Single-Molecule Study of Transcriptional Pausing and Arrest by
            <i>E. coli</i>
            RNA Polymerase

Robinson, John; Davenport, Anthony P.; Wuite, Gijs J. L.; Landick, Robert; Bustamante, Carlos

doi:10.1126/science.287.5462.2497

Cited by 318 publications

(253 citation statements)

References 22 publications

Supporting

Mentioning

233

Contrasting

Order By: Relevance

“…The average progress determined from this exponential function was 660 bp which, when divided by the incubation time, 60 s, produced an estimated average rate of elongation of 10.3 bp/s. This estimate agrees with previously reported in vitro rates at comparable NTP concentrations 24, 25, 26…”

Section: Resultssupporting

confidence: 93%

Proteins mediating DNA loops effectively block transcription

et al. 2017

View full text Add to dashboard Cite

Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop‐mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.

show abstract

Section: Resultssupporting

confidence: 93%

Proteins mediating DNA loops effectively block transcription

et al. 2017

View full text Add to dashboard Cite

show abstract

“…pJP101 [ PR promoter] was generated by inserting a PCR product containing the PR promoter (oligonucleotide primer oJP033 and oJP034 with pPIA2-6 as template [Davenport et al 2000]) into the SacII site of pJB103 (Bath et al 2000).…”

Section: Plasmid Constructionmentioning

confidence: 99%

SpoIIIE strips proteins off the DNA during chromosome translocation

Marquis¹,

Nollmann²,

Ptacin³

et al. 2008

Genes Dev.

Self Cite

View full text Add to dashboard Cite

The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division. An extreme example of this post-cytokinetic DNA segregation occurs during spore formation in the bacterium Bacillus subtilis, where SpoIIIE pumps three-quarters of the chromosome (>3 megabases) into one of the two daughter cells. Here, we investigate the fate of the proteins associated with the translocated DNA. Taking advantage of several unique features of Bacillus sporulation, we demonstrate that RNA polymerase, transcription factors, and chromosome remodeling proteins are stripped off the DNA during translocation of the chromosome into the forespore compartment. Furthermore, we show that in vitro the soluble ATPase domain of SpoIIIE can displace RNA polymerase bound to DNA, suggesting that SpoIIIE alone is capable of this wire-stripping activity. Our data suggest that the bulk of the forespore chromosome is translocated naked into the forespore compartment. We propose that the translocation-stripping activity of SpoIIIE plays a key role in reprogramming developmental gene expression in the forespore.[Keywords: Chromosome segregation; chromosome translocation; sporulation; FtsK; AAA+ ATPase] Supplemental material is available at http://www.genesdev.org.

show abstract

“…This simple model can be used to describe the biological activity of RNA polymerase, which has recently been studied on the single molecule level [33].…”

mentioning

confidence: 99%

“…One-dimensional stochastic processes [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] are widely used to describe dynamics in biological, chemical, and physical systems [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. Quite ubiquitous among these, are nearest neighbor hopping processes on finite discrete lattices (chains).…”

mentioning

confidence: 99%

Closed-Form Solutions for Continuous Time Random Walks on Finite Chains

Flomenbom

Klafter

2005

Phys. Rev. Lett.

View full text Add to dashboard Cite

Continuous time random walks (CTRWs) on finite arbitrarily inhomogeneous chains are studied. By introducing a technique of counting all possible trajectories, we derive closed-form solutions in Laplace space for the Green's function (propagator) and for the first passage time probability density function (PDF) for nearest neighbor CTRWs in terms of the input waiting time PDFs. These solutions are also the Laplace space solutions of the generalized master equation (GME). Moreover, based on our counting technique, we introduce the adaptor function for expressing higher order propagators (joint PDFs of time-position variables) for CTRWs in terms of Green's functions.Using the derived formulae, an escape problem from a biased chain is considered.

show abstract

Single-Molecule Study of Transcriptional Pausing and Arrest by E. coli RNA Polymerase

Cited by 318 publications

References 22 publications

Proteins mediating DNA loops effectively block transcription

Proteins mediating DNA loops effectively block transcription

SpoIIIE strips proteins off the DNA during chromosome translocation

Closed-Form Solutions for Continuous Time Random Walks on Finite Chains

Contact Info

Product

Resources

About