Mutations induced by Bleomycin, 4-nitroquinoline-1-oxide, and hydrogen peroxide in the rpoB gene of Escherichia coli: Perspective on Mutational Hotspots

Fernandez, Kristen; D’Souza, Sara; Ahn, Jenny J.; Singh, Summer; Bacasen, Erin Mae; Mashiach, Daniel; Mishail, Daniel; Kao, Timothy; Thai, Jasmine; Hwang, Spring; Yaramada, Lekha; Miller, Jeffrey H

doi:10.1016/j.mrfmmm.2020.111702

Cited by 5 publications

(6 citation statements)

References 42 publications

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“…However, the experimental group (pGEX-BaRecJ) yielded a broader spectrum with a more uniform distribution of transitions and transversions and a marked increase in the number of A-C, A-T, and C-G transitions than the control (Figure 1D). BaRecJ mutation method obtained 49 different types of base substitution mutations (Figure 1E), significantly higher than mutagenesis methods such as 5-azacytidine (5AZ), ethyl methanesulfonate (EMS), and 2-aminopurine (2AP) (Fernandez et al, 2020).…”

Section: Resultsmentioning

confidence: 96%

“…We applied the BaRecJ in vivo mutagenesis method to E. coli , achieving the broadest mutation spectrum in rpoB (Fernandez et al, 2020; Badran and Liu, 2015). For S. cerevisiae , using the BaRecJ mutagenesis approach combined with Adaptive Laboratory Evolution (ALE), mutants with high tolerance to acetic acid and ethanol were obtained.…”

Section: Introductionmentioning

confidence: 99%

“…We applied the BaRecJ in vivo mutagenesis method to E. coli, achieving the broadest mutation spectrum in rpoB (Fernandez et al, 2020;Badran and Liu, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

Shang,

Zhang,

et al. 2024

Preprint

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With the continual advancement of technologies such as microbial cultivation, DNA sequencing, bioinformatics, and genetic engineering, methods for microbial breeding have become increasingly diverse. We identified a RecJ enzyme (BaRecJ) with both endonuclease and exonuclease activities from B. alcalophilus. Differing from traditional physical-chemical mutagenesis approaches and the methods based on perturbation factor. this research established a novel mutagenesis method utilizing the endonuclease and exonuclease activities of BaRecJ. Mutagenesis of E. coli was conducted using the BaRecJ method, followed by screening for rifampicin-resistant mutants, rpoB sequencing results demonstrated a broader, more uniform spectrum of mutations and a higher frequency of substitution mutations with this mutagenesis approach. Furthermore, this mutagenesis method was applied to S cerevisiae, resulting in mutants with enhanced tolerance to acetic acid and ethanol, exhibiting improved fermentation performance and flocculation abilities Genomic resequencing analysis summarized genes possibly associated with the tolerance of mutants. Therefore, this approach not only holds immense potential in microbial mutagenesis breeding and adaptive evolution but also, when coupled with genomic resequencing, allows for the rapid identification of genetic loci associated with specific traits.

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Section: Resultsmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

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Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

Shang,

Zhang,

et al. 2024

Preprint

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“…The fingerprint of a mutagen is determined by not only its preference for certain types of mutations, but also for its preference for specific sites even though the same base change is involved. Sometimes these preferential sites have the same nearest neighbors, but often there are strong preferences among the sites with the same nearest neighbors (see Fernandez et al, 2020 for a discussion of this point). Mutational “hotspots” were first described by Benzer (1961), and subsequently by a series of other investigations (Coulondre et al, 1978; Coulondre & Miller, 1977; Farabaugh et al, 1978; Garibyan et al, 2003; Viswanathan et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

“…However, analysis of mutations in rpoB occurring as a result of Pol IV and Pol V induction do not show a preference for A:T→C:G substitutions (Curti et al, 2009; Wolff et al, 2004). Moreover, other relatively weak mutagens, such as bleomycin, do show mutations in rpoB attributable to Pol IV or Pol V, but do not show mutations at the A:T→C:G hotspots seen with AZT, DIDA, and STAV (Fernandez et al, 2020). What is common to all three is that they are chain breakers, and this probably leads, ultimately, to a specific type of oxidative damage, or a specific type of replication error.…”

Section: Discussionmentioning

confidence: 99%

The antiretroviral agents azidothymidine, stavudine, and didanosine have the identical mutational fingerprint in the rpoB region of Escherichia coli

Yaramada¹,

Singh²,

Ge³

et al. 2022

Environ and Mol Mutagen

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We looked at the mutational fingerprints of three antiretroviral (anti-HIV) agents, azidothymidine (AZT), stavudine (STAV), and didanosine (DIDA) in the rpoB system of Escherichia coli and compared them with each other and with the fingerprints of trimethoprim and of spontaneous mutations in a wild-type and a mutT background. All three agents gave virtually identical fingerprints in the wild-type background, causing only A: T!C:G changes at 3 of the 12 A:T!C:G possible sites among the total of 92 possible base substitution mutations, even though AZT and STAV are thymidine analogs but DIDA is an adenosine analog. As all three agents are reverse transcriptase inhibitors, and act as chain blockers, the common fingerprint may be a property of chain blocking agents.anti-HIV agents, bacterial systems, mutagenesis | INTRODUCTIONAzidothymidine (AZT; Zidovudine; 3 0 -azido-3 0 -deoxythymidine), stavudine (STAV; 2 0 ,3 0 -dideoxythymidine), and didanosine (DIDA; 2 0 ,3 0 -dideoxyinosine), depicted in Figure 1, are reverse transcriptase

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High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota

Lee,

Tiffany,

Mahan

et al. 2024

Cell

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Mutations induced by Bleomycin, 4-nitroquinoline-1-oxide, and hydrogen peroxide in the rpoB gene of Escherichia coli: Perspective on Mutational Hotspots

Cited by 5 publications

References 42 publications

Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

The antiretroviral agents azidothymidine, stavudine, and didanosine have the identical mutational fingerprint in the rpoB region of Escherichia coli

High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota

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