Single-molecule dynamics of transcription of the lar promoter

Abstract

We measured the in vivo production of RNA molecules tagged with MS2d-GFP in Escherichia coli, driven by the lar promoter, under weak and medium induction. The distributions of intervals between consecutive productions of RNAs are found to be sub-exponential, and the process of RNA production is found to be sub-Poissonian. We discuss possible models of transcription initiation and, based on our results and previous in vitro measurements, find that a sequential two-step model of transcription initiation at the promoter region explains well the results.

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

“…Two studies reported in vivo measurements of the kinetics of P lac/ara-1 [21,22]. In these, the RNA is visible shortly after transcription occurs by tagging them with MS2d-GFP proteins [23].…”

Effects of multimerization on the temporal variability of protein complex abundance

“…With proper parameter values, the gamma distribution well approximates recent live cell measurements of intervals between productions of consecutive RNAs in E. coli [13,20]. We fitted the measurements of time intervals in [20] with the three-exponential model proposed in that work, and with a gamma distribution. The latter results in ( α M , ( α M k M ) -1 ) of (2.27183, 1070.57) and (2.51171, 565.956) for the low and medium induction levels, respectively.…”

“…In our implementation, each time this reaction occurs, a value of τ S is drawn from a gamma distribution with mean of k M -1 and coefficient of variation (variance over the mean) of ${\alpha }_M^{MathClass-bin-1MathClass-bin/2}$. With proper parameter values, the gamma distribution well approximates recent live cell measurements of intervals between productions of consecutive RNAs in E. coli [13,20]. We fitted the measurements of time intervals in [20] with the three-exponential model proposed in that work, and with a gamma distribution.…”

“…This approximation assumes that the elongation time is negligible, which relies on observation that the durations of the closed and the open complex formations (in the order of 10 3 s) [1,2,13,20] are much longer than elongation (in the order of 10 1 or 10 2 s) [21,22]. Moreover, in prokaryotes, translation is coupled to transcription [23], and can initiate as soon as the ribosome binding site region (RBS) of the RNA is formed (Shine-Dalgarno sequence) [24].…”

“…Setting α M = 1 yields Poisson distributed mRNA numbers M ~ Poi( k M d M -1 ), while α M > 1 and α M < 1 result in sub- and super-Poissonian distributions of RNA numbers, respectively (both of which have been reported in E. coli [6,20]). We note that, for integer values of α M , the parameter has a physical interpretation: namely, it represents a sequential process with α M elementary steps, each of duration ( α M k M ) -1 , which is in accordance with a sequential process of transcription initiation [1].…”