Cellular and molecular phenotypes depending upon the RNA repair system RtcAB of<i>Escherichia coli</i>

Engl, Christoph; Schaefer, Jorrit; Kotta‐Loizou, Ioly; Buck, Martin

doi:10.1093/nar/gkw628

Cited by 27 publications

(46 citation statements)

References 27 publications

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“…In contrast, the σ 54 family contains only one member, σ 54 (also known as σ N ), which binds to similar regions of RNAP, but has no discernible sequence homology and has significant differences in structure (with the exception of the helix-turn-helix motifs) and modes of RNAP regulation [3,6,7]. σ 54 is present in an estimated 60% of bacterial genomes [8], and there are over 135 genes in Escherichia coli regulated by σ 54 that cover a diverse range of stress responses [9], including nitrogen assimilation during starvation, response to antibiotics, carbon metabolism and loss of membrane integrity [10][11][12][13][14]. σ 54 recognises the -12 (GG) and -24 (TGC) promoter regions and binds to the RNAP to form a stable closed complex that rarely spontaneously converts to open complex [15].…”

Section: Introductionmentioning

confidence: 99%

“…Together with structures of the closed complex, an intermediate state where DNA is partially loaded into the RNAP cleft and the open promoter complex, a mechanistic understanding of how bEBPs use ATP to activate transcription can now be proposed. This review summarises current structural models and the emerging understanding of how this special class of AAA + proteins utilises ATPase activities to allow σ 54 -dependent transcription initiation.Biomolecules 2020, 10, 351 2 of 12 during starvation, response to antibiotics, carbon metabolism and loss of membrane integrity [10][11][12][13][14]. σ 54 recognises the -12 (GG) and -24 (TGC) promoter regions and binds to the RNAP to form a stable closed complex that rarely spontaneously converts to open complex [15].Transcriptionally competent open complex formation by the σ 54 holoenzyme requires the actions of activators bound remotely upstream from the transcription start site.…”

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confidence: 99%

“…Biomolecules 2020, 10, 351 2 of 12 during starvation, response to antibiotics, carbon metabolism and loss of membrane integrity [10][11][12][13][14]. σ 54 recognises the -12 (GG) and -24 (TGC) promoter regions and binds to the RNAP to form a stable closed complex that rarely spontaneously converts to open complex [15].…”

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confidence: 99%

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Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

Gao

Danson

et al. 2020

Biomolecules

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Bacterial enhancer-binding proteins (bEBPs) are specialised transcriptional activators. bEBPs are hexameric AAA+ ATPases and use ATPase activities to remodel RNA polymerase (RNAP) complexes that contain the major variant sigma factor, σ54 to convert the initial closed complex to the transcription competent open complex. Earlier crystal structures of AAA+ domains alone have led to proposals of how nucleotide-bound states are sensed and propagated to substrate interactions. Recently, the structure of the AAA+ domain of a bEBP bound to RNAP-σ54-promoter DNA was revealed. Together with structures of the closed complex, an intermediate state where DNA is partially loaded into the RNAP cleft and the open promoter complex, a mechanistic understanding of how bEBPs use ATP to activate transcription can now be proposed. This review summarises current structural models and the emerging understanding of how this special class of AAA+ proteins utilises ATPase activities to allow σ54-dependent transcription initiation.

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Section: Introductionmentioning

confidence: 99%

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Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

Gao

Danson

et al. 2020

Biomolecules

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“…In contrast to a recent report that indicates a shift in the sedimentation of 70S ribosomes in the absence of rtcB (21), we directly analyzed the ribosome profile by separating the ribosomal subunits, 70S monosomes and polysomes from S30 extracts of the respective strains on 10–30% sucrose gradients. As shown in Supplementary Figure S1A, the absence or overexpression of rtcB did not affect the relative positions of ribosomes and subunits.…”

Section: Resultsmentioning

confidence: 99%

The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity inEscherichia coli

et al. 2016

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When Escherichia coli encounters stress, the endoribonuclease MazF initiates a post-transcriptional response that results in the reprogramming of protein synthesis. By removing the 3΄-terminus of the 16S rRNA, MazF generates specialized ribosomes that selectively translate mRNAs likewise processed by MazF. Given the energy required for de novo ribosome biosynthesis, we considered the existence of a repair mechanism operating upon stress relief to recycle the modified ribosomes. Here, we show that the stress-ribosomes and the 3΄-terminal 16S rRNA fragment are stable during adverse conditions. Moreover, employing in vitro and in vivo approaches we demonstrate that the RNA ligase RtcB catalyzes the re-ligation of the truncated 16S rRNA present in specialized ribosomes Thereby their ability to translate canonical mRNAs is fully restored. Together, our findings not only provide a physiological function for the RNA ligase RtcB in bacteria but highlight the reversibility of ribosome heterogeneity, a crucial but hitherto undescribed concept for translational regulation.

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“…57) and that its human counterpart is a catalytic subunit of the tRNA-splicing ligase originally identified by us in the early 1980s (54). This "epilogue" was extended very recently by the publication of data on a possible role of the rtcAB operon in E. coli in RNA repair and the maintenance of ribosome homeostasis (58,59) and, in one specific case, in the re-ligation by RtcB of 16S rRNA cleaved by a stress-induced endoribonuclease (59). Equally inspiring are recent findings implicating cyclase/RtcA in neuronal functions in metazoa, in association with either RNA transport in mouse neurites (60) or the regulation of axon regeneration in Drosophila and rodent neurons (61).…”

Section: Chasing Functions Of the Rna 3-phosphate Cyclase And Other Rmentioning

confidence: 97%

Traversing the RNA world

Filipowicz

2017

Journal of Biological Chemistry

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An invitation to write a "Reflections" type of article creates a certain ambivalence: it is a great honor, but it also infers the end of your professional career. Before you vanish for good, your colleagues look forward to an interesting but entertaining account of the ups-and-downs of your past research and your views on science in general, peppered with indiscrete anecdotes about your former competitors and collaborators. What follows will disappoint those who await complaint and criticism, for example, about the difficulties of doing research in the 1960s and 1970s in Eastern Europe, or those seeking very personal revelations. My scientific life has in fact seen many happy coincidences, much good fortune, and several lucky escapes from situations that at the time were quite scary. I have also been fortunate with regard to competitors and collaborators, particularly because, whenever possible, I tried to "neutralize" my rivals by collaborating with them -to the benefit of all. I recommend this strategy to young researchers to dispel the nightmares that can occur when competing against powerful contenders. I have been blessed with the selection of my research topic: RNA biology. Over the last five decades, new and unexpected RNA-related phenomena emerged almost yearly. I experienced them very personally while studying transcription, translation, RNA splicing, ribosome biogenesis, and more recently, different classes of regulatory non-coding RNAs, including microRNAs. Some selected research and para-research stories, also covering many wonderful people I had a privilege to work with, are summarized below.My mother told me that I was born with a caul (in Polish, w czepku urodzony, which literally means "born in a bonnet"). This is traditionally the sign of a person who will always enjoy good luck. I am not sure that it turned out that way for others with this rare birth phenomenon, e.g. Lord Byron, Charlemagne, Sigmund Freud, and Napoleon, but my survival as a one-year-old of the 1944 Warsaw Uprising and the ensuing destruction of the city by German troops does nothing to destroy the hypothesis. My parents were actually very courageous to conceive me in that hell, where my father served in the underground army (Armia Krajowa) controlled by the Londonbased Polish government-in-exile. In 1946, with Warsaw destroyed, my family moved to the industrial city of Lodz, and my father became involved in setting up a Department of General and Physiological Chemistry at the newly formed Medical University of Lodz. He became its chairman in the early 1950s.Given my father's position, I was exposed to biology and chemistry since my early childhood, and this greatly influenced my professional future. Our rather spacious apartment served as an extension of his laboratory and was usually full of mice. The poor animals were often not so attractive given that part of his research concerned vitamin deficiencies. Laying the white mice out on our black grand piano as a backdrop for photographic documentation didn't necessarily improve...

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Cellular and molecular phenotypes depending upon the RNA repair system RtcAB ofEscherichia coli

Cited by 27 publications

References 27 publications

Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity inEscherichia coli

Traversing the RNA world

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