RNA Polymerase Inhibitors with Activity against Rifampin-Resistant Mutants of Staphylococcus aureus

ABSTRACT A collection of rifampin-resistant mutants of Staphylococcus aureus with characterized RNA polymerase β-subunit (rpoB) gene mutations was cross-screened against a number of other RNA polymerase inhibitors to correlate susceptibility with specific rpoB genotypes. The rpoB mutants were cross-resistant to streptolydigin and sorangicin A. In contrast, thiolutin, holomycin, corallopyronin A, and ripostatin A retained activity against the rpoB mutants. The second group of inhibitors may be of interest as drug development candidates.

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A Mutation of RNA Polymerase β′ Subunit (RpoC) Converts Heterogeneously Vancomycin-Intermediate Staphylococcus aureus (hVISA) into “Slow VISA”

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00135-15 ◽

2015 ◽

Vol 59 (7) ◽

pp. 4215-4225 ◽

Cited By ~ 13

Author(s):

Miki Matsuo ◽

Tomomi Hishinuma ◽

Yuki Katayama ◽

Keiichi Hiramatsu

Keyword(s):

Staphylococcus Aureus ◽

Cell Wall ◽

Rna Polymerase ◽

Stringent Response ◽

Whole Genome ◽

Multicopy Plasmid ◽

Β Subunit ◽

Whole Genome Analysis ◽

Content Type ◽

Peptidoglycan Biosynthesis

ABSTRACTVarious mutations in therpoBgene, which encodes the RNA polymerase β subunit, are associated with increased vancomycin (VAN) resistance in vancomycin-intermediateStaphylococcus aureus(VISA) and heterogeneously VISA (hVISA) strains. We reported thatrpoBmutations are also linked to the expression of the recently found “slow VISA” (sVISA) phenotype (M. Saito, Y. Katayama, T. Hishinuma, A. Iwamoto, Y. Aiba, K Kuwahara-Arai, L. Cui, M. Matsuo, N. Aritaka, and K. Hiramatsu, Antimicrob Agents Chemother 58:5024–5035, 2014,http://dx.doi.org/10.1128/AAC.02470-13). Because RpoC and RpoB are components of RNA polymerase, we examined the effect of therpoC(P440L) mutation on the expression of the sVISA phenotype in the Mu3fdh2*V6-5 strain (V6-5), which was derived from a previously reported hVISA strain with the VISA phenotype. V6-5 had an extremely prolonged doubling time (DT) (72 min) and high vancomycin MIC (16 mg/liter). However, the phenotype of V6-5 was unstable, and the strain frequently reverted to hVISA with concomitant loss of low growth rate, cell wall thickness, and reduced autolysis. Whole-genome sequencing of phenotypic revertant strain V6-5-L1 and comparison with V6-5 revealed a second mutation, F562L, inrpoC. Introduction of the wild-type (WT)rpoCgene using a multicopy plasmid resolved the sVISA phenotype of V6-5, indicating that therpoC(P440L) mutant expressed the sVISA phenotype in hVISA. To investigate the mechanisms of resistance in the sVISA strain, we independently isolated an additional 10 revertants to hVISA and VISA. In subsequent whole-genome analysis, we identified compensatory mutations in the genes of three distinct functional categories: therpoCgene itself as regulatory mutations, peptidoglycan biosynthesis genes, andrelQ, which is involved in the stringent response. It appears that therpoC(P440L) mutation causes the sVISA phenotype by augmenting cell wall peptidoglycan synthesis and through the control of the stringent response.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01060-12 ◽

2012 ◽

Vol 56 (12) ◽

pp. 6250-6255 ◽

Cited By ~ 16

Author(s):

Aashish Srivastava ◽

David Degen ◽

Yon W. Ebright ◽

Richard H. Ebright

Keyword(s):

Staphylococcus Aureus ◽

Binding Site ◽

Frequency Spectrum ◽

Resistance Rate ◽

Cross Resistance ◽

Β Subunit ◽

Fitness Costs ◽

Switch Region ◽

Content Type ◽

Resistant Mutants

ABSTRACTThe 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 inStaphylococcus aureus. The resistance rate for Myx is 4 × 10−8to 7 × 10−8per generation, which is equal within error to the resistance rate for Rif (3 × 10−8to 10 × 10−8per 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 inStaphylococcus aureusRNAP and, in parentheses, as inEscherichia coliRNAP). 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.

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Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice

ACS Infectious Diseases ◽

10.1021/acsinfecdis.0c00034 ◽

2020 ◽

Vol 6 (10) ◽

pp. 2573-2581

Author(s):

Jörg Haupenthal ◽

Yannik Kautz ◽

Walid A. M. Elgaher ◽

Linda Pätzold ◽

Teresa Röhrig ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Rna Polymerase ◽

Wound Infection ◽

Infection Model ◽

Polymerase Inhibitors ◽

Bacterial Rna

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Activity of and Development of Resistance to Corallopyronin A, an Inhibitor of RNA Polymerase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01742-10 ◽

2011 ◽

Vol 55 (5) ◽

pp. 2413-2416 ◽

Cited By ~ 17

Author(s):

Katherine Mariner ◽

Martin McPhillie ◽

Rachel Trowbridge ◽

Catriona Smith ◽

Alex J. O'Neill ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antibacterial Activity ◽

Rna Polymerase ◽

Inhibitory Concentration ◽

Drug Candidate ◽

Antibacterial Drug ◽

Content Type ◽

Development Of Resistance ◽

Bacterial Rna ◽

Resistant Mutants

ABSTRACTWe explored the properties of corallopyronin A (CorA), a poorly characterized inhibitor of bacterial RNA polymerase (RNAP). It displayed a 50% inhibitory concentration of 0.73 μM against RNAP, compared with 11.5 nM for rifampin. The antibacterial activity of CorA was also inferior to rifampin, and resistant mutants ofStaphylococcus aureuswere easily selected. The mutations conferring resistance resided in therpoBandrpoCsubunits of RNAP. We conclude that CorA is not a promising antibacterial drug candidate.

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Biochemical and structural analyses reveal critical residues in δ subunit affecting its bindings to β′ subunit of Staphylococcus aureus RNA polymerase

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2021.01.078 ◽

2021 ◽

Vol 545 ◽

pp. 98-104

Author(s):

Zhaozhu Lin ◽

Fulin Wang ◽

Zhuo Shang ◽

Wei Lin

Keyword(s):

Staphylococcus Aureus ◽

Rna Polymerase ◽

Β Subunit ◽

Critical Residues

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Mutation of RNA Polymerase β-Subunit Gene Promotes Heterogeneous-to-Homogeneous Conversion of β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00720-13 ◽

2013 ◽

Vol 57 (10) ◽

pp. 4861-4871 ◽

Cited By ~ 21

Author(s):

Yoshifumi Aiba ◽

Yuki Katayama ◽

Tomomi Hishinuma ◽

Hiroko Murakami-Kuroda ◽

Longzhu Cui ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Rna Polymerase ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phenotypic Expression ◽

Amino Acid Replacement ◽

Whole Genome ◽

Β Subunit ◽

Methicillin Resistant ◽

Content Type

ABSTRACTThree types of phenotypic expression of β-lactam resistance have been reported in methicillin-resistantStaphylococcus aureus(MRSA): heterogeneous, homogeneous, and Eagle-type resistance. Heterogeneous-to-homogeneous conversion of β-lactam resistance is postulated to be caused by a chromosomal mutation (chr*) in addition to the expression of themecAgene. Eagle-type resistance is a unique phenotype ofchr*occurring in pre-MRSA strain N315 whosemecAgene expression is strongly repressed by an intactmecIgene. We here report that certain mutations of therpoBgene, encoding the RNA polymerase β subunit, belong tochr*. We studied homogeneous MRSA (homo-MRSA) strain N315ΔIP-H5 (abbreviated as ΔIP-H5), which was obtained from hetero-MRSA strain N315ΔIP by selection with 8 mg/liter imipenem. Whole-genome sequencing of ΔIP-H5 revealed the presence of a unique mutation in therpoBgene,rpoB(N967I), causing the amino acid replacement of Asn by Ile at position 967 of RpoB. The effect of therpoB(N967I) mutation was confirmed by constructing a revertant H5rpoB(I967N) strain as well as an N315-derived mutant, N315rpoB(N967I). H5rpoB(I967N) regained the hetero-resistance phenotype, and the N315rpoB(N967I) strain showed an Eagle-type phenotype similar to that of the typical Eagle-type MRSA strain N315h4. Furthermore, subsequent whole-genome sequencing revealed that N315h4 also had a missense mutation ofrpoB(R644H). Introduction of therpoB(N967I) mutation was accompanied by decreased autolysis, prolonged doubling time, and tolerance to bactericidal concentrations of methicillin. We consider thatrpoBmutations are the major cause for heterogeneous-to-homogeneous phenotypic conversion of β-lactam resistance in MRSA strain N315 and its derived strains.

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