Membrane and Actin Tethering Transitions Help IQGAP1 Coordinate GTPase and Lipid Messenger Signaling.

The coordination of lipid messenger signaling with cytoskeletal regulation is central to many organelle-specific regulatory processes. This coupling often depends on the function of multidomain scaffolds that orchestrate transient interactions among multiple signaling intermediates and regulatory proteins on organelles. The number of possible scaffold interaction partners and the ability for these interactions to occur at different timescales makes investigations of scaffold functions challenging. This work employs live cell imaging to probe how the multidomain scaffold IQ motif containing GTPase activating protein 1 (IQGAP1) coordinates the activities of proteins affecting local actin polymerization, membrane processing, and phosphoinositide signaling. Using endosomes that are confined by a local actin network as a model system, we demonstrate that IQGAP1 can transition between different actin and endosomal membrane tethered states. Fast scaffold binding/disassociation transitions are shown to be driven by interactions between C-terminal scaffold domains and Rho GTPases at the membrane. Fluctuations in these binding modes are linked to negative regulation of actin polymerization. Although this control governs core elements of IQGAP1 dynamics, actin binding by the N-terminal calponin homology domain of the scaffold is shown to help the scaffold track the temporal development of endosome membrane markers, implying actin associations bolster membrane and actin coordination. Importantly, these effects are not easily distilled purely through standard (static) co-localization analyses or traditional pathway perturbations methods and were resolved by performing dynamic correlation and multiple regression analyses of IQGAP1 scaffold mutants. Using these capabilities with pharmacological inhibition, we provide evidence that membrane tethering is dependent on the activities of the lipid kinase phosphoinositide 3-kinase in addition to the Rho GTPases Rac1 and Cdc42. Overall, these methods and results point to a scaffold tethering mechanism that allows IQGAP1 to help control the amplitude of phosphoinositide lipid messenger signaling by coordinating signaling intermediate activities with the development and disassembly of local actin cytoskeletal networks.

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms.

Recent evidence suggests that transcript elongation by RNA polymerase II (RNAPII) is regulated by mechanical cues affecting the entry into, and exit from, transcriptionally inactive states, including pausing and arrest. We present a single-molecule optical-trapping study of the interactions of RNAPII with transcription elongation factors TFIIS and TFIIF, which affect these processes. By monitoring the response of elongation complexes containing RNAPII and combinations of TFIIF and TFIIS to controlled mechanical loads, we find that both transcription factors are independently capable of restoring arrested RNAPII to productive elongation. TFIIS, in addition to its established role in promoting transcript cleavage, is found to relieve arrest by a second, cleavage-independent mechanism. TFIIF synergistically enhances some, but not all, of the activities of TFIIS. These studies also uncovered unexpected insights into the mechanisms underlying transient pauses. The direct visualization of pauses at near-base-pair resolution, together with the load dependence of the pause-entry phase, suggests that two distinct mechanisms may be at play: backtracking under forces that hinder transcription and a backtrack-independent activity under assisting loads. The measured pause lifetime distributions are inconsistent with prevailing views of backtracking as a purely diffusive process, suggesting instead that the extent of backtracking may be modulated by mechanisms intrinsic to RNAPII. Pauses triggered by inosine triphosphate misincorporation led to backtracking, even under assisting loads, and their lifetimes were reduced by TFIIS, particularly when aided by TFIIF. Overall, these experiments provide additional insights into how obstacles to transcription may be overcome by the concerted actions of multiple accessory factors.

Single-molecule studies of RNAPII elongation.

Elongation, the transcriptional phase in which RNA polymerase (RNAP) moves processively along a DNA template, occurs via a fundamental enzymatic mechanism that is thought to be universally conserved among multi-subunit polymerases in all kingdoms of life. Beyond this basic mechanism, a multitude of processes are integrated into transcript elongation, among them fidelity control, gene regulatory interactions involving elongation factors, RNA splicing or processing factors, and regulatory mechanisms associated with chromatin structure. Many kinetic and molecular details of the mechanism of the nucleotide addition cycle and its regulation, however, remain elusive and generate continued interest and even controversy. Recently, single-molecule approaches have emerged as powerful tools for the study of transcription in eukaryotic organisms. Here, we review recent progress and discuss some of the unresolved questions and ongoing debates, while anticipating future developments in the field. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.

Multiphoton photoelectron emission microscopy of single Au nanorods: combined experimental and theoretical study of rod morphology and dielectric environment on localized surface plasmon resonances.

Multiphoton photoelectron emission from individual Au nanorods deposited on indium tin oxide (ITO) substrates is studied via scanning photoionization microscopy, based on femtosecond laser excitation at frequencies near the rod longitudinal surface plasmon resonance (LSPR). The observed resonances in photoemission correlate strongly with plasmon resonances measured in dark field microscopy (DFM), thus establishing a novel scheme for wavelength-resolved study of plasmons in isolated metallic nanoparticles based on highly sensitive electron counting methods. In this work, we explore experimental and theoretical effects of (i) morphology and (ii) aspect ratio (AR) for longitudinal plasmon resonance behavior in Au nanorods. A quasilinear dependence between LSPR and aspect ratio (AR) is experimentally determined [Δλ≈ +100(10) nm/AR unit] for Au nanorods on ITO, in excellent agreement with the first principles value from finite element computer modeling [Δλ = +108(5) nm/AR unit]. Interestingly, however, LSPR values for larger vs. smaller diameter rods (w≈ 20 nm and 10 nm) are systematically red-shifted [ΔE≈-0.03(1) eV; Δλ≈ +15(5) nm at λ≈ 800 nm], indicating that electromagnetic retardation effects must also be considered for highest accuracy in LSPR position. To augment these results, the influence of the dielectric environment on the rod LSPR has been explored both experimentally and numerically. In particular, detailed finite-element simulations for ITO supported Au nanorods are found to yield plasmon resonances in near quantitative agreement (ΔE≈±0.04 eV) with experiment, with residual differences arising from uncertainty in the refractive index of the ITO thin film. Furthermore, the results indicate that plasmon resonance predictions based on infinitely thick ITO substrates are reliable to a few meV for film thicknesses larger than approximately twice the rod width.

The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks.

IQGAP1 is a large, multi-domain scaffold that helps orchestrate cell signaling and cytoskeletal mechanics by controlling interactions among a spectrum of receptors, signaling intermediates, and cytoskeletal proteins. While this coordination is known to impact cell morphology, motility, cell adhesion, and vesicular traffic, among other functions, the spatiotemporal properties and regulatory mechanisms of IQGAP1 have not been fully resolved. Herein, we describe a series of super-resolution and live-cell imaging analyses that identified a role for IQGAP1 in the regulation of an actin cytoskeletal shell surrounding a novel membranous compartment that localizes selectively to the basal cortex of polarized epithelial cells (MCF-10A). We also show that IQGAP1 appears to both stabilize the actin coating and constrain its growth. Loss of compartmental IQGAP1 initiates a disassembly mechanism involving rapid and unconstrained actin polymerization around the compartment and dispersal of its vesicle contents. Together, these findings suggest IQGAP1 achieves this control by harnessing both stabilizing and antagonistic interactions with actin. They also demonstrate the utility of these compartments for image-based investigations of the spatial and temporal dynamics of IQGAP1 within endosome-specific actin networks.

Coherent multiphoton photoelectron emission from single au nanorods: the critical role of plasmonic electric near-field enhancement.

Electron emission from individual Au nanorods deposited on indium-tin-oxide (ITO) following excitation with femtosecond laser pulses near the rod longitudinal plasmon resonance is studied via scanning photoionization microscopy. The measured electron signal is observed to strongly depend on the excitation laser polarization and wavelength. Correlated secondary electron microscopy (SEM) and dark-field microscopy (DFM) studies of the same nanorods unambiguously confirm that maximum electron emission results from (i) laser polarization aligned with the rod long axis and (ii) laser wavelength resonant with the localized surface plasmon resonance. The experimental results are in good agreement with quantitative predictions for a coherent multiphoton photoelectric effect, which is identified as the predominant electron emission mechanism for metal nanoparticles under employed excitation conditions. According to this mechanism, the multiphoton photoemission rate is increased by over 10 orders of magnitude in the vicinity of a localized surface plasmon resonance, due to enhancement of the incident electromagnetic field in the particle near-field. These findings identify multiphoton photoemission as an extremely sensitive metric of local electric fields (i.e., "hot spots") in plasmonic nanoparticles/structures that can potentially be exploited for direct quantitation of local electric field enhancement factors.

Polarization-dependent scanning photoionization microscopy: ultrafast plasmon-mediated electron ejection dynamics in single Au nanorods.

This work investigates plasmon-enhanced multiphoton scanning photoelectron emission microscopy (SPIM) of single gold nanorods under vacuum conditions. Striking differences in their photoemission properties are observed for nanorods deposited either on 2 nm thick Pt films or 10 nm thick indium tin oxide (ITO) films. On a Pt support, the Au nanorods display fourth-order photoionization when excited at 800 nm, a wavelength corresponding to their plasmon resonance in aqueous solution. A cos(8)(θ) dependence of the photoelectron flux on laser polarization implies photoemission mediated by the dipolar plasmon; however, no plasmon resonance signature is exhibited over the 750-880 nm range. Electromagnetic simulations confirm that the resonance is severely broadened compared to aqueous solution, indicative of strong interactions between the Au nanorod and propagating surface plasmon modes in the Pt substrate. On ITO substrates, by way of contrast, sharp plasmon resonances in the photoemission from individual Au nanorods are observed, with widths limited only by fundamental internal electron collision processes. Furthermore, the ensemble-averaged plasmon resonance for Au nanorods on ITO is almost unshifted compared to its frequency in solution. Both findings suggest that plasmonic particle-substrate interactions are suppressed in the Au/ITO system. However, Au nanorods on ITO exhibit a surprising third-order photoemission (observed neither in Au nor ITO by itself), indicating that electrostatic interactions introduce a substantial shift in the work function for this fundamental nanoparticle-substrate system.