An Alternate Mechanism of Abortive Release Marked by the Formation of Very Long Abortive Transcripts

Chander, Monica; Austin, Karyn M.; Aye-Han, Nwe-Nwe; Sircar, Piya; Hsu, Lilian M.

doi:10.1021/bi701236f

Cited by 9 publications

(31 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4). The transition from abortive to productive elongation, marked by release of σ 70 from promoter contacts (or from RNAP contacts), occurs within the first 20 nt of transcript elongation (Chander et al, 2007; Revyakin et al, 2006). Known cases of σ 70 -stimulated pausing in vivo occur no later than +25 (Ring et al, 1996).…”

Section: Discussionmentioning

confidence: 99%

Regulator Trafficking on Bacterial Transcription Units In Vivo

et al. 2009

View full text Add to dashboard Cite

Summary The in vivo trafficking patterns on DNA by the bacterial regulators of transcript elongation σ70, ρ, NusA, and NusG and the explanation for high promoter-proximal levels or peaks of RNA polymerase (RNAP) are unknown. Genome-wide ChIP-chip on E. coli revealed distinct association patterns of regulators as RNAP transcribes away from promoters (ρ first, then NusA, and then NusG). However, the interactions of elongating complexes with these regulators, including a weak interaction with σ70, did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from σ70 peaks in the direction of transcription and co-occurred with NusA and ρ peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of ρ did not increase RNAP levels within genes downstream of the RNAP peaks, suggesting the peaks are caused by a mechanism other than simple ρ-dependent attenuation.

show abstract

Section: Discussionmentioning

confidence: 99%

Regulator Trafficking on Bacterial Transcription Units In Vivo

et al. 2009

View full text Add to dashboard Cite

show abstract

“…S1). We note the accumulation of abortive RNA products in reactions performed with template #2, which we attribute to the two base pair substitutions in the initial transcribed region; initial transcribed region alterations can have dramatic effects on abortive transcript production (Hsu et al 2003;Chander et al 2007). The ;116-nt terminated transcript (T) is indicated, and the asterisk (*) indicates a shorter terminated transcript that is the result of transcription initiating under the control of the promoter-distal extended À10 element.…”

mentioning

confidence: 86%

Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex

Deighan¹,

Pukhrambam²,

Nickels³

et al. 2011

Genes Dev.

View full text Add to dashboard Cite

The bacterial RNA polymerase (RNAP) holoenzyme consists of a catalytic core enzyme (a 2 bb'v) in complex with a s factor that is essential for promoter recognition and transcription initiation. During early elongation, the stability of interactions between s and the remainder of the transcription complex decreases. Nevertheless, there is no mechanistic requirement for release of s upon the transition to elongation. Furthermore, s can remain associated with RNAP during transcription elongation and influence regulatory events that occur during transcription elongation. Here we demonstrate that promoter-like DNA sequence elements within the initial transcribed region that are known to induce early elongation pausing through sequence-specific interactions with s also function to increase the s content of downstream elongation complexes. Our findings establish s-dependent pausing as a mechanism by which initial transcribed region sequences can influence the composition and functional properties of the transcription elongation complex over distances of at least 700 base pairs.[Keywords: RNA polymerase; s factor; transcription initiation; promoter-proximal pausing; transcription elongation complex] Supplemental material is available for this article. The s subunit of bacterial RNA polymerase (RNAP) is required for promoter-specific transcription initiation (Gross et al. 1998). When complexed with the RNAP core enzyme (subunit structure a 2 bb9v), different s factors specify the recognition of different classes of promoters (Gruber and Gross 2003). The primary s factor in Escherichia coli, s 70 , typically directs transcription initiation from promoters defined by two conserved hexameric DNA sequence elements, termed the À10 and À35 elements for their relationship to the transcription start site (position +1). During the transition from transcription initiation to transcription elongation, the growth of the nascent RNA destabilizes the interaction between s 70 and the RNAP core enzyme (Mekler et al. 2002;Murakami et al. 2002;Vassylyev et al. 2002;Nickels et al. 2005), but the complete release of s 70 is not required for entry into the elongation phase of transcription (Ring et al. 1996;Bar-Nahum and Nudler 2001;Mukhopadhyay et al. 2001;Mooney et al. 2005). Thus, although historically defined as an initiation factor, s 70 can also remain associated with the transcription elongation complex and influence the transcription process during elongation. A functional role for s 70 during elongation was first established in the context of bacteriophage l late gene transcription (for review, see Roberts et al. 1998). Specifically, the expression of the phage late genes under the control of the lQ anti-terminator protein depends on a s 70 -dependent pause that occurs during early elongation, shortly after the s 70 -containing RNAP holoenzyme has escaped the late promoter P R9 . Formation of this paused early elongation complex, which contains a stably bound nascent RNA that is 16 or 17 nucleotides (nt) in length, depends on an int...

show abstract

“…Kammerer et al (59) showed that the bacteriophage T5 N25 promoter and its derivative, the N25 antipromoter, exhibit very different rates of promoter escape (roughly 1.7 and 0.6 min –1 , respectively) and ratios of abortive to productive transcripts (40 and 300, respectively), despite differing only in the initial portion of their transcribed sequences (+3 to +20). Chander et al (60) demonstrated finer tuning using individual mutations to the 20-nucleotide sequence. These changes should in principle introduce a vertical scaling of the expression response curve.…”

Section: Biological Options For Tuningmentioning

confidence: 99%

Tuning Response Curves for Synthetic Biology

et al. 2013

View full text Add to dashboard Cite

Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system’s dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.

show abstract

An Alternate Mechanism of Abortive Release Marked by the Formation of Very Long Abortive Transcripts

Cited by 9 publications

References 54 publications

Regulator Trafficking on Bacterial Transcription Units In Vivo

Regulator Trafficking on Bacterial Transcription Units In Vivo

Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex

Tuning Response Curves for Synthetic Biology

Contact Info

Product

Resources

About