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Article ; Online: tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector.

Jain, Ishita / Kolesnik, Matvey / Kuznedelov, Konstantin / Minakhin, Leonid / Morozova, Natalia / Shiriaeva, Anna / Kirillov, Alexandr / Medvedeva, Sofia / Livenskyi, Alexei / Kazieva, Laura / Makarova, Kira S / Koonin, Eugene V / Borukhov, Sergei / Severinov, Konstantin / Semenova, Ekaterina

Science advances

2024 Volume 10, Issue 17, Page(s) eadl0164

Abstract: Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA-guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes ... ...

Abstract	Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA-guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by
MeSH term(s)	RNA, Transfer/genetics ; RNA, Transfer/metabolism ; CRISPR-Cas Systems ; Anticodon/genetics ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Leptotrichia/genetics ; Leptotrichia/metabolism ; CRISPR-Associated Proteins/metabolism ; CRISPR-Associated Proteins/genetics ; Bacteriophages/genetics ; RNA Cleavage
Chemical Substances	RNA, Transfer (9014-25-9) ; Anticodon ; CRISPR-Associated Proteins
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adl0164
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors.

Arseniev, Anatolii / Panfilov, Mikhail / Pobegalov, Georgii / Potyseva, Alina / Pavlinova, Polina / Yakunina, Maria / Lee, Jookyung / Borukhov, Sergei / Severinov, Konstantin / Khodorkovskii, Mikhail

bioRxiv : the preprint server for biology

2023

Abstract: Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of ... ...

Abstract	Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes of RNAP (ECs) in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway elemental paused state of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the streptolydigin-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl-pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.05.542125
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Article: Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.

Lee, Jookyung / Borukhov, Sergei

Frontiers in molecular biosciences

2016 Volume 3, Page(s) 73

Abstract: DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and ...

Abstract	DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
Language	English
Publishing date	2016-11-09
Publishing country	Switzerland
Document type	Review ; Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2016.00073
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Article ; Online: Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.

Chaban, Anastasiia / Minakhin, Leonid / Goldobina, Ekaterina / Bae, Brain / Hao, Yue / Borukhov, Sergei / Putzeys, Leena / Boon, Maarten / Kabinger, Florian / Lavigne, Rob / Makarova, Kira S / Koonin, Eugene V / Nair, Satish K / Tagami, Shunsuke / Severinov, Konstantin / Sokolova, Maria L

Nature communications

2024 Volume 15, Issue 1, Page(s) 317

Abstract: Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) ... ...

Abstract	Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
MeSH term(s)	Pyridinolcarbamate ; Virion/genetics ; Bacteriophages/genetics ; Bacterial Typing Techniques ; DNA-Directed RNA Polymerases/genetics
Chemical Substances	Pyridinolcarbamate (81R511UV73) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44630-z
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Article ; Online: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.

Fraser, Alec / Sokolova, Maria L / Drobysheva, Arina V / Gordeeva, Julia V / Borukhov, Sergei / Jumper, John / Severinov, Konstantin V / Leiman, Petr G

Nature communications

2022 Volume 13, Issue 1, Page(s) 3526

Abstract: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 ... ...

Abstract	Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
MeSH term(s)	DNA-Directed RNA Polymerases/metabolism ; Deoxyuridine ; Promoter Regions, Genetic/genetics ; RNA, Viral ; Sigma Factor/metabolism ; Transcription, Genetic ; Viral Replicase Complex Proteins
Chemical Substances	RNA, Viral ; Sigma Factor ; Viral Replicase Complex Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Deoxyuridine (W78I7AY22C)
Language	English
Publishing date	2022-06-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31214-6
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Article ; Online: Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli.

Sutormin, Dmitry / Galivondzhyan, Alina / Musharova, Olga / Travin, Dmitrii / Rusanova, Anastasiia / Obraztsova, Kseniya / Borukhov, Sergei / Severinov, Konstantin

Nature communications

2022 Volume 13, Issue 1, Page(s) 4524

Abstract: Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is colocalized, genome- ...

Abstract	Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is colocalized, genome-wide, with transcribing RNA polymerase (RNAP). Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, colocalization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched upstream (within up to 12-15 kb) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP:EcTopoI interaction by either overexpression of EcTopoI competitor (CTD or inactive EcTopoI Y319F mutant) or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, uncoupling of the RNAP:EcTopoI interaction leads to R-loops accumulation genome-wide, indicating that this interaction is required for prevention of R-loops formation.
MeSH term(s)	DNA Topoisomerases, Type I/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; R-Loop Structures ; Transcription, Genetic
Chemical Substances	Escherichia coli Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2022-08-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-32106-5
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Article ; Online: Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli

Dmitry Sutormin / Alina Galivondzhyan / Olga Musharova / Dmitrii Travin / Anastasiia Rusanova / Kseniya Obraztsova / Sergei Borukhov / Konstantin Severinov

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 19

Abstract: In E. coli, disruption of TopoI and RNAP interaction decreases cells viability and leads to hypernegative DNA supercoiling and R loops accumulation. TopoI and DNA gyrase bind around transcription units and TopoI recognizes cleavage sites by a specific ... ...

Abstract	In E. coli, disruption of TopoI and RNAP interaction decreases cells viability and leads to hypernegative DNA supercoiling and R loops accumulation. TopoI and DNA gyrase bind around transcription units and TopoI recognizes cleavage sites by a specific motif and negative supercoiling.
Keywords	Science ; Q
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bacterial RNA polymerase-DNA interaction - the driving force of gene expression and the target for drug action

Sergei Borukhov / Jookyung Lee

Frontiers in Molecular Biosciences, Vol

2016 Volume 3

Abstract	DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
Keywords	RNA Polymerase I ; Transcription Factors ; Transcription ; Genetic ; Transcriptional Activation ; crp ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2016-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail

Anastasiia Chaban / Leonid Minakhin / Ekaterina Goldobina / Brain Bae / Yue Hao / Sergei Borukhov / Leena Putzeys / Maarten Boon / Florian Kabinger / Rob Lavigne / Kira S. Makarova / Eugene V. Koonin / Satish K. Nair / Shunsuke Tagami / Konstantin Severinov / Maria L. Sokolova

Nature Communications, Vol 15, Iss 1, Pp 1-

2024 Volume 12

Abstract: Abstract Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA ... ...

Abstract	Abstract Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
Keywords	Science ; Q
Subject code	612
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: GNAT toxins evolve toward narrow tRNA target specificities.

Bikmetov, Dmitry / Hall, Alexander M J / Livenskyi, Alexei / Gollan, Bridget / Ovchinnikov, Stepan / Gilep, Konstantin / Kim, Jenny Y / Larrouy-Maumus, Gerald / Zgoda, Viktor / Borukhov, Sergei / Severinov, Konstantin / Helaine, Sophie / Dubiley, Svetlana

Nucleic acids research

2022 Volume 50, Issue 10, Page(s) 5807–5817

Abstract: Type II toxin-antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via ... ...

Abstract	Type II toxin-antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via acetylation of aminoacyl-tRNAs. In this work, we explored the evolutionary trajectory of GNAT toxins. Using LC/MS detection of acetylated aminoacyl-tRNAs combined with ribosome profiling, we systematically investigated the in vivo substrate specificity of an array of diverse GNAT toxins. Our functional data show that the majority of GNAT toxins are specific to Gly-tRNA isoacceptors. However, the phylogenetic analysis shows that the ancestor of GNAT toxins was likely a relaxed specificity enzyme capable of acetylating multiple elongator tRNAs. Together, our data provide a remarkable snapshot of the evolution of substrate specificity.
MeSH term(s)	Antitoxins/genetics ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Phylogeny ; RNA, Transfer/genetics ; RNA, Transfer, Amino Acyl/genetics ; Toxin-Antitoxin Systems/genetics
Chemical Substances	Antitoxins ; Bacterial Proteins ; Bacterial Toxins ; RNA, Transfer, Amino Acyl ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2022-06-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac356
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