Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g., from a 7-base transcript) were markedly slower than from earlier stages (e.g., from a 2-or 4-base transcript). In addition, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states. Further examination with magnetic tweezers transcription experiments showed that RNAP adopted a long-lived backtracked state during initiation and that the pausedbacktracked initiation intermediate was populated abundantly at physiologically relevant nucleoside triphosphate (NTP) concentrations. The paused intermediate population was further increased when the NTP concentration was decreased and/or when an imbalance in NTP concentration was introduced (situations that mimic stress). Our results confirm the existence of a previously hypothesized paused and backtracked RNAP initiation intermediate and suggest it is biologically relevant; furthermore, such intermediates could be exploited for therapeutic purposes and may reflect a conserved state among paused, initiating eukaryotic RNA polymerase II enzymes.T ranscription in Escherichia coli comprises three stages: initiation, elongation and termination. Initiation, which is typically the rate-limiting and the most regulated stage of transcription, is by itself a complex, multistep process consisting of the following successive steps (1, 2): (i) association of RNA polymerase (RNAP) core enzyme (subunit composition α2ββ′ω) with the promoter specificity factor σ (such as σ70 for transcription of housekeeping genes) to form RNAP holoenzyme; (ii) binding of holoenzyme to the −10 and −35 DNA elements in the promoter recognition sequence (PRS) upstream to the transcription start site (TSS) to form closed promoter complex (RPc); (iii) isomerization of RPc through multiple intermediates into an open promoter complex (RPo), in which a ∼12-bp DNA stretch (bases at registers −10 to +2) is melted to form a transcription bubble, the template DNA strand is inserted into RNAP major cleft positioning the base at register +1 of TSS at the active site, the nontemplate strand is tightly bound by σ70 and the downstream DNA duplex (bases +3 up to +20) is loaded into RNAP β′ DNA-binding clamp; (iv) an abortive initiation step (AI), where binding of nucleoside triphosphate (NTPs) and the start of RNA synthesis leads to formation of an initial transcribing complex (RP ITC ) followed by RNAP cycling through multiple polymerization trials via a DNA scrunching mechanism (3, 4), release of short "abortive transcripts" and repositioning itself in RP O for a new synthesis trial (5-7); and finally, (v) RNAP promoter escape, when enough strain is built in the enzyme, the σ70 undergoes structural transition to relieve blockage of ...

Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement’s dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.

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Biological reactions in the cellular environment differ physicochemically from those performed in dilute buffer solutions due to, in part, slower diffusion of various components in the cellular milieu, increase in their chemical activities, and modulation of their binding affinities and conformational stabilities. In vivo transcription is therefore expected to be strongly influenced by the 'crowdedness' of the cell. Previous studies of transcription under macromolecular crowding conditions have focused mainly on multiple cycles of RNAP-Promoter associations, assuming that the association is the rate-determining step of the entire transcription process. However, recent reports demonstrated that late initiation and promoter escape could be the rate-determining steps for some promoter DNA sequences. The investigation of crowding effects on these steps under single-round conditions is therefore crucial for better understanding of transcription initiation in vivo. Here, we have implemented an in vitro transcription quenched-kinetics single-molecule assay to investigate the dependence of transcription reaction rates on the sizes and concentrations of crowders. Our results demonstrate an expected slowdown of transcription kinetics due to increased viscosity, and an unexpected enhancement in transcription kinetics by large crowding agents (at a given viscosity). More importantly, the enhancement's dependence on crowder size significantly deviates from hard-sphere model (scaled-particle theory) predictions, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions are affected by crowding conditions in the cellular milieu.

Introduction and Objective: Robot-assisted radical nephrectomy (RRN) is increasingly utilized as an alternative to laparoscopic radical nephrectomy (LRN), but there are concerns over costs and objective benefit. In the setting of very large renal masses (>10 cm), comparison between techniques is limited and it is unclear whether a robotic approach confers any perioperative benefit over LRN or open radical nephrectomy (ORN). In this study, perioperative outcomes of RRN, LRN, and ORN for very large renal masses are compared. Methods: Using the National Cancer Database, patients were identified who underwent radical nephrectomy for kidney tumors >10 cm diagnosed from 2010 to 2015. Patients were analyzed according to surgical approach. Perioperative outcomes, including conversion to open, length of stay, readmission rates, positive surgical margins, and 30-and 90-day mortality were compared among cohorts. Results: A total of 9288 patients met inclusion criteria (RRN = 842, LRN = 2326, ORN = 6120). Compared with ORN, recipients of RRN or LRN had similar rates of 30-day readmission and 30-and 90-day mortality. Length of hospital stay was significantly shorter in RRN (-1.73 days -0.19; p < 0.0001) and LRN (-1.40 days -0.12; p < 0.0001) compared with ORN. LRN had a higher rate of conversion to open compared with RRN (odds ratio 1.48; 95% confidence interval 1.10-1.98; p = 0.0087). Conversion to open from RRN or LRN added 1.3 additional days of inpatient stay. Over the study period, RRN use increased from 4.1% to 14.8%, LRN from 20.9% to 25.6%, whereas ORN use decreased from 75% to 59.6%. Conclusions: Minimally invasive approaches are increasingly utilized in very large renal masses. RRN has lower rates of conversion to open but produces comparable perioperative outcomes to LRN. Minimally invasive approaches have a shorter length of inpatient stay but otherwise report similar surgical margin status, readmission rates, and mortality rates compared with ORN.