DNA-dependent RNA polymerase of Escherichia coli induces bending or an increased flexibility of DNA by specific complex formation.

Heumann, Hermann; Ricchetti, Miria; Werel, W.

doi:10.1002/j.1460-2075.1988.tb03336.x

Cited by 67 publications

(51 citation statements)

References 26 publications

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“…A nucleosome-like model in which the promoter is wrapped around RNA polymerase was originally proposed by Buc et al (28) for the lac UV5 open complex based on the crosslinking (29) and footprinting (25) data. The observations that RNA polymerase appears to induce a DNA bending in several promoters are consistent with the wrapping model (30)(31)(32)(33). A similar model (caging of RNA polymerase) is also described by Adhya et al (34).…”

Section: Discussionsupporting

confidence: 83%

Role of CRP in transcription activation atEscherichia coli lacpromoter: CRP is dispensable after the formation of open complex

Tagami

Aiba

1995

Nucl Acids Res

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Section: Discussionsupporting

confidence: 83%

Role of CRP in transcription activation atEscherichia coli lacpromoter: CRP is dispensable after the formation of open complex

Tagami

Aiba

1995

Nucl Acids Res

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“…T7 RNAP by itself can bend the promoter DNA to cause spontaneous melting in a region from Ϫ4 to ϩ2, similar to what is observed with Rpo41-Mtf1 (25). DNA bending of bacterial promoters requires the presence of both the core RNAP subunit and the accessory sigma factor (40). Transcription factors induced DNA bending near the TATA element is an essential step for the recruitment of archaeal RNAP or eukaryotic RNAP II to the promoter (41,42).…”

Section: Discussionmentioning

confidence: 67%

Transcription Factor-dependent DNA Bending Governs Promoter Recognition by the Mitochondrial RNA Polymerase

Tang

Deshpande

Patel

2011

Journal of Biological Chemistry

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Promoter recognition is the first and the most important step during gene expression. Our studies of the yeast (Saccharomyces cerevisiae) mitochondrial (mt) transcription machinery provide mechanistic understandings on the basic problem of how the mt RNA polymerase (RNAP) with the help of the initiation factor discriminates between promoter and non-promoter sequences. We have used fluorescence-based approaches to quantify DNA binding, bending, and opening steps by the core mtRNAP subunit (Rpo41) and the transcription factor (Mtf1). Our results show that promoter recognition is not achieved by tight and selective binding to the promoter sequence. Instead, promoter recognition is achieved by an induced-fit mechanism of transcription factor-dependent differential conformational changes in the promoter and non-promoter DNAs. While Rpo41 induces a slight bend upon binding both the DNAs, addition of the Mtf1 results in severe bending of the promoter and unbending of the non-promoter DNA. Only the sharply bent DNA results in the catalytically active open complex. Such an induced-fit mechanism serves three purposes: 1) assures catalysis at promoter sites, 2) prevents RNA synthesis at non-promoter sites, and 3) provides a conformational state at the non-promoter sites that would aid in facile translocation to scan for specific sites.DNA-dependent RNA synthesis initiates with the specific binding of the RNA polymerase (RNAP) 2 to its promoter. During this process of promoter selection, the RNAP is able to seek out active promoters within vast stretches of non-promoter sequences in the genome. The multi-subunit RNAPs of the bacteria, archaea, and eukarya rely on transcription factors for promoter selection and specific transcription (1-3) whereas the single subunits RNAPs of bacteriophages are able to carry out the same functions without any accessory factors (4). The RNAPs that transcribe the mitochondrial genomes are unique in that they are homologous to the single subunit RNAPs of bacteriophages, but they require one or more transcription factors for promoter-specific initiation (5-9). The transcription factors modulate various steps of initiation and play a key role in open complex formation (10,11).In this study, we have investigated the transcription machinery of the yeast (Saccharomyces cerevisiae) mitochondria, which consists of a nuclear encoded ϳ153 kDa core subunit Rpo41 (12) and a ϳ45 kDa transcription factor Mtf1 (13, 14). The two proteins are sufficient to catalyze transcription from the conserved nona-nucleotide promoter (5Ј-ATATA-AGTA(ϩ1)) of the yeast mitochondria that directs the synthesis of rRNA, tRNA, and respiratory chain protein mRNAs (15). Rpo41 cannot initiate specific transcription on duplex promoters without Mtf1 (13,16,17). However, when the DNA is negatively supercoiled or premelted, then Rpo41 can initiate specific transcription without Mtf1 (18). Based on these results, it was proposed that Rpo41 has the intrinsic ability to recognize the promoter. A similar conclusion was made for its homolo...

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“…4 provides a framework for interpretation of genetic, biochemical, and structural data on RNAPII-dependent transcription initiation and regulation. Based on similarities between RNAPII and other multisubunit RNA polymerases (i.e., RNA polymerases I and III, E. coli RNA polymerase) in threedimensional structure (39,40), subunit primary structure (41,42), DNA crosslinking (43)(44)(45)(46)(47), DNA bending (48)(49)(50)(51), and DNA wrapping (51-54), we suggest that the model in Fig. 4 may apply generally to multisubunit RNA polymerases.…”

Section: Discussionmentioning

confidence: 92%

Trajectory of DNA in the RNA polymerase II transcription preinitiation complex

Kim

Lagrange

Wang

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

111

124

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By using site-specific protein-DNA photocrosslinking, we define the positions of TATA-binding protein, transcription factor IIB, transcription factor IIF, and subunits of RNA polymerase II (RNAPII) relative to promoter DNA within the human transcription preinitiation complex. The results indicate that the interface between the largest and second-largest subunits of RNAPII forms an extended, Ϸ240 Å channel that interacts with promoter DNA both upstream and downstream of the transcription start. By using electron microscopy, we show that RNAPII compacts promoter DNA by the equivalent of Ϸ50 bp. Together with the published structure of RNAPII, the results indicate that RNAPII wraps DNA around its surface and suggest a specific model for the trajectory of the wrapped DNA.Transcription initiation at a eukaryotic protein-encoding gene involves assembly on promoter DNA of a complex consisting of RNA polymerase II (RNAPII) and six general transcription factors: IIA, IIB, IID (or TATA-element binding protein, TBP), IIE, IIF, and IIH (1-3). A subcomplex containing TBP, IIB, IIF, RNAPII, and promoter DNA is stable (4, 5), and, under certain conditions (e.g., conditions that promote DNA melting), is fully competent for transcription initiation (6-11). Results of DNA footprinting experiments indicate that the TBP-IIB-IIF-RNAPII-promoter complex with linear DNA at 30°C involves interactions both upstream and downstream of the transcription start (positions Ϫ42 to ϩ17; H. Lu and D.R., unpublished data) and involves unmelted DNA (11). Thus, the TBP-IIB-IIF-RNAPII-promoter complex with linear DNA at 30°C appears to correspond to the RNA polymerase-promoter ''intermediate complex'' characterized in studies of Escherichia coli RNA polymerase (RP i or RP c2 ; refs. 12-15).The TBP-IIB-IIF-RNAPII-promoter complex contains at least 14 distinct polypeptides (one in TBP, one in IIB, two in IIF, and at least 10 in RNAPII) and has a molecular mass in excess of 700 kDa (1-3). High-resolution structures have been determined for the TBP-DNA and TBP-IIB-DNA complexes (16-18). However, the TBP-IIB-IIF-RNAPII-promoter complex is too large for high-resolution structure determination by current methods. Therefore, information about the structure of the TBP-IIB-IIF-RNAPII-promoter complex must rely on low-resolution structure determination (19,20) supplemented by biochemical and imaging data.In the work in this report, we have used site-specific protein-DNA photocrosslinking and electron microscopy to define protein-DNA interactions within the human TBP-IIB-IIF-RNAPIIpromoter complex. MATERIALS AND METHODSDerivatized Promoter DNA Fragments. Derivatized promoter DNA fragments were prepared essentially as in ref. 21. Oligodeoxyribonucleotides containing phosphorothioate 5Ј to the third nucleotide were synthesized by using solid-phase ␤-cyanoethylphosphoramidite chemistry and tetraethylthiuram disulfide (Applied Biosystems), purified on OPC (Applied Biosystems), and derivatized with azidophenacyl bromide (Sigma; ref. 22). Derivatized oligodeo...

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DNA-dependent RNA polymerase of Escherichia coli induces bending or an increased flexibility of DNA by specific complex formation.

Cited by 67 publications

References 26 publications

Role of CRP in transcription activation atEscherichia coli lacpromoter: CRP is dispensable after the formation of open complex

Role of CRP in transcription activation atEscherichia coli lacpromoter: CRP is dispensable after the formation of open complex

Transcription Factor-dependent DNA Bending Governs Promoter Recognition by the Mitochondrial RNA Polymerase

Trajectory of DNA in the RNA polymerase II transcription preinitiation complex

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