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Yulia Yuzenkova

About Yulia Yuzenkova:
No description specified

SEEK ID: https://fairdomhub.org/people/373

Location:  United Kingdom

Expertise: Molecular Biology, Biochemistry

Tools: phage techniques, protein purification, Molecular biology techniques (RNA/DNA/Protein), protein-DNA interactions; gel shifts; footprints; in vitro transcription protein ligan interactions

ORCID: Not specified

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Project positions

Noisy-Strep (University of Newcastle)

Related items

Noisy-Strep

Bistable switches are the key elements of the regulatory networks governing cell development, differentiation and life-strategy decisions. Transcriptional noise is a main determinant that causes switching between different states in bistable systems. By using the human pathogen Streptococcus pneumoniae as a model bacterium, we will investigate how transcriptional fidelity and processivity influence (noisy) gene expression and participate in bistability. To study this question, we will use both
...

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=163

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae
Noisy-Strep

Abstract (Expand)

Transcription by RNA polymerase may be interrupted by pauses caused by backtracking or misincorporation that can be resolved by the conserved bacterial Gre-factors. However, the consequences of such … pausing in the living cell remain obscure. Here, we developed molecular biology and transcriptome sequencing tools in the human pathogen Streptococcus pneumoniae and provide evidence that transcription elongation is rate-limiting on highly expressed genes. Our results suggest that transcription elongation may be a highly regulated step of gene expression in S. pneumoniae. Regulation is accomplished via long-living elongation pauses and their resolution by elongation factor GreA. Interestingly, mathematical modeling indicates that long-living pauses cause queuing of RNA polymerases, which results in 'transcription traffic jams' on the gene and thus blocks its expression. Together, our results suggest that long-living pauses and RNA polymerase queues caused by them are a major problem on highly expressed genes and are detrimental for cell viability. The major and possibly sole function of GreA in S. pneumoniae is to prevent formation of backtracked elongation complexes.

Authors: Yulia Yuzenkova, Pamela Gamba, M. Herber, L. Attaiech, Sulman Shafeeq, Oscar Kuipers, S. Klumpp, Nikolay Zenkin, Jan-Willem Veening

Date Published: 6th Sep 2014

Journal: Nucleic Acids Res

Multiple active centers of multi-subunit RNA polymerases
Noisy-Strep

Abstract (Expand)

The active center of multi-subunit RNA polymerase consists of two modules, the Mg(2+) module, holding the catalytic Mg(2+) ion, and a module made of a flexible domain, the Trigger Loop. Uniquely, the … TL module can be substituted by alternative modules, thus changing the catalytic properties of the active center.

Authors: Yulia Yuzenkova, Mohammad Roghanian, Nikolay Zenkin

Date Published: 10th Jul 2012

Journal: Transcription

Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence
Noisy-Strep

Abstract (Expand)

Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined … by the ability of the elongating RNA polymerase to recognize the sequence of the RNA-DNA hybrid. We show that, independently of thermodynamic stability of the elongation complex, RNA polymerase directly 'senses' the shape and/or identity of base pairs of the RNA-DNA hybrid. Recognition of the RNA-DNA hybrid sequence delays translocation by RNA polymerase, and thus slows down the nucleotide addition cycle through 'in pathway' mechanism. We show that this phenomenon is conserved among bacterial and eukaryotic RNA polymerases, and is involved in regulatory pauses, such as a pause regulating the production of virulence factors in some bacteria and a pause regulating transcription/replication of HIV-1. The results indicate that recognition of RNA-DNA hybrid sequence by multi-subunit RNA polymerases is involved in transcription regulation and may determine the overall rate of transcription elongation.

Authors: Aleksandra Bochkareva, Yulia Yuzenkova, Vasisht R Tadigotla, Nikolay Zenkin

Date Published: 29th Nov 2011

Journal: EMBO J.

A new basal promoter element recognized by RNA polymerase core enzyme
Noisy-Strep

Abstract (Expand)

Bacterial promoters are recognized by RNA polymerase (RNAP) σ subunit, which specifically interacts with the -10 and -35 promoter elements. Here, we provide evidence that the β' zipper, an … evolutionarily conserved loop of the largest subunit of RNAP core, interacts with promoter spacer, a DNA segment that separates the -10 and -35 promoter elements, and facilitates the formation of stable closed promoter complex. Depending on the spacer sequence, the proposed interaction of the β' zipper with the spacer can also facilitate open promoter complex formation and even substitute for interactions of the σ subunit with the -35 element. These results suggest that there exists a novel class of promoters that rely on interaction of the β' zipper with promoter spacer, along with or instead of interactions of σ subunit with the -35 element, for their activity. Finally, our data suggest that sequence-dependent interactions of the β' zipper with DNA can contribute to promoter-proximal σ-dependent RNAP pausing, a recently recognized important step of transcription control.

Authors: Yulia Yuzenkova, Vasisht R Tadigotla, Konstantin Severinov, Nikolay Zenkin

Date Published: 26th Jul 2011

Journal: EMBO J.

Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre
Noisy-Strep

Abstract (Expand)

The highly processive transcription by multi-subunit RNA polymerases (RNAP) can be interrupted by misincorporation or backtracking events that may stall transcription or lead to erroneous transcripts. … Backtracked/misincorporated complexes can be resolved via hydrolysis of the transcript. Here, we show that, in response to misincorporation and/or backtracking, the catalytic domain of RNAP active centre, the trigger loop (TL), is substituted by transcription factor Gre. This substitution turns off the intrinsic TL-dependent hydrolytic activity of RNAP active centre, and exchanges it to a far more efficient Gre-dependent mechanism of RNA hydrolysis. Replacement of the TL by Gre factor occurs only in backtracked/misincorporated complexes, and not in correctly elongating complexes. This controlled switching of RNAP activities allows the processivity of elongation to be unaffected by the hydrolytic activity of Gre, while ensuring efficient proofreading of transcription and resolution of backtracked complexes.

Authors: Mohammad Roghanian, Yulia Yuzenkova, Nikolay Zenkin

Date Published: 27th Jan 2011

Journal: Not specified

Stepwise mechanism for transcription fidelity
Noisy-Strep

Abstract (Expand)

Transcription is the first step of gene expression and is characterized by a high fidelity of RNA synthesis. During transcription, the RNA polymerase active centre discriminates against not just … non-complementary ribo NTP substrates but also against complementary 2'- and 3'-deoxy NTPs. A flexible domain of the RNA polymerase active centre, the Trigger Loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive.

Authors: Yulia Yuzenkova, Aleksandra Bochkareva, Vasisht R Tadigotla, Mohammad Roghanian, Savva Zorov, Konstantin Severinov, Nikolay Zenkin

Date Published: 1st Apr 2010

Journal: BMC Biol.

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