Changes in Escherichia coli transcriptome during acclimatization at low temperature

Polissi, Alessandra; Laurentis, Walter De; Zangrossi, Sandro; Briani, Federica; Longhi, Vera; Pesole, Graziano; Dehò, Gianni

doi:10.1016/s0923-2508(03)00167-0

Cited by 98 publications

(70 citation statements)

References 40 publications

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“…In a pnp mutant, expression of CspA homologs was significantly prolonged upon cold shock. 87,116 PNPase has been shown to be associated with endonuclease RNase E and other proteins in the RNA degradosome. [117][118][119] In vitro, PNPase catalyzes phosphorolytic degradation of RNA, releasing nucleoside ©2 0 1 1 L a n d e s B i o s c i e n c e .…”

Section: Discussionmentioning

confidence: 99%

RNA remodeling and gene regulation by cold shock proteins

2010

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Section: Discussionmentioning

confidence: 99%

RNA remodeling and gene regulation by cold shock proteins

2010

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“…Chaperone proteins are defined by the fact they do not required a sequence-specific interaction, a specific RNA structure, or an energy source, and the protein is not required to be present after the RNA has been unfolded in order to maintain the correct RNA structure (Portman and Dreyfuss 1994;Herschlag 1995;Rein et al 1998;Cristofari and Darlix 2002). Bacterial CSPs are important for cellular adaptation to cold stress, and their function at low temperature is directly related to their role as chaperone proteins (Jiang et al 1997;Polissi et al 2003). Eukaryotic proteins that contain CSDs have also been shown to act as RNA chaperones and can complement CSP function in vivo (Nakaminami et al 2006;Kim et al 2007).…”

Section: Discussionmentioning

confidence: 99%

gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16

Ammerman¹,

Fisk²,

Read³

2008

RNA

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Editing in trypanosomes involves the addition or deletion of uridines at specific sites to produce translatable mitochondrial mRNAs. RBP16 is an accessory factor from Trypanosoma brucei that affects mitochondrial RNA editing in vivo and also stimulates editing in vitro. We report here experiments aimed at elucidating the biochemical activities of RBP16 involved in modulating RNA editing. In vitro RNA annealing assays demonstrate that RBP16 significantly stimulates the annealing of gRNAs to cognate pre-mRNAs. In addition, RBP16 also facilitates hybridization of partially complementary RNAs unrelated to the editing process. The RNA annealing activity of RBP16 is independent of its high-affinity binding to gRNA oligo(U) tails, consistent with the previously reported in vitro editing stimulatory properties of the protein. In vivo studies expressing recombinant RBP16 in mutant Escherichia coli strains demonstrate that RBP16 is an RNA chaperone and that in addition to RNA annealing activity, it contains RNA unwinding activity. Our data suggest that the mechanism by which RBP16 facilitates RNA editing involves its capacity to modulate RNA secondary structure and promote gRNA/pre-mRNA annealing.

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“…Therefore, although full-length, enzymatically active PNPase is clearly required for optimal growth of Yersinia at low temperature (see below), at higher temperatures it appears to be dispensable for maximal growth in most laboratory conditions. At low temperatures, or in cells recovering from a cold shock, PNPase plays a central role in reprogramming cellular metabolism (4,5,31). Following a cold shock, restart of growth in both E. coli and Y. enterocolitica is preceded by PNPase-mediated degradation of transcripts encoding socalled CSPs (5,31).…”

Section: Discussionmentioning

confidence: 99%

“…At low temperatures, or in cells recovering from a cold shock, PNPase plays a central role in reprogramming cellular metabolism (4,5,31). Following a cold shock, restart of growth in both E. coli and Y. enterocolitica is preceded by PNPase-mediated degradation of transcripts encoding socalled CSPs (5,31). It is believed that PNPase might act to free ribosomes that are inactivated by bound CSP-encoding transcripts.…”

Section: Discussionmentioning

confidence: 99%

Modulation of Yersinia Type Three Secretion System by the S1 Domain of Polynucleotide Phosphorylase

Rosenzweig

Weltman

Plano

et al. 2005

Journal of Biological Chemistry

120

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Both low temperatures and encounters with host phagocytes are two stresses that have been relatively well studied in many species of bacteria. Previous work has shown that the exoribonuclease polynucleotide phosphorylase (PNPase) is required for Yersiniae to grow at low temperatures. Here, we show that PNPase also enhances the ability of Yersinia pseudotuberculosis and Yersinia pestis to withstand the killing activities of murine macrophages. PNPase is required for the optimal functioning of the Yersinia type three secretion system (TTSS), an organelle that injects effector proteins directly into host cells. Unexpectedly, the effect of PNPase on the TTSS is independent of its ribonuclease activity and instead requires its S1 RNA binding domain. In contrast, catalytically inactive enzyme does not enhance the low temperature growth effect of PNPase. Surprisingly, wild-type-like TTSS functioning was restored to the pnp mutant strain by expressing just the ϳ70 amino acid S1 domains from either PNPase, RNase R, RNase II, or RpsA. Our findings suggest that PNPase plays multifaceted roles in enhancing Yersinia survival in response to stressful conditions.

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Changes in Escherichia coli transcriptome during acclimatization at low temperature

Cited by 98 publications

References 40 publications

RNA remodeling and gene regulation by cold shock proteins

RNA remodeling and gene regulation by cold shock proteins

gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16

Modulation of Yersinia Type Three Secretion System by the S1 Domain of Polynucleotide Phosphorylase

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