<scp><scp>Nus</scp></scp> transcription elongation factors and <scp>RNase III</scp> modulate small ribosome subunit biogenesis in <i><scp>E</scp>scherichia coli</i>

Bubunenko, Mikhail; Court, Donald L.; Refaii, Abdalla Al; Saxena, Shivalika; Korepanov, Alexey P.; Friedman, David I.; Gottesman, Max E.; Alix, Jean‐Hervé

doi:10.1111/mmi.12105

Cited by 45 publications

(60 citation statements)

References 78 publications

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“…NusE, which is now known to be ribosomal small subunit protein S10, binds NusG and as such is thought to be involved in ensuring that a ribosome closely follows the transcribing RNA polymerase, thus coupling translation to transcription (Burmann et al , 2010; McGary and Nudler, 2013). In addition, NusA interacts with translesion DNA polymerases to affect DNA repair (Cohen et al , 2009), and with NusB it may even be involved in intracellular RNA folding and processing (Bubunenko et al , 2013). Thus, these early lambda-host interaction genetic studies revealed previously unsuspected complexities of transcription and led directly to the discovery and characterization of factors that control RNA polymerase elongation and termination.…”

Section: Historical Importance and Recent Progressmentioning

confidence: 99%

Bacteriophage lambda: Early pioneer and still relevant

2015

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Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives have continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.

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Section: Historical Importance and Recent Progressmentioning

confidence: 99%

Bacteriophage lambda: Early pioneer and still relevant

2015

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“…The examples of on/off regulation at the transcript elongation stage, such as promoter-proximal pauses in metazoans (Adelman and Lis, 2012) and antitermination in prokaryotes (Santangelo and Artsimovitch, 2011), are also known. In other cases, transcription elongation control is mediated by coupling of transcription to downstream processes, such as RNA translation, processing, and folding (Proshkin et al, 2010; Bubunenko et al, 2013). The multisubunit RNAPs evolved to elongate relatively inefficiently in the absence of proper coupling, thereby enabling the downstream processes to control the elongation rate.…”

Section: Introductionmentioning

confidence: 99%

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

Turtola

Belogurov

2016

eLife

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Universally conserved factors from NusG family bind at the upstream fork junction of transcription elongation complexes and modulate RNA synthesis in response to translation, processing, and folding of the nascent RNA. Escherichia coli NusG enhances transcription elongation in vitro by a poorly understood mechanism. Here we report that E. coli NusG slows Gre factor-stimulated cleavage of the nascent RNA, but does not measurably change the rates of single nucleotide addition and translocation by a non-paused RNA polymerase. We demonstrate that NusG slows RNA cleavage by inhibiting backtracking. This activity is abolished by mismatches in the upstream DNA and is independent of the gate and rudder loops, but is partially dependent on the lid loop. Our comprehensive mapping of the upstream fork junction by base analogue fluorescence and nucleic acids crosslinking suggests that NusG inhibits backtracking by stabilizing the minimal transcription bubble.DOI: http://dx.doi.org/10.7554/eLife.18096.001

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“…Both NusA and NusB are important for rRNA synthesis and ribosome biogenesis (Bubunenko et al, 2013). Only NusA binds to RNA Pol in vitro .…”

Section: Rna Pol Foci Are Transcription Factories For Rrna Synthesis mentioning

confidence: 99%

Nucleolus-like compartmentalization of the transcription machinery in fast-growing bacterial cells

Jin

Martín-Franco

Sun

et al. 2016

Critical Reviews in Biochemistry and Molecular Biology

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Overview. We have learned a great deal about RNA polymerase (RNA Pol), transcription factors, and the transcriptional regulation mechanisms in prokaryotes for specific genes, operons, or transcriptomes. However, we have only begun to understand how the transcription machinery is 3-dimensionally (3D) organized into bacterial chromosome territories to orchestrate the transcription process and to maintain harmony with the replication machinery in the cell. Much progress has been made recently in our understanding of the spatial organization of the transcription machinery in fast-growing Escherichia coli cells using state-of-the-art superresolution imaging techniques. Co-imaging of RNA polymerase (RNA Pol) with DNA and transcription elongation factors involved in ribosomal RNA (rRNA) synthesis and ribosome biogenesis has revealed similarities between bacteria and eukaryotes in the spatial organization of the transcription machinery for growth genes, most of which are rRNA genes. Evidence supports the notion that RNA Pol molecules are concentrated, forming foci at the clustering of rRNA operons resembling the eukaryotic nucleolus. RNA Pol foci are proposed to be active transcription factories for both rRNA genes expression and ribosome biogenesis to support maximal growth in optimal growing conditions. Thus, in fast-growing bacterial cells, RNA Pol foci mimic eukaryotic Pol I activity, and transcription factories resemble nucleolus-like compartmentation. In addition, the transcription and replication machineries are mostly segregated in space to avoid the conflict between the two major cellular functions in fast-growing cells.

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Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli

Cited by 45 publications

References 78 publications

Bacteriophage lambda: Early pioneer and still relevant

Bacteriophage lambda: Early pioneer and still relevant

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

Nucleolus-like compartmentalization of the transcription machinery in fast-growing bacterial cells

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