Transcription Antitermination by Translation Initiation Factor IF1

Phadtare, Sangita; Kazakov, Teymur; Bubunenko, Mikhail; Court, Donald L.; Pestova, Tatyana V.; Severinov, Konstantin

doi:10.1128/jb.00188-07

Cited by 26 publications

(43 citation statements)

References 45 publications

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“…These results suggest that the transcription antitermination activity of S10 is independent of ribosomes or ribosome-bound S10, in agreement with our finding that S10 cannot bind to NusB and the 30S subunit at the same time. The above results also suggest that under normal growth conditions, rRNA transcription antitermination is not essential and that proteins involved in antitermination are required because of their role in other cellular processes, as recently also shown for other antitermination factors (Bubunenko et al, 2007; Phadtare et al, 2007). …”

Section: Discussionsupporting

confidence: 77%

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

et al. 2008

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Summary Protein S10 is a component of the 30S ribosomal subunit and participates together with NusB protein in processive transcription antitermination. The molecular mechanisms by which S10 can act as a translation or a transcription factor are not understood. We used complementation assays and recombineering to delineate regions of S10 dispensable for antitermination, and determined the crystal structure of a transcriptionally active NusB-S10 complex. In this complex, S10 adopts the same fold as in the 30S subunit and is blocked from simultaneous association with the ribosome. Mass spectrometric mapping of UV-induced crosslinks revealed that the NusB-S10 complex presents an intermolecular, composite and contiguous binding surface for RNAs containing BoxA antitermination signals. Furthermore, S10 overproduction complemented a nusB null phenotype. These data demonstrate that S10 and NusB together form a BoxA-binding module; that NusB facilitates entry of S10 into the transcription machinery; and that S10 represents a central hub in processive antitermination.

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Section: Discussionsupporting

confidence: 77%

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

et al. 2008

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“…It should be noted that the structure of the CSD domains is very similar to the structure of the S1 domain. On the basis of this similarity, the CSD and S1 domains are grouped into the OB (oligomer binding) fold (33), and the S1 domain proteins have been shown to exhibit in vivo and in vitro activities similar to those of CSD domain proteins (38,56,58). Therefore, it can be concluded that RNase R actually contains three CSD domains.…”

Section: Resultsmentioning

confidence: 99%

“…RNase R has three cold shock domains, the CSD1, CSD2, and S1 domains. Our previous study showed that CSD domains can act as nucleic acid chaperones and unwind RNAs (4,(36)(37)(38)(39)(40). Based on the in vivo data, the CSD2 domain seems to be critical for the helicase activity of RNase R and either the CSD1 or S1 domain is required for optimal activity.…”

Section: Resultsmentioning

confidence: 99%

Escherichia coliRNase R Has Dual Activities, Helicase and RNase

et al. 2010

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In Escherichia coli, the cold shock response occurs when there is a temperature downshift from 37°C to 15°C, and this response is characterized by induction of several cold shock proteins, including the DEAD-box helicase CsdA, during the acclimation phase. CsdA is involved in a variety of cellular processes. Our previous studies showed that the helicase activity of CsdA is critical for its function in cold shock acclimation of cells and that the only proteins that were able to complement its function were another helicase, RhlE, an RNA chaperone, CspA, and a cold-inducible exoribonuclease, RNase R. Interestingly, other major 3-to-5 processing exoribonucleases of E. coli, such as polynucleotide phosphorylase and RNase II, cannot complement the cold shock function of CsdA. Here we carried out a domain analysis of RNase R and showed that this protein has two distinct activities, RNase and helicase, which are independent of each other and are due to different domains. Mutant RNase R proteins that lack the RNase activity but exhibit the helicase activity were able to complement the cold shock function of CsdA, suggesting that only the helicase activity of RNase R is essential for complementation of the cold shock function of CsdA. We also observed that in vivo deletion of the two cold shock domains resulted in a loss of the ability of RNase R to complement the cold shock function of CsdA. We further demonstrated that RNase R exhibits helicase activity in vitro independent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases in E. coli.When exponentially growing cells of Escherichia coli are shifted from 37°C to a low temperature, such as 15°C, a cold shock response is elicited. This response is characterized by a transient arrest of cell growth termed the acclimation phase, followed by resumption of growth at the low temperature. During the acclimation phase there is severe inhibition of general protein synthesis. However, several cold shock proteins are induced during this phase, including CspA (19) and its homologues, such as CspB (26) CsdA is a DEAD-box protein that belongs to the large family of putative RNA helicases. Members of this family are conserved in organisms from bacteria to humans (29) and play important roles in many cellular processes, such as processing, transport, or degradation of RNA or ribosome biogenesis (for a review, see reference 21). CsdA has been identified as a multifunctional protein, and it has been proposed that this protein participates in a variety of processes, such as ribosome biogenesis, mRNA decay, translation initiation, and gene regulation. CsdA is essential at low temperatures, and deletion of its gene impairs growth when there is a cold shock (8, 24). On the other hand, it is dispensable at 37°C. Previously, we showed that the helicase activity of CsdA is pivotal in its role at low temperature (3). Our in vivo genetic screening of an E. coli strain revealed that another DEAD-box RNA helicase, RhlE...

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“…IF1 is active in trans-splicing, it rescues the splicing of a misfolded intron in vivo, and it resolves a terminator stem in vitro and in vivo. 29,69 CspA has further striking similarity (43% sequence identity) to the cold shock domain of the Y-box factors, which are eukaryotic nucleic acid binding proteins involved in transcriptional and translational regulation. 70 One well-studied member is the major messenger ribonucleoprotein particle protein p50, also known as YB-1, which is a general regulator of translation by modulating mRNA structural rearrangements and packaging.…”

Section: Classification Of Proteins With Rna Chaperone Activitymentioning

confidence: 98%

RNA Chaperones, RNA Annealers and RNA Helicases

Rajkowitsch¹,

Chen²,

Stampfl³

et al. 2007

RNA Biology

293

283

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RNA molecules face difficulties when folding into their native structures. In the cell, proteins can assist RNAs in reaching their functionally active states by binding and stabilizing a specific structure or, in a quite opposite way, by interacting in a non-specific manner. These proteins can either facilitate RNA-RNA interactions in a reaction termed RNA annealing, or they can resolve non-functional inhibitory structures. The latter is defined as "RNA chaperone activity" and is the main topic of this review. Here we define RNA chaperone activity in a stringent way and we review those proteins for which RNA chaperone activity has been clearly demonstrated. These proteins belong to quite diverse families such as hnRNPs, histone-like proteins, ribosomal proteins, cold shock domain proteins and viral nucleocapsid proteins. DExD/H-box containing RNA helicases are discussed as a special family of enzymes that restructure RNA or RNPs in an ATP-dependent manner. We further address the different mechanisms RNA chaperones might use to promote folding including the recently proposed theory of protein disorder as a key element in triggering RNA-protein interactions. Finally, we present a new website for proteins with RNA chaperone activity which compiles all the information on these proteins with the perspective to promote the understanding of their activity.

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Transcription Antitermination by Translation Initiation Factor IF1

Cited by 26 publications

References 45 publications

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

Escherichia coliRNase R Has Dual Activities, Helicase and RNase

RNA Chaperones, RNA Annealers and RNA Helicases

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