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  1. Article: Transcription-coupled global genomic repair in E. coli.

    Nudler, Evgeny

    Trends in biochemical sciences

    2023  Volume 48, Issue 10, Page(s) 873–882

    Abstract: The nucleotide excision repair (NER) pathway removes helix-distorting lesions from DNA in all organisms. Escherichia coli has long been a model for understanding NER, which is traditionally divided into major and minor subpathways known as global genome ... ...

    Abstract The nucleotide excision repair (NER) pathway removes helix-distorting lesions from DNA in all organisms. Escherichia coli has long been a model for understanding NER, which is traditionally divided into major and minor subpathways known as global genome repair (GGR) and transcription-coupled repair (TCR), respectively. TCR has been assumed to be mediated exclusively by Mfd, a DNA translocase of minimal NER phenotype. This review summarizes the evidence that shaped the traditional view of NER in bacteria, and reviews data supporting a new model in which GGR and TCR are inseparable. In this new model, RNA polymerase serves both as the essential primary sensor of bulky DNA lesions genome-wide and as the delivery platform for the assembly of functional NER complexes in living cells.
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Transcription, Genetic ; DNA Repair ; DNA Damage ; DNA/metabolism ; Genomics ; Receptors, Antigen, T-Cell
    Chemical Substances DNA (9007-49-2) ; Receptors, Antigen, T-Cell
    Language English
    Publishing date 2023-08-07
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2023.07.007
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  2. Article ; Online: Transcription-coupled global genomic repair in E. coli

    Nudler, Evgeny

    Trends in Biochemical Sciences. 2023 Aug. 07,

    2023  

    Abstract: The nucleotide excision repair (NER) pathway removes helix-distorting lesions from DNA in all organisms. Escherichia coli has long been a model for understanding NER, which is traditionally divided into major and minor subpathways known as global genome ... ...

    Abstract The nucleotide excision repair (NER) pathway removes helix-distorting lesions from DNA in all organisms. Escherichia coli has long been a model for understanding NER, which is traditionally divided into major and minor subpathways known as global genome repair (GGR) and transcription-coupled repair (TCR), respectively. TCR has been assumed to be mediated exclusively by Mfd, a DNA translocase of minimal NER phenotype. This review summarizes the evidence that shaped the traditional view of NER in bacteria, and reviews data supporting a new model in which GGR and TCR are inseparable. In this new model, RNA polymerase serves both as the essential primary sensor of bulky DNA lesions genome-wide and as the delivery platform for the assembly of functional NER complexes in living cells.
    Keywords DNA ; DNA repair ; DNA-directed RNA polymerase ; Escherichia coli ; genome ; genomics ; models ; phenotype ; nucleotide excision repair (NER) ; transcription-coupled repair (TCR) ; UvrABCD ; transcription elongation/termination/antitermination ; backtracking ; ppGpp
    Language English
    Dates of publication 2023-0807
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2023.07.007
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  3. Article ; Online: Bacterial histones unveiled.

    Pani, Bibhusita / Nudler, Evgeny

    Nature microbiology

    2023  Volume 8, Issue 11, Page(s) 1939–1941

    MeSH term(s) Histones ; Bacteria ; Immunity, Innate
    Chemical Substances Histones
    Language English
    Publishing date 2023-10-19
    Publishing country England
    Document type Journal Article
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01509-5
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  4. Article ; Online: RNA polymerase and ppGpp deliver a one-two punch to antibiotics.

    Rasouly, Aviram / Nudler, Evgeny

    Molecular cell

    2023  Volume 83, Issue 8, Page(s) 1204–1205

    Abstract: Mutation rates are elevated in response to sub-inhibitory concentrations of antibiotics. In this issue, Zhai et al. ...

    Abstract Mutation rates are elevated in response to sub-inhibitory concentrations of antibiotics. In this issue, Zhai et al.
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Guanosine Tetraphosphate/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; DNA-Directed RNA Polymerases/genetics ; Gene Expression Regulation, Bacterial
    Chemical Substances Escherichia coli Proteins ; Guanosine Tetraphosphate (33503-72-9) ; Anti-Bacterial Agents ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2023-04-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2023.03.024
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  5. Article ; Online: The very hungry bactericidal antibiotics.

    Rasouly, Aviram / Nudler, Evgeny

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 28, Page(s) e2208035119

    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacteria/enzymology ; Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Phosphoenolpyruvate Sugar Phosphotransferase System/metabolism
    Chemical Substances Anti-Bacterial Agents ; Phosphoenolpyruvate Sugar Phosphotransferase System (EC 2.7.1.-)
    Language English
    Publishing date 2022-07-08
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2208035119
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  6. Article ; Online: RNA polymerase and ppGpp deliver a one-two punch to antibiotics

    Rasouly, Aviram / Nudler, Evgeny

    Molecular Cell. 2023 Apr., v. 83, no. 8 p.1204-1205

    2023  

    Abstract: Mutation rates are elevated in response to sub-inhibitory concentrations of antibiotics. In this issue, Zhai et al.¹ report a role for both ppGpp binding sites on RNAP in stress-induced mutagenesis. ...

    Abstract Mutation rates are elevated in response to sub-inhibitory concentrations of antibiotics. In this issue, Zhai et al.¹ report a role for both ppGpp binding sites on RNAP in stress-induced mutagenesis.
    Keywords DNA-directed RNA polymerase ; antibiotics ; binding sites ; cells ; mutagenesis ; mutation rate
    Language English
    Dates of publication 2023-04
    Size p. 1204-1205.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2023.03.024
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  7. Article ; Online: General transcription factor from Escherichia coli with a distinct mechanism of action.

    Vasilyev, Nikita / Liu, Mengjie M J / Epshtein, Vitaly / Shamovsky, Ilya / Nudler, Evgeny

    Nature structural & molecular biology

    2024  Volume 31, Issue 1, Page(s) 141–149

    Abstract: Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) ... ...

    Abstract Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) σ
    MeSH term(s) Escherichia coli/metabolism ; Sigma Factor/chemistry ; Sigma Factor/genetics ; Sigma Factor/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Escherichia coli Proteins/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Transcription Factors, General/genetics ; Transcription Factors, General/metabolism ; Transcription, Genetic ; Bacterial Proteins/metabolism
    Chemical Substances Sigma Factor ; Transcription Factors ; Escherichia coli Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Transcription Factors, General ; Bacterial Proteins
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-023-01154-w
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  8. Article ; Online: Reactive oxygen species as the long arm of bactericidal antibiotics.

    Rasouly, Aviram / Nudler, Evgeny

    Proceedings of the National Academy of Sciences of the United States of America

    2019  Volume 116, Issue 20, Page(s) 9696–9698

    MeSH term(s) Anti-Bacterial Agents ; Bacteria ; Cell Death ; Reactive Oxygen Species
    Chemical Substances Anti-Bacterial Agents ; Reactive Oxygen Species
    Language English
    Publishing date 2019-05-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1905291116
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  9. Article ; Online: Towards the unified principles of transcription termination.

    Svetlov, Vladimir / Nudler, Evgeny

    The EMBO journal

    2019  Volume 39, Issue 3, Page(s) e104112

    Abstract: Discovery of the role of bacterial RNase J1 in termination of transcription suggests common allosteric principles and mechanistic congruency of termination between bacteria and eukaryotes, in which an unrelated RNase Xrn2/Rat1 plays a similar role. ...

    Abstract Discovery of the role of bacterial RNase J1 in termination of transcription suggests common allosteric principles and mechanistic congruency of termination between bacteria and eukaryotes, in which an unrelated RNase Xrn2/Rat1 plays a similar role.
    MeSH term(s) Animals ; Bacillus subtilis ; Exoribonucleases ; Torpedo ; Transcription Termination, Genetic ; Transcription, Genetic
    Chemical Substances Exoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2019-12-30
    Publishing country England
    Document type News ; Comment
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.15252/embj.2019104112
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  10. Article ; Online: Persistence of backtracking by human RNA polymerase II.

    Yang, Kevin B / Rasouly, Aviram / Epshtein, Vitaly / Martinez, Criseyda / Nguyen, Thao / Shamovsky, Ilya / Nudler, Evgeny

    Molecular cell

    2024  Volume 84, Issue 5, Page(s) 897–909.e4

    Abstract: RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide ... ...

    Abstract RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown. Consequently, we developed a method to directly sequence the extruded, "backtracked" 3' RNA. Our data show that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctions and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking can potentially affect diverse gene expression programs.
    MeSH term(s) Humans ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA/genetics ; Transcription, Genetic ; DNA-Directed RNA Polymerases/genetics
    Chemical Substances RNA Polymerase II (EC 2.7.7.-) ; RNA (63231-63-0) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2024-02-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.01.019
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