Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors

Nadratowska-Wesołowska, Beata; Słomińska-Wojewódzka, Monika; Łyżeń, Robert; Węgrzyn, Alicja; Szalewska-Pałasz, Agnieszka; Węgrzyn, Grzegorz

doi:10.1007/s00438-010-0567-y

Cited by 12 publications

(11 citation statements)

References 73 publications

(132 reference statements)

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“…The interaction of different proteins of the degradosome is required for efficient degradation of RNA, and the disruption of the complex has stabilizing effects on bacterial transcripts (19). No further experimental evidence was found for a role of Bd3464 coding for the poly(A) polymerase PcnB; however, it is intriguing that this gene also encodes an enzyme that catalyzes RNA polyadenylation at the 3Ј end, which leads to its faster degradation (24). Inactivation of pcnB significantly increased the half-lives of various specific transcripts in E. coli.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genes Essential for Prey-Independent Growth of Bdellovibrio bacteriovorus HD100

et al. 2011

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Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that attacks and invades Gram-negative bacteria. The predator requires living bacteria to survive as growth and replication take place inside the bacterial prey. It is possible to isolate mutants that grow and replicate outside prey bacteria. Such mutants are designated host or prey independent, and their nutritional requirements vary. Some mutants are saprophytic and require prey extracts for extracellular growth, whereas other mutants grow axenically, which denotes the formation of colonies on complete medium in the absence of any prey components. The initial events leading to prey-independent growth are still under debate, and several genes may be involved. We selected new mutants by three different methods: spontaneous mutation, transposon mutagenesis, and targeted gene knockout. By all approaches we isolated mutants of the hit (host interaction) locus. As the relevance of this locus for the development of prey independence has been questioned, we performed whole-genome sequencing of five prey-independent mutants. Three mutants were saprophytic, and two mutants could grow axenically. Wholegenome analysis revealed that the mutation of a small open reading frame of the hit locus is sufficient for the conversion from predatory to saprophytic growth. Complementation experiments were performed by introduction of a plasmid carrying the wild-type hit gene into saprophytic mutants, and predatory growth could be restored. Whole-genome sequencing of two axenic mutants demonstrated that in addition to the hit mutation the colony formation on complete medium was shown to be influenced by the mutations of two genes involved in RNA processing. Complementation experiments with a wild-type gene encoding an RNA helicase, RhlB, abolished the ability to form colonies on complete medium, indicating that stability of RNA influences axenic growth.

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Section: Discussionmentioning

confidence: 99%

Identification of Genes Essential for Prey-Independent Growth of Bdellovibrio bacteriovorus HD100

et al. 2011

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“…Briefly, 1 mg of MS2 RNA and 10 pmol of PemK Sa were incubated at 37°C in 10 mM Tris-HCl (pH 8.0) containing 10 mM EGTA in a total volume of 10 ml for 30 min. Primer extension was performed as described by Nadratowska-Wesolowska et al 42 with slight modifications. Briefly, toxin-digested MS2 RNA was mixed with 0.5 pmol of 32 P-labelled primer (Supplementary Table S5), incubated for 20 min at 70°C, then slowly cooled to 40°C and transferred to an ice bath.…”

Section: Methodsmentioning

confidence: 99%

A regulatory role for Staphylococcus aureus toxin–antitoxin system PemIKSa

et al. 2013

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Toxin-antitoxin systems were shown to be involved in plasmid maintenance when they were initially discovered, but other roles have been demonstrated since. Here we identify and characterize a novel toxin-antitoxin system (pemIK Sa ) located on Staphylococcus aureus plasmid pCH91. The toxin (PemK Sa ) is a sequence-specific endoribonuclease recognizing the tetrad sequence UkAUU, and the antitoxin (PemI Sa ) inhibits toxin activity by physical interaction. Although the toxin-antitoxin system is responsible for stable plasmid maintenance our data suggest the participation of pemIK Sa in global regulation of staphylococcal virulence by alteration of the translation of large pools of genes. We propose a common mechanism of reversible activation of toxin-antitoxin systems based on antitoxin transcript resistance to toxin cleavage. Elucidation of this mechanism is particularly interesting because reversible activation is a prerequisite for the proposed general regulatory role of toxin-antitoxin systems.

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“…The activities of at least two of them are inversely dependent on the growth rate, which is manifested by an increase in the abundance of PAP I and higher levels of RNA polyadenylation observed in slowly growing bacteria [48,49]. The intricate regulation of pcnB transcription in E. coli was shown to be dependent on two sigma factors, s 70 and s S , responsible for promoter recognition by RNA polymerase, and on ppGpp and DksA, two effectors of the stringent response produced in response to amino acid starvation [46]. Moreover, transcriptional control of pcnB expression in other bacteria seems to also involve additional transcription factors [50].…”

Section: Regulation Of Poly(a) Polymerase I Level and Activitymentioning

confidence: 99%

RNA polyadenylation and its consequences in prokaryotes

Hajnsdorf

Kaberdin

2018

Phil. Trans. R. Soc. B

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One contribution of 11 to a theme issue '5 0 and 3 0 modifications controlling RNA degradation'.Post-transcriptional addition of poly(A) tails to the 3 0 end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development.Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5 0 and 3 0 modifications controlling RNA degradation'.

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Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors

Cited by 12 publications

References 73 publications

Identification of Genes Essential for Prey-Independent Growth of Bdellovibrio bacteriovorus HD100

Identification of Genes Essential for Prey-Independent Growth of Bdellovibrio bacteriovorus HD100

A regulatory role for Staphylococcus aureus toxin–antitoxin system PemIKSa

RNA polyadenylation and its consequences in prokaryotes

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