2016
Prevalence of mutations in genes associated with rifampicin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates Muthaiah, Muthuraj; Shivekar, Smita Sunil; Cuppusamy Kapalamurthy, Vidya Raj Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, Vol. 8 https://doi.org/10.1016/j.jctube.2017.06.001	journal	August 2017
Frequency of multi-drug resistance and mutations in Mycobacterium tuberculosis isolates from Punjab state of India Singhal, Ritu; Arora, Jyoti; Sah, Grish C. Journal of Epidemiology and Global Health, Vol. 7, Issue 3 https://doi.org/10.1016/j.jegh.2017.05.002	journal	September 2017
Comprehensive Analysis of Distinctive Polyketide and Nonribosomal Peptide Structural Motifs Encoded in Microbial Genomes Minowa, Yohsuke; Araki, Michihiro; Kanehisa, Minoru Journal of Molecular Biology, Vol. 368, Issue 5 https://doi.org/10.1016/j.jmb.2007.02.099	journal	May 2007
Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition Lin, Wei; Mandal, Soma; Degen, David Molecular Cell, Vol. 66, Issue 2 https://doi.org/10.1016/j.molcel.2017.03.001	journal	April 2017
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase Campbell, Elizabeth A.; Korzheva, Nataliya; Mustaev, Arkady Cell, Vol. 104, Issue 6, p. 901-912 https://doi.org/10.1016/s0092-8674(01)00286-0	journal	March 2001
Pyrosequencing enumerates and contrasts soil microbial diversity Roesch, Luiz F. W.; Fulthorpe, Roberta R.; Riva, Alberto The ISME Journal, Vol. 1, Issue 4 https://doi.org/10.1038/ismej.2007.53	journal	July 2007
The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review Floss, Heinz G.; Yu, Tin-Wein; Arakawa, Kenji The Journal of Antibiotics, Vol. 64, Issue 1 https://doi.org/10.1038/ja.2010.139	journal	November 2010
Resistance to rifampicin: a review Goldstein, Beth P. The Journal of Antibiotics, Vol. 67, Issue 9 https://doi.org/10.1038/ja.2014.107	journal	August 2014
Antibiotic resistance is ancient D’Costa, Vanessa M.; King, Christine E.; Kalan, Lindsay Nature, Vol. 477, Issue 7365 https://doi.org/10.1038/nature10388	journal	August 2011
Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules Brady, Sean F. Nature Protocols, Vol. 2, Issue 5 https://doi.org/10.1038/nprot.2007.195	journal	May 2007
The metagenomics of soil Daniel, Rolf Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1160	journal	June 2005
Cutting the Gordian knot: early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation Jarmusch, Scott A.; Feldmann, Ingo; Blank-Landeshammer, Bernhard The Journal of Antibiotics, Vol. 73, Issue 11 https://doi.org/10.1038/s41429-020-00369-z	journal	September 2020
Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis He, Si Mei; Song, Wan Ling; Cong, Kun Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-08672-w	journal	August 2017
Molecular genetic basis of antimicrobial agent resistance inMycobacterium tuberculosis: 1998 update Ramaswamy, S.; Musser, J. M. Tubercle and Lung Disease, Vol. 79, Issue 1 https://doi.org/10.1054/tuld.1998.0002	journal	January 1998
Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center Feklistov, A.; Mekler, V.; Jiang, Q. Proceedings of the National Academy of Sciences, Vol. 105, Issue 39 https://doi.org/10.1073/pnas.0802822105	journal	September 2008
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors Owen, Jeremy G.; Charlop-Powers, Zachary; Smith, Alexandra G. Proceedings of the National Academy of Sciences, Vol. 112, Issue 14 https://doi.org/10.1073/pnas.1501124112	journal	March 2015
Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme Basu, Ritwika S.; Warner, Brittany A.; Molodtsov, Vadim Journal of Biological Chemistry, Vol. 289, Issue 35 https://doi.org/10.1074/jbc.m114.584037	journal	June 2014
Molecular Cloning and Characterization of CYP719, a Methylenedioxy Bridge-forming Enzyme That Belongs to a Novel P450 Family, from cultured Coptis japonica Cells Ikezawa, Nobuhiro; Tanaka, Masaru; Nagayoshi, Masanori Journal of Biological Chemistry, Vol. 278, Issue 40 https://doi.org/10.1074/jbc.m302470200	journal	May 2003
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
History of the Development of Rifampin Sensi, P. Clinical Infectious Diseases, Vol. 5, Issue Supplement_3 https://doi.org/10.1093/clinids/5.supplement_3.s402	journal	July 1983
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Ab initio gene identification in metagenomic sequences Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark Nucleic Acids Research, Vol. 38, Issue 12 https://doi.org/10.1093/nar/gkq275	journal	April 2010
Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD Davis, Elizabeth; Chen, James; Leon, Katherine Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1231	journal	December 2014
Engineering the acyltransferase substrate specificity of assembly line polyketide synthases Dunn, Briana J.; Khosla, Chaitan Journal of The Royal Society Interface, Vol. 10, Issue 85 https://doi.org/10.1098/rsif.2013.0297	journal	August 2013
The rRNA Operons of Mycobacterium Smegmatis and Mycobacterium Tuberculosis: Comparison of Promoter Elements and of Neighbouring Upstream Genes Gonzalez-y-Merchand, J. A.; Colston, M. J.; Cox, R. A. Microbiology, Vol. 142, Issue 3 https://doi.org/10.1099/13500872-142-3-667	journal	March 1996
Tuberculosis Drug Development: History and Evolution of the Mechanism-Based Paradigm : Figure 1. Chakraborty, Sumit; Rhee, Kyu Y. Cold Spring Harbor Perspectives in Medicine, Vol. 5, Issue 8 https://doi.org/10.1101/cshperspect.a021147	journal	April 2015
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/s0907444904019158	journal	November 2004
PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16 Wood, S. A.; Kirby, B. M.; Goodwin, C. M. Journal of Applied Microbiology, Vol. 102, Issue 1 https://doi.org/10.1111/j.1365-2672.2006.03043.x	journal	January 2007
PCR screening of 3-amino-5-hydroxybenzoic acid synthase gene leads to identification of ansamycins and AHBA-related antibiotic producers in Actinomycetes Huitu, Z.; Linzhuan, W.; Aiming, L. Journal of Applied Microbiology, Vol. 106, Issue 3 https://doi.org/10.1111/j.1365-2672.2008.04010.x	journal	March 2009
PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes Wang, H. -X.; Chen, Y. -Y.; Ge, L. Journal of Applied Microbiology, Vol. 115, Issue 1 https://doi.org/10.1111/jam.12217	journal	May 2013
Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis : Structural basis for rifamycin resistance of bacterial RNA polymerase Molodtsov, Vadim; Scharf, Nathan T.; Stefan, Maxwell A. Molecular Microbiology, Vol. 103, Issue 6 https://doi.org/10.1111/mmi.13606	journal	January 2017
Biosynthetic Gene Cluster for the Polyenoyltetramic Acid -Lipomycin Bihlmaier, C.; Welle, E.; Hofmann, C. Antimicrobial Agents and Chemotherapy, Vol. 50, Issue 6 https://doi.org/10.1128/aac.00007-06	journal	May 2006
Frequency, Spectrum, and Nonzero Fitness Costs of Resistance to Myxopyronin in Staphylococcus aureus Srivastava, Aashish; Degen, David; Ebright, Yon W. Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 12 https://doi.org/10.1128/aac.01060-12	journal	September 2012
Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes Reddy, Boojala Vijay B.; Kallifidas, Dimitris; Kim, Jeffrey H. Applied and Environmental Microbiology, Vol. 78, Issue 10 https://doi.org/10.1128/aem.00102-12	journal	March 2012
Identification of Two Genes from Streptomyces argillaceus Encoding Glycosyltransferases Involved in Transfer of a Disaccharide during Biosynthesis of the Antitumor Drug Mithramycin Fernández, Ernestina; Weißbach, Ulrike; Reillo, César Sánchez Journal of Bacteriology, Vol. 180, Issue 18 https://doi.org/10.1128/jb.180.18.4929-4937.1998	journal	September 1998
Direct Detection of Multidrug-Resistant Mycobacterium tuberculosis in Clinical Specimens in Low- and High-Incidence Countries by Line Probe Assay Johansen, I. S.; Lundgren, B.; Sosnovskaja, A. Journal of Clinical Microbiology, Vol. 41, Issue 9 https://doi.org/10.1128/jcm.41.9.4454-4456.2003	journal	September 2003
Molecular Characterization of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis Strains Isolated in Poland Sajduda, A.; Brzostek, A.; Poplawska, M. Journal of Clinical Microbiology, Vol. 42, Issue 6 https://doi.org/10.1128/jcm.42.6.2425-2431.2004	journal	June 2004
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome Bhullar, Kirandeep; Waglechner, Nicholas; Pawlowski, Andrew PLoS ONE, Vol. 7, Issue 4 https://doi.org/10.1371/journal.pone.0034953	journal	April 2012
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Isolation and structure of a new ansamycin antibiotic kanglemycin A from a Nocardia. Wang, Nan-Jin; Fu, Yuan; Yan, Gui-Hua The Journal of Antibiotics, Vol. 41, Issue 2 https://doi.org/10.7164/antibiotics.41.264	journal	January 1988
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/elife.01456	journal	September 2013
Global biogeographic sampling of bacterial secondary metabolism Charlop-Powers, Zachary; Owen, Jeremy G.; Reddy, Boojala Vijay B. eLife, Vol. 4 https://doi.org/10.7554/elife.05048	journal	January 2015
Natural-Product Sugar Biosynthesis and Enzymatic Glycodiversification Thibodeaux, Christopher J.; Melançon, Charles E.; Liu, Hung-wen Angewandte Chemie International Edition, Vol. 47, Issue 51 https://doi.org/10.1002/anie.200801204	journal	December 2008
The Structural Diversity of Acidic Lipopeptide Antibiotics Strieker, Matthias; Marahiel, Mohamed A. ChemBioChem, Vol. 10, Issue 4 https://doi.org/10.1002/cbic.200800546	journal	January 2009
Selective Isolation and Ansamycin-Targeted Screenings of Commensal Actinomycetes from the “Maytansinoids-Producing” Arboreal Trewia nudiflora Zhu, Na; Zhao, Peiji; Shen, Yuemao Current Microbiology, Vol. 58, Issue 1 https://doi.org/10.1007/s00284-008-9284-8	journal	October 2008
Studies of the binding of Escherichia coli RNA polymerase to DNA Hinkle, David C.; Mangel, Walter F.; Chamberlin, Michael J. Journal of Molecular Biology, Vol. 70, Issue 2 https://doi.org/10.1016/0022-2836(72)90534-7	journal	September 1972
Rifamycins: an insight into biological activity based on structural investigations Brufani, M.; Cerrini, S.; Fedeli, W. Journal of Molecular Biology, Vol. 87, Issue 3 https://doi.org/10.1016/0022-2836(74)90094-1	journal	August 1974
7.24 - Antimycobacterium Agents Ma, Z.; Ginsberg, A. M.; Spigelman, M. Comprehensive Medicinal Chemistry II, p. 699-730 https://doi.org/10.1016/B0-08-045044-X/00224-8	book	April 2007
On the mechanism of rifampicin inhibition of RNA synthesis. McClure, W. R.; Cech, C. L. Journal of Biological Chemistry, Vol. 253, Issue 24 https://doi.org/10.1016/S0021-9258(17)34269-2	journal	December 1978
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase Campbell, Elizabeth A.; Korzheva, Nataliya; Mustaev, Arkady Cell, Vol. 104, Issue 6, p. 901-912 https://doi.org/10.1016/S0092-8674(01)00286-0	journal	March 2001
The WHO 2014 Global tuberculosis report—further to go Zumla, Alimuddin; George, Andrew; Sharma, Virendra The Lancet Global Health, Vol. 3, Issue 1 https://doi.org/10.1016/S2214-109X(14)70361-4	journal	January 2015
Allosteric Modulation of the RNA Polymerase Catalytic Reaction Is an Essential Component of Transcription Control by Rifamycins Artsimovitch, Irina; Vassylyeva, Marina N.; Svetlov, Dmitri Cell, Vol. 122, Issue 3 https://doi.org/10.1016/j.cell.2005.07.014	journal	August 2005
Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F. Chemistry & Biology, Vol. 21, Issue 9 https://doi.org/10.1016/j.chembiol.2014.08.006	journal	September 2014
Drug resistance-conferring mutations in Mycobacterium tuberculosis from pulmonary tuberculosis patients in Southwest Ethiopia Tadesse, Mulualem; Aragaw, Dossegnaw; Dimah, Belayneh International Journal of Mycobacteriology, Vol. 5, Issue 2 https://doi.org/10.1016/j.ijmyco.2016.02.009	journal	June 2016
Prevalence of mutations in genes associated with rifampicin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates Muthaiah, Muthuraj; Shivekar, Smita Sunil; Cuppusamy Kapalamurthy, Vidya Raj Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, Vol. 8 https://doi.org/10.1016/j.jctube.2017.06.001	journal	August 2017
Frequency of multi-drug resistance and mutations in Mycobacterium tuberculosis isolates from Punjab state of India Singhal, Ritu; Arora, Jyoti; Sah, Grish C. Journal of Epidemiology and Global Health, Vol. 7, Issue 3 https://doi.org/10.1016/j.jegh.2017.05.002	journal	September 2017
Molecular analysis of rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis isolates by multiple allele specific polymerase chain reaction in Puducherry, South India Thirumurugan, Ravibalan; Kathirvel, Maruthai; Vallayyachari, Kommoju Journal of Infection and Public Health, Vol. 8, Issue 6 https://doi.org/10.1016/j.jiph.2015.05.003	journal	November 2015
Comprehensive Analysis of Distinctive Polyketide and Nonribosomal Peptide Structural Motifs Encoded in Microbial Genomes Minowa, Yohsuke; Araki, Michihiro; Kanehisa, Minoru Journal of Molecular Biology, Vol. 368, Issue 5 https://doi.org/10.1016/j.jmb.2007.02.099	journal	May 2007
Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition Lin, Wei; Mandal, Soma; Degen, David Molecular Cell, Vol. 66, Issue 2 https://doi.org/10.1016/j.molcel.2017.03.001	journal	April 2017
Glycopeptide and Lipoglycopeptide Antibiotics Kahne, Dan; Leimkuhler, Catherine; Lu, Wei Chemical Reviews, Vol. 105, Issue 2 https://doi.org/10.1021/cr030103a	journal	February 2005
Comprehensive Study on Structure−Activity Relationships of Rifamycins: Discussion of Molecular and Crystal Structure and Spectroscopic and Thermochemical Properties of Rifamycin O Bacchi, Alessia; Pelizzi, Giancarlo; Nebuloni, Marino Journal of Medicinal Chemistry, Vol. 41, Issue 13 https://doi.org/10.1021/jm970791o	journal	June 1998
Chaxamycins A–D, Bioactive Ansamycins from a Hyper-arid Desert Streptomyces sp. Rateb, Mostafa E.; Houssen, Wael E.; Arnold, Markus Journal of Natural Products, Vol. 74, Issue 6 https://doi.org/10.1021/np200320u	journal	June 2011
Pyrosequencing enumerates and contrasts soil microbial diversity Roesch, Luiz F. W.; Fulthorpe, Roberta R.; Riva, Alberto The ISME Journal, Vol. 1, Issue 4 https://doi.org/10.1038/ismej.2007.53	journal	July 2007
The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review Floss, Heinz G.; Yu, Tin-Wein; Arakawa, Kenji The Journal of Antibiotics, Vol. 64, Issue 1 https://doi.org/10.1038/ja.2010.139	journal	November 2010
Resistance to rifampicin: a review Goldstein, Beth P. The Journal of Antibiotics, Vol. 67, Issue 9 https://doi.org/10.1038/ja.2014.107	journal	August 2014
Antibiotic resistance is ancient D’Costa, Vanessa M.; King, Christine E.; Kalan, Lindsay Nature, Vol. 477, Issue 7365 https://doi.org/10.1038/nature10388	journal	August 2011
NIH Image to ImageJ: 25 years of image analysis Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W. Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2089	journal	June 2012
Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules Brady, Sean F. Nature Protocols, Vol. 2, Issue 5 https://doi.org/10.1038/nprot.2007.195	journal	May 2007
The metagenomics of soil Daniel, Rolf Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1160	journal	June 2005
Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis He, Si Mei; Song, Wan Ling; Cong, Kun Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-08672-w	journal	August 2017
Bisintercalator natural products with potential therapeutic applications: isolation, structure determination, synthetic and biological studies Dawson, Simon; Malkinson, John P.; Paumier, David Nat. Prod. Rep., Vol. 24, Issue 1 https://doi.org/10.1039/B516347C	journal	January 2007
Molecular genetic basis of antimicrobial agent resistance inMycobacterium tuberculosis: 1998 update Ramaswamy, S.; Musser, J. M. Tubercle and Lung Disease, Vol. 79, Issue 1 https://doi.org/10.1054/tuld.1998.0002	journal	January 1998
Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center Feklistov, A.; Mekler, V.; Jiang, Q. Proceedings of the National Academy of Sciences, Vol. 105, Issue 39 https://doi.org/10.1073/pnas.0802822105	journal	September 2008
Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products Owen, J. G.; Reddy, B. V. B.; Ternei, M. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 29 https://doi.org/10.1073/pnas.1222159110	journal	July 2013
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors Owen, Jeremy G.; Charlop-Powers, Zachary; Smith, Alexandra G. Proceedings of the National Academy of Sciences, Vol. 112, Issue 14 https://doi.org/10.1073/pnas.1501124112	journal	March 2015
Cation-pi interactions in structural biology Gallivan, J. P.; Dougherty, D. A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 17 https://doi.org/10.1073/pnas.96.17.9459	journal	August 1999
Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme Basu, Ritwika S.; Warner, Brittany A.; Molodtsov, Vadim Journal of Biological Chemistry, Vol. 289, Issue 35 https://doi.org/10.1074/jbc.M114.584037	journal	June 2014
Molecular Cloning and Characterization of CYP719, a Methylenedioxy Bridge-forming Enzyme That Belongs to a Novel P450 Family, from cultured Coptis japonica Cells Ikezawa, Nobuhiro; Tanaka, Masaru; Nagayoshi, Masanori Journal of Biological Chemistry, Vol. 278, Issue 40 https://doi.org/10.1074/jbc.M302470200	journal	May 2003
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
History of the Development of Rifampin Sensi, P. Clinical Infectious Diseases, Vol. 5, Issue Supplement_3 https://doi.org/10.1093/clinids/5.Supplement_3.S402	journal	July 1983
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Ab initio gene identification in metagenomic sequences Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark Nucleic Acids Research, Vol. 38, Issue 12 https://doi.org/10.1093/nar/gkq275	journal	April 2010
Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape Pupov, Danil; Kuzin, Ivan; Bass, Irina Nucleic Acids Research, Vol. 42, Issue 7 https://doi.org/10.1093/nar/gkt1384	journal	January 2014
Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD Davis, Elizabeth; Chen, James; Leon, Katherine Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1231	journal	December 2014
Engineering the acyltransferase substrate specificity of assembly line polyketide synthases Dunn, Briana J.; Khosla, Chaitan Journal of The Royal Society Interface, Vol. 10, Issue 85 https://doi.org/10.1098/rsif.2013.0297	journal	August 2013
The rRNA Operons of Mycobacterium Smegmatis and Mycobacterium Tuberculosis: Comparison of Promoter Elements and of Neighbouring Upstream Genes Gonzalez-y-Merchand, J. A.; Colston, M. J.; Cox, R. A. Microbiology, Vol. 142, Issue 3 https://doi.org/10.1099/13500872-142-3-667	journal	March 1996
Tuberculosis Drug Development: History and Evolution of the Mechanism-Based Paradigm : Figure 1. Chakraborty, Sumit; Rhee, Kyu Y. Cold Spring Harbor Perspectives in Medicine, Vol. 5, Issue 8 https://doi.org/10.1101/cshperspect.a021147	journal	April 2015
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16 Wood, S. A.; Kirby, B. M.; Goodwin, C. M. Journal of Applied Microbiology, Vol. 102, Issue 1 https://doi.org/10.1111/j.1365-2672.2006.03043.x	journal	January 2007
PCR screening of 3-amino-5-hydroxybenzoic acid synthase gene leads to identification of ansamycins and AHBA-related antibiotic producers in Actinomycetes Huitu, Z.; Linzhuan, W.; Aiming, L. Journal of Applied Microbiology, Vol. 106, Issue 3 https://doi.org/10.1111/j.1365-2672.2008.04010.x	journal	March 2009
Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov: Three new Amycolatopsis species Everest, G. J.; Meyers, P. R. Journal of Applied Microbiology, Vol. 111, Issue 2 https://doi.org/10.1111/j.1365-2672.2011.05058.x	journal	June 2011
Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets van Kessel, Julia C.; Hatfull, Graham F. Molecular Microbiology, Vol. 67, Issue 5 https://doi.org/10.1111/j.1365-2958.2008.06109.x	journal	March 2008
PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes Wang, H. -X.; Chen, Y. -Y.; Ge, L. Journal of Applied Microbiology, Vol. 115, Issue 1 https://doi.org/10.1111/jam.12217	journal	May 2013
Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis : Structural basis for rifamycin resistance of bacterial RNA polymerase Molodtsov, Vadim; Scharf, Nathan T.; Stefan, Maxwell A. Molecular Microbiology, Vol. 103, Issue 6 https://doi.org/10.1111/mmi.13606	journal	January 2017
Biosynthetic Gene Cluster for the Polyenoyltetramic Acid -Lipomycin Bihlmaier, C.; Welle, E.; Hofmann, C. Antimicrobial Agents and Chemotherapy, Vol. 50, Issue 6 https://doi.org/10.1128/AAC.00007-06	journal	May 2006
Frequency, Spectrum, and Nonzero Fitness Costs of Resistance to Myxopyronin in Staphylococcus aureus Srivastava, Aashish; Degen, David; Ebright, Yon W. Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 12 https://doi.org/10.1128/AAC.01060-12	journal	September 2012
Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes Reddy, Boojala Vijay B.; Kallifidas, Dimitris; Kim, Jeffrey H. Applied and Environmental Microbiology, Vol. 78, Issue 10 https://doi.org/10.1128/AEM.00102-12	journal	March 2012
Identification of Two Genes from Streptomyces argillaceus Encoding Glycosyltransferases Involved in Transfer of a Disaccharide during Biosynthesis of the Antitumor Drug Mithramycin Fernández, Ernestina; Weißbach, Ulrike; Reillo, César Sánchez Journal of Bacteriology, Vol. 180, Issue 18 https://doi.org/10.1128/JB.180.18.4929-4937.1998	journal	September 1998
Performance of the Genotype MTBDR Line Probe Assay for Detection of Resistance to Rifampin and Isoniazid in Strains of Mycobacterium tuberculosis with Low- and High-Level Resistance Brossier, F.; Veziris, N.; Truffot-Pernot, C. Journal of Clinical Microbiology, Vol. 44, Issue 10 https://doi.org/10.1128/JCM.01054-06	journal	October 2006
Characterization of rpoB Mutations in Rifampin-Resistant Clinical Isolates of Mycobacterium tuberculosis from Turkey by DNA Sequencing and Line Probe Assay Cavusoglu, C.; Hilmioglu, S.; Guneri, S. Journal of Clinical Microbiology, Vol. 40, Issue 12 https://doi.org/10.1128/JCM.40.12.4435-4438.2002	journal	December 2002
Direct Detection of Multidrug-Resistant Mycobacterium tuberculosis in Clinical Specimens in Low- and High-Incidence Countries by Line Probe Assay Johansen, I. S.; Lundgren, B.; Sosnovskaja, A. Journal of Clinical Microbiology, Vol. 41, Issue 9 https://doi.org/10.1128/JCM.41.9.4454-4456.2003	journal	September 2003
Molecular Characterization of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis Strains Isolated in Poland Sajduda, A.; Brzostek, A.; Poplawska, M. Journal of Clinical Microbiology, Vol. 42, Issue 6 https://doi.org/10.1128/JCM.42.6.2425-2431.2004	journal	June 2004
Rapid Molecular Screening for Multidrug-Resistant Tuberculosis in a High-Volume Public Health Laboratory in South Africa Barnard, Marinus; Albert, Heidi; Coetzee, Gerrit American Journal of Respiratory and Critical Care Medicine, Vol. 177, Issue 7 https://doi.org/10.1164/rccm.200709-1436OC	journal	April 2008
BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler Zhang, Tongwu; Luo, Yingfeng; Chen, Yaping BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-567	journal	January 2012
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome Bhullar, Kirandeep; Waglechner, Nicholas; Pawlowski, Andrew PLoS ONE, Vol. 7, Issue 4 https://doi.org/10.1371/journal.pone.0034953	journal	April 2012
Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics Perron, Gabriel G.; Whyte, Lyle; Turnbaugh, Peter J. PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0069533	journal	March 2015
Isolation and structure of a new ansamycin antibiotic kanglemycin A from a Nocardia. Wang, Nan-Jin; Fu, Yuan; Yan, Gui-Hua The Journal of Antibiotics, Vol. 41, Issue 2 https://doi.org/10.7164/antibiotics.41.264	journal	January 1988
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
Global biogeographic sampling of bacterial secondary metabolism Charlop-Powers, Zachary; Owen, Jeremy G.; Reddy, Boojala Vijay B. eLife, Vol. 4 https://doi.org/10.7554/eLife.05048	journal	January 2015
Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA Hubin, Elizabeth A.; Fay, Allison; Xu, Catherine eLife, Vol. 6 https://doi.org/10.7554/eLife.22520	journal	January 2017

Similar Records

The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase

Journal Article · 2020 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1763105

Lilic, Mirjana; Chen, James; Boyaci, Hande; +8 more

Rifamycin Antibiotic Resistance by ADP-Ribosylation: Structure and Diversity of Arr

Journal Article · 2007 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:980437

Baysarowich, J; Koteva, K; Hughes, D; +5 more

Structural, Functional, and Genetic Analysis of Sorangicin Inhibition of Bacterial RNA Polymerase

Journal Article · 2004 · EMBO J. · OSTI ID:913857

Campbell, E; Pavlova, O; Zenkin, N; +5 more

Related Subjects

99 GENERAL AND MISCELLANEOUS
Bacterial transcription
Metagenomics
Natural products
X-ray crystallography

Title: Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism

Citation Formats

References (127)

Similar Records

Related Subjects