RNA remodeling and gene regulation by cold shock proteins

Phadtare, Sangita; Severinov, Konstantin

doi:10.4161/rna.7.6.13482

Cited by 144 publications

(127 citation statements)

References 124 publications

(115 reference statements)

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“…For example, the up-regulation of cold shock domain RNA binding proteins during low temperature growth destabilizes RNA structures that would otherwise impair transcription elongation and translation initiation at low temperatures (14). Moreover, over-expression of cold shock proteins and other RNA chaperones buffered deleterious mutations in E. coli (15), suggesting that such proteins broadly mitigate the effects of RNA misfolding.…”

Section: Introductionmentioning

confidence: 99%

Proteins That Chaperone RNA Regulation

Woodson¹,

Panja²,

Santiago-Frangos

2018

Microbiol Spectr

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RNA-binding proteins chaperone the biological functions of non-coding RNA by reducing RNA misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality control over RNP biogenesis. Recent studies of E. coli CspA, HIV NCp and E. coli Hfq, are beginning to show how RNA-binding proteins remodel RNA structures. These different protein families use common strategies for disrupting or annealing RNA double helices, which can be used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in bacteria.

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Section: Introductionmentioning

confidence: 99%

Proteins That Chaperone RNA Regulation

Woodson¹,

Panja²,

Santiago-Frangos

2018

Microbiol Spectr

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“…The formation of such secondary structures is thermodynamically favored at lower temperatures. Therefore, RNA helicases play an important role for the adaptation to the cold (44). To test whether the B. subtilis DEAD-box RNA helicases are involved in this process, we compared growth of the wild-type and isogenic helicase mutant strains at standard laboratory and reduced temperatures (37 and 16°C, respectively).…”

Section: Consequences Of Deletions Of Individual Dead-box Helicase Gementioning

confidence: 99%

DEAD-Box RNA Helicases in Bacillus subtilis Have Multiple Functions and Act Independently from Each Other

Lehnik-Habrink¹,

Rempeters²,

Kovács³

et al. 2012

Journal of Bacteriology

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d DEAD-box RNA helicases play important roles in remodeling RNA molecules and in facilitating a variety of RNA-protein interactions that are key to many essential cellular processes. In spite of the importance of RNA, our knowledge about RNA helicases is limited. In this study, we investigated the role of the four DEAD-box RNA helicases in the Gram-positive model organism Bacillus subtilis. A strain deleted of all RNA helicases is able to grow at 37°C but not at lower temperatures. The deletion of cshA, cshB, or yfmL in particular leads to cold-sensitive phenotypes. Moreover, these mutant strains exhibit unique defects in ribosome biogenesis, suggesting distinct functions for the individual enzymes in this process. Based on protein accumulation, severity of the cold-sensitive phenotype, and the interaction with components of the RNA degradosome, CshA is the major RNA helicase of B. subtilis. To unravel the functions of CshA in addition to ribosome biogenesis, we conducted microarray analysis and identified the ysbAB and frlBONMD mRNAs as targets that are strongly affected by the deletion of the cshA gene. Our findings suggest that the different helicases make distinct contributions to the physiology of B. subtilis. Ribosome biogenesis and RNA degradation are two of their major tasks in B. subtilis. RNA molecules participate in a large number of cellular processes. Due to their relative simplicity (they are composed of only four different nucleic acid building blocks) and the molecular crowding found in the cytoplasm of cells, RNAs are prone to form undesired inter-and intramolecular interactions. In order to prevent these interactions, every cell expresses proteins that assist the RNA molecules to function properly. A major class of these proteins are DEAD-box RNA helicases (1).DEAD-box RNA helicases are ubiquitous enzymes that consist of a highly conserved helicase core comprising two RecA-like domains. Within the two domains, 12 characteristic sequence motifs have been identified. These motifs are involved in ATP and RNA binding, ATP hydrolysis, and the communication between the different sites. Motif II contains the name-giving Asp-Glu-AlaAsp, or DEAD, amino acid sequence (for reviews, see references 1 and 2). In addition to the conserved helicase core, most DEADbox proteins contain variable N-or C-terminal extensions. These additional domains often confer specificity for their substrates and interaction partners and are thus involved in the specific functional output and regulation of the DEAD-box protein (3,4,5,6).

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“…For example, a precise and optimum temperature is essential for hatching of bird eggs, which, of course, are stem cells. Temperature effects are modulated at the cellular level by stress-response pathways that include heat-shock and cold-shock proteins (9,10). In contrast to heat-shock proteins (HSP), which are induced by increased temperatures, cold-shock proteins (CSP) are induced by lowering the temperatures but are downregulated when temperatures are elevated (11,12).…”

Section: Introductionmentioning

confidence: 99%

Stress-Response Protein RBM3 Attenuates the Stem-like Properties of Prostate Cancer Cells by Interfering with CD44 Variant Splicing

et al. 2013

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Stress-response pathways play an important role in cancer. The cold-inducible RNA-binding protein RBM3 is upregulated in several types of cancer, including prostate cancer, but its pathogenic contributions are undetermined. RBM3 is expressed at low basal levels in human fetal prostate or in CD133 þ prostate epithelial cells (PrEC), compared with the adult prostate or CD133-PrEC, and RBM3 is downregulated in cells cultured in soft agar or exposed to stress. Notably, RBM3 overexpression in prostate cancer cells attenuated their stem celllike properties in vitro as well as their tumorigenic potential in vivo. Interestingly, either overexpressing RBM3 or culturing cells at 32 C suppressed RNA splicing of the CD44 variant v8-v10 and increased expression of the standard CD44 (CD44s) isoform. Conversely, silencing RBM3 or culturing cells in soft agar (under conditions that enrich for stem cell-like cells) increased the ratio of CD44v8-v10 to CD44s mRNA. Mechanistic investigations showed that elevating CD44v8-v10 interfered with MMP9-mediated cleavage of CD44s and suppressed expression of cyclin D1, whereas siRNA-mediated silencing of CD44v8-v10 impaired the ability of prostate cancer cells to form colonies in soft agar. Together, these findings suggested that RBM3 contributed to stem cell-like character in prostate cancer by inhibiting CD44v8-v10 splicing. Our work uncovers a hitherto unappreciated role of RBM3 in linking stress-regulated RNA splicing to tumorigenesis, with potential prognostic and therapeutic implications in prostate cancer. Cancer Res; 73(13); 4123-33. Ó2013 AACR.

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RNA remodeling and gene regulation by cold shock proteins

Cited by 144 publications

References 124 publications

Proteins That Chaperone RNA Regulation

Proteins That Chaperone RNA Regulation

DEAD-Box RNA Helicases in Bacillus subtilis Have Multiple Functions and Act Independently from Each Other

Stress-Response Protein RBM3 Attenuates the Stem-like Properties of Prostate Cancer Cells by Interfering with CD44 Variant Splicing

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