Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from <i>Thermus thermophilus</i>

Reay, Paul; Yamasaki, Kazuhiko; Terada, Takaho; Kuramitsu, Seiki; Shirouzu, Mikako; Yokoyama, Shigeyuki

doi:10.1002/prot.20054

Cited by 32 publications

(34 citation statements)

References 57 publications

(75 reference statements)

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“…However, this model is inconsistent with an independent crystal structure of A. aeolicus NusG 145 , solution structures of A. aeolicus, E. coli, and Thermus thermophilus NusGs 92,152,155 , and functional studies of E. coli NusG 92 .…”

Section: Nusg Family Of Regulatorsmentioning

confidence: 82%

“…For example, NusG is not essential in B. subtilis 164 or Staphylococcus aureus 165 , and, unlike the E. coli NusG, B. subtilis NusG strongly increases pausing at some regulatory sites in vivo and in vitro 166 . T. thermophilus NusG does not bind to Rho 152 and slows down rather than facilitates elongation by its cognate RNAP, even though it binds to the nontemplate DNA strand, competes with σ A , and induces forward translocation by RNAP 111 , properties shared with E. coli RfaH and NusG. NusGs may also differ in their regulatory interactions: T. maritima NusG is the only member of this family known to bind nonspecifically and cooperatively to nucleic acids 153 , and one of three NusG paralogs in Thermoanaerobacter tengcongensis interacts with DnaA 167 .…”

Section: Nusg Family Of Regulatorsmentioning

confidence: 99%

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NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

Tomar

Artsimovitch

2013

Chem. Rev.

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Section: Nusg Family Of Regulatorsmentioning

confidence: 82%

Section: Nusg Family Of Regulatorsmentioning

confidence: 99%

NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

Tomar

Artsimovitch

2013

Chem. Rev.

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“…Deletions of yeast KOW2 and KOW4-KOW5 are associated with severe growth defects in yeast (10,11,17), indicating important functions of the KOW domains in vivo. Structural studies have shown that isolated KOW domains of NusG and both archaeal (30,(32)(33)(34) and human Spt5 (Protein Data Bank [PDB] IDs 2E6Z, 2E70, and 3H7H) all adopt the same fold as the ␤-barrel of Tudor domains. Tudor domains are structurally compact (ϳ50-amino-acid) modules that mediate protein-protein and protein-NA interactions in diverse molecular systems (35).…”

mentioning

confidence: 99%

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5

Meyer

Zhang

et al. 2015

Molecular and Cellular Biology

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The eukaryotic Spt4-Spt5 heterodimer forms a higher-order complex with RNA polymerase II (and I) to regulate transcription elongation. Extensive genetic and functional data have revealed diverse roles of Spt4-Spt5 in coupling elongation with chromatin modification and RNA-processing pathways. A mechanistic understanding of the diverse functions of Spt4-Spt5 is hampered by challenges in resolving the distribution of functions among its structural domains, including the five KOW domains in Spt5, and a lack of their high-resolution structures. We present high-resolution crystallographic results demonstrating that distinct structures are formed by the first through third KOW domains (KOW1-Linker1 [K1L1] and KOW2-KOW3) of Saccharomyces cerevisiae Spt5. The structure reveals that K1L1 displays a positively charged patch (PCP) on its surface, which binds nucleic acids in vitro, as shown in biochemical assays, and is important for in vivo function, as shown in growth assays. Furthermore, assays in yeast have shown that the PCP has a function that partially overlaps that of Spt4. Synthesis of our results with previous evidence suggests a model in which Spt4 and the K1L1 domain of Spt5 form functionally overlapping interactions with nucleic acids upstream of the transcription bubble, and this mechanism may confer robustness on processes associated with transcription elongation.T ranscription by RNA polymerase (RNAP) II is a regulated process that requires over 60 different accessory factors that interact dynamically with the polymerase as it proceeds through the three main stages of transcription: initiation, elongation, and termination (1). Each RNAP II complex is structurally and biochemically tuned to cope with a set of conditions (e.g., the chromatin state) and to accomplish specific functions (e.g., promoter-dependent initiation) associated with a particular stage of transcription. In eukaryotes, the processes of RNAP II elongation and termination interact closely with pathways of pre-mRNA processing, 3=-end formation, and RNA export (2-4) and thus form temporally and spatially coupled activities that together determine transcriptional responses to intrinsic and extrinsic signaling and regulate RNA metabolism. The heterodimeric complex of Spt4-Spt5 is one of several protein factors that participate in all of the steps that follow transcription initiation. Saccharomyces cerevisiae Spt4-Spt5 is known to coordinate transcription elongation with chromatin remodeling and histone modification; it functions as a general elongation factor for both RNAP II and RNAP I and coordinates with 5= capping, splicing, and 3=-end processing of transcripts (reviewed by Hartzog and Fu [5]). The metazoan homolog of Spt4-Spt5, DSIF, partners with NELF and additional RNAP IIassociated complexes (e.g., P-TEFb and Mediator) to impart a pause-and-release mechanism that regulates RNAP II activity during the initiation-to-elongation transition near promoterproximal regions (6-8). While facilitative for transcription elongation, Spt4-Spt5 also pl...

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“…The Nus and Gre factors have been studied intensively for many years, and much is known about how these factors regulate transcription elongation (4,23,37,40,49,52). The Nus (N utilization substance) factors were first discovered due to their role in formation of terminator-resistant complexes during phage transcription, but they have since been found to be essential for regulation of host cell (Escherichia coli) transcription and are highly conserved proteins in both gram-positive and gram-negative organisms (3,28,37,39).NusA is an essential protein that plays a role in both transcription antitermination and pausing (37,40). Although the precise mechanism by which NusA is able to exert these contradictory activities has not been fully elucidated, it is dependent, in part, on the activities of other elongation factors (13,19,40).…”

mentioning

confidence: 99%

Subcellular Partitioning of Transcription Factors inBacillus subtilis

2006

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RNA polymerase (RNAP) requires the interaction of various transcription elongation factors to efficiently transcribe RNA. During transcription of rRNA operons, RNAP forms highly processive antitermination complexes by interacting with NusA, NusB, NusG, NusE, and possibly several unidentified factors to increase elongation rates to around twice those observed for mRNA. In previous work we used cytological assays with Bacillus subtilis to identify the major sites of rRNA synthesis within the cell, which are called transcription foci. Using this cytological assay, in conjunction with both quantitative native polyacrylamide gel electrophoresis and Western blotting, we investigated the total protein levels and the ratios of NusB and NusG to RNAP in both antitermination and mRNA transcription complexes. We determined that the ratio of RNAP to NusG was 1:1 in both antitermination and mRNA transcription complexes, suggesting that NusG plays important regulatory roles in both complexes. A ratio of NusB to RNAP of 1:1 was calculated for antitermination complexes with just a 0.3:1 ratio in mRNA complexes, suggesting that NusB is restricted to antitermination complexes. We also investigated the cellular abundance and subcellular localization of transcription restart factor GreA. We found no evidence which suggests that GreA is involved in antitermination complex formation and that it has a cellular abundance which is around twice that of RNAP. Surprisingly, we found that the vast majority of GreA is associated with RNAP, suggesting that there is more than one binding site for GreA on RNAP. These results indicate that transcription elongation complexes are highly dynamic and are differentially segregated within the nucleoid according to their functions.Unlike the situation in eukaryotes, a single RNA polymerase (RNAP) is responsible for carrying out transcription of all classes of genes in prokaryotes. As rRNA synthesis is the rate-determining step in ribosome assembly, the efficiency of this process determines the rate at which organisms can produce proteins and ultimately divide (23, 37). The rate of rRNA transcription has also been found to be around twice the rate of mRNA transcription (52), and this is due to the types of transcription elongation complexes (EC) formed during these two types of transcription. The vast majority of stable RNA (rRNA and tRNA) is produced by antitermination ECs that are resistant to transcription pause signals and ensure that full-length transcripts are efficiently produced (1, 11, 52), although transcription of tRNA genes that are located outside rRNA operons does not appear to depend on the same regulatory sequences that are responsible for the antitermination complex formation that occurs in rRNA operons (Doherty, unpublished data). mRNA is produced by ECs that tend to be highly susceptible to pausing, and this appears, among other things, to help ensure the close coupling of transcription and translation, transcription fidelity, to enhance responsiveness to transcription attenuators (5, ...

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Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus

Cited by 32 publications

References 57 publications

NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5

Subcellular Partitioning of Transcription Factors inBacillus subtilis

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