Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer.

Photosynthetic species evolved to protect their light-harvesting apparatus from photoxidative damage driven by intracellular redox conditions or environmental conditions. The Fenna-Matthews-Olson (FMO) pigment-protein complex from green sulfur bacteria exhibits redox-dependent quenching behavior partially due to two internal cysteine residues. Here, we show evidence that a photosynthetic complex exploits the quantum mechanics of vibronic mixing to activate an oxidative photoprotective mechanism. We use two-dimensional electronic spectroscopy (2DES) to capture energy transfer dynamics in wild-type and cysteine-deficient FMO mutant proteins under both reducing and oxidizing conditions. Under reducing conditions, we find equal energy transfer through the exciton 4-1 and 4-2-1 pathways because the exciton 4-1 energy gap is vibronically coupled with a bacteriochlorophyll-a vibrational mode. Under oxidizing conditions, however, the resonance of the exciton 4-1 energy gap is detuned from the vibrational mode, causing excitons to preferentially steer through the indirect 4-2-1 pathway to increase the likelihood of exciton quenching. We use a Redfield model to show that the complex achieves this effect by tuning the site III energy via the redox state of its internal cysteine residues. This result shows how pigment-protein complexes exploit the quantum mechanics of vibronic coupling to steer energy transfer.

Redox conditions correlated with vibronic coupling modulate quantum beats in photosynthetic pigment-protein complexes.

Quantum coherences, observed as time-dependent beats in ultrafast spectroscopic experiments, arise when light-matter interactions prepare systems in superpositions of states with differing energy and fixed phase across the ensemble. Such coherences have been observed in photosynthetic systems following ultrafast laser excitation, but what these coherences imply about the underlying energy transfer dynamics remains subject to debate. Recent work showed that redox conditions tune vibronic coupling in the Fenna-Matthews-Olson (FMO) pigment-protein complex in green sulfur bacteria, raising the question of whether redox conditions may also affect the long-lived (>100 fs) quantum coherences observed in this complex. In this work, we perform ultrafast two-dimensional electronic spectroscopy measurements on the FMO complex under both oxidizing and reducing conditions. We observe that many excited-state coherences are exclusively present in reducing conditions and are absent or attenuated in oxidizing conditions. Reducing conditions mimic the natural conditions of the complex more closely. Further, the presence of these coherences correlates with the vibronic coupling that produces faster, more efficient energy transfer through the complex under reducing conditions. The growth of coherences across the waiting time and the number of beating frequencies across hundreds of wavenumbers in the power spectra suggest that the beats are excited-state coherences with a mostly vibrational character whose phase relationship is maintained through the energy transfer process. Our results suggest that excitonic energy transfer proceeds through a coherent mechanism in this complex and that the coherences may provide a tool to disentangle coherent relaxation from energy transfer driven by stochastic environmental fluctuations.

Phycobilisome's Exciton Transfer Efficiency Relies on an Energetic Funnel Driven by Chromophore-Linker Protein Interactions.

The phycobilisome is the primary light-harvesting antenna in cyanobacterial and red algal oxygenic photosynthesis. It maintains near-unity efficiency of energy transfer to reaction centers despite relying on slow exciton hopping along a relatively sparse network of highly fluorescent phycobilin chromophores. How the complex maintains this high efficiency remains unexplained. Using a two-dimensional electronic spectroscopy polarization scheme that enhances energy transfer features, we directly watch energy flow in the phycobilisome complex of Synechocystis sp. PCC 6803 from the outer phycocyanin rods to the allophycocyanin core. The observed downhill flow of energy, previously hidden within congested spectra, is faster than timescales predicted by Förster hopping along single rod chromophores. We attribute the fast, 8 ps energy transfer to interactions between rod-core linker proteins and terminal rod chromophores, which facilitate unidirectionally downhill energy flow to the core. This mechanism drives the high energy transfer efficiency in the phycobilisome and suggests that linker protein-chromophore interactions have likely evolved to shape its energetic landscape.

Leveraging Dynamical Symmetries in Two-Dimensional Electronic Spectra to Extract Population Transfer Pathways.

We present a method to deterministically isolate population transfer kinetics from two-dimensional electronic spectroscopic signals. Central to this analysis is the characterization of how all possible subensembles of excited state systems evolve through the population time. When these dynamics are diagrammatically mapped by using double-sided Feynman pathways where population time dynamics are included, a useful symmetry emerges between excited state absorption and ground state bleach recovery dynamics of diagonal and below diagonal cross-peak signals. This symmetry allows removal of pathways from the spectra to isolate signals that evolve according to energy transfer kinetics. We describe a regression procedure to fit to energy transfer time constants and characterize the accuracy of the method in a variety of complex excited state systems using simulated two-dimensional spectra. Our results show that the method is robust for extracting ultrafast energy transfer in multistate excitonic systems, systems containing dark states that affect the signal kinetics, and systems with interfering vibrational relaxation pathways. This procedure can be used to accurately extract energy transfer kinetics from a wide variety of condensed phase systems.

Accumulation of Mitochondrial RPPH1 RNA Is Associated with Cellular Senescence.

Post-transcriptional gene regulation is an important step in the regulation of eukaryotic gene expression. Subcellular compartmentalization of RNA species plays a crucial role in the control of mRNA turnover, spatial restriction of protein synthesis, and the formation of macromolecular complexes. Although long noncoding RNAs (lncRNAs) are one of the key regulators of post-transcriptional gene expression, it is not heavily studied whether localization of lncRNAs in subcellular organelles has functional consequences. Here, we report on mitochondrial lncRNAs whose expression fluctuates in the process of cellular senescence. One of the mitochondrial lncRNAs, RPPH1 RNA, is overexpressed and accumulates in mitochondria of senescent fibroblasts, possibly modulated by the RNA-binding protein AUF1. In addition, RPPH1 RNA overexpression promotes spontaneous replicative cellular senescence in proliferating fibroblasts. Using MS2 aptamer-based RNA affinity purification strategy, we identified putative target mRNAs of RPPH1 RNA and revealed that partial complementarity of RPPH1 RNA to its target mRNAs prevents those mRNAs decay in proliferating fibroblasts. Altogether, our results demonstrate the role of mitochondrial noncoding RNA in the regulation of mRNA stability and cellular senescence.

Leveraging scatter in two-dimensional spectroscopy: passive phase drift correction enables a global phasing protocol.

Phase stability between pulse pairs defining Fourier-transform time delays can limit resolution and complicates development and adoption of multidimensional coherent spectroscopies. We demonstrate a data processing procedure to correct the long-term phase drift of the nonlinear signal during two-dimensional (2D) experiments based on the relative phase between scattered excitation pulses and a global phasing procedure to generate fully absorptive 2D electronic spectra of wafer-scale monolayer MoS2. Our correction results in a ∼30-fold increase in effective long-term signal phase stability, from ∼λ/2 to ∼λ/70 with negligible extra experimental time and no additional optical components. This scatter-based drift correction should be applicable to other interferometric techniques as well, significantly lowering the practical experimental requirements for this class of measurements.

AUF1 facilitates microRNA-mediated gene silencing.

Eukaryotic mRNA decay is tightly modulated by RNA-binding proteins (RBPs) and microRNAs (miRNAs). RBP AU-binding factor 1 (AUF1) has four isoforms resulting from alternative splicing and is critical for miRNA-mediated gene silencing with a distinct preference of target miRNAs. Previously, we have shown that AUF1 facilitates miRNA loading to Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex. Here, we further demonstrate that depletion of AUF1 abolishes the global interaction of miRNAs and AGO2. Single-molecule analysis revealed that AUF1 slowed down assembly of AGO2-let-7b-mRNA complex unexpectedly. However, target mRNAs recognized by both miRNA and AUF1 are less abundant upon AUF1 overexpression implying that AUF1 is a decay-promoting factor influencing multiple steps in AGO2-miRNA-mediated mRNA decay. Our findings indicate that AUF1 functions in promoting miRNA-mediated mRNA decay globally.

Competition between Hydrophilic and Argyrophilic Interactions in Surface Enhanced Raman Spectroscopy.

The competition for binding and charge-transfer (CT) from the nitrogen containing heterocycle pyrimidine to either silver or to water in surface enhanced Raman spectroscopy (SERS) is discussed. The correlation between the shifting observed for vibrational normal modes and CT is analyzed both experimentally using Raman spectroscopy and theoretically using electronic structure theory. Discrete features in the Raman spectrum correspond to the binding of either water or silver to each of pyrimidine's nitrogen atoms with comparable frequency shifts. Natural bond orbital (NBO) calculations in each chemical environment reveal that the magnitude of charge transfer from pyrimidine to adjacent silver atoms is only about twice that for water alone. These results suggest that the choice of solvent plays a role in determining the vibrational frequencies of nitrogen containing molecules in SERS experiments.

Annihilation of Excess Excitations along Phycocyanin Rods Precedes Downhill Flow to Allophycocyanin Cores in the Phycobilisome of Synechococcus elongatus PCC 7942.

Cyanobacterial phycobilisome complexes absorb visible sunlight and funnel photogenerated excitons to the photosystems where charge separation occurs. In the phycobilisome complex of Synechococcus elongatus PCC 7942, phycocyanin protein rods that absorb bluer wavelengths are assembled on allophycocyanin cores that absorb redder wavelengths. This arrangement creates a natural energy gradient toward the reaction centers of the photosystems. Here, we employ broadband pump-probe spectroscopy to observe the fate of excess excitations in the phycobilisome complex of this organism. We show that excess excitons are quenched through exciton-exciton annihilation along the phycocyanin rods prior to transfer to the allophycocyanin cores. Our observations are especially relevant in comparison to other antenna proteins, where exciton annihilation primarily occurs in the lowest-energy chlorophylls. The observed effect could play a limited photoprotective role in physiological light fluences. The exciton decay dynamics is faster in the intact phycobilisome than in isolated C-phycocyanin trimers studied in earlier work, confirming that this effect is an emergent property of the complex assembly. Using the obtained annihilation data, we calculate exciton hopping times of 2.2-6.4 ps in the phycocyanin rods. This value agrees with earlier FRET calculations of exciton hopping times along phycocyanin hexamers by Sauer and Scheer.

Sub-10 fs Intervalley Exciton Coupling in Monolayer MoS2 Revealed by Helicity-Resolved Two-Dimensional Electronic Spectroscopy.

The valley pseudospin at the K and K' high-symmetry points in monolayer transition metal dichalcogenides (TMDs) has potential as an optically addressable degree of freedom in next-generation optoelectronics. However, intervalley scattering and relaxation of charge carriers leads to valley depolarization and limits practical applications. In addition, enhanced Coulomb interactions lead to pronounced excitonic effects that dominate the optical response and initial valley depolarization dynamics but complicate the interpretation of ultrafast spectroscopic experiments at short time delays. Employing broadband helicity-resolved two-dimensional electronic spectroscopy (2DES), we observe ultrafast (∼10 fs) intervalley coupling between all A and B valley exciton states that results in a complete breakdown of the valley index in large-area monolayer MoS2 films. These couplings and subsequent dynamics exhibit minimal excitation fluence or temperature dependence and are robust toward changes in sample grain size and inherent strain. Our observations strongly suggest that this direct intervalley coupling on the time scale of optical excitation is an inherent property of large-area MoS2 distinct from dynamic carrier or exciton scattering, phonon-driven processes, and multiexciton effects. This ultrafast intervalley coupling poses a fundamental challenge for exciton-based valleytronics in monolayer TMDs and must be overcome to fully realize large-area valleytronic devices.

Time-Domain Line-Shape Analysis from 2D Spectroscopy to Precisely Determine Hamiltonian Parameters for a Photosynthetic Complex.

Optical signals come from coherences between quantum states, with spectral line widths determined by the coherences' dephasing dynamics. Using a 2D electronic spectrometer, we observe weak coherence- and rephasing-time-domain signals persisting to 1 ps in the Fenna-Matthews-Olson complex at 77 K. These are coherences between the ground and excited states prepared after the complex interacts once or three times with light, rather than zero-quantum coherences that are more frequently investigated following two interactions. Here, we use these small but persistent signal components to isolate spectral contributions with narrowed peaks and reveal the system's eigenenergies.

Evidence for the Dominance of Carrier-Induced Band Gap Renormalization over Biexciton Formation in Cryogenic Ultrafast Experiments on MoS2 Monolayers.

Transition-metal dichalcogenides (TMDs) such as MoS2 display promising electrical and optical properties in the monolayer limit. Due to strong quantum confinement, TMDs provide an ideal environment for exploring excitonic physics using ultrafast spectroscopy. However, the interplay between collective excitation effects on single excitons such as band gap renormalization/exciton binding energy (BGR/EBE) change and multiexciton effects such biexciton formation remains poorly understood. Using two-dimensional electronic spectroscopy, we observe the dominance of single-exciton BGR/EBE signals over optically induced biexciton formation. We make this determination based on a lack of strong PIA features at T = 0 fs in the cryogenic spectra. By means of nodal line slope analysis, we determine that spectral diffusion occurs faster than BGR/EBE change, indicative of distinct processes. These results indicate that at higher sub-Mott limit fluences, collective effects on single excitons dominate biexciton formation.

Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency.

DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.

eIF4E phosphorylation by MST1 reduces translation of a subset of mRNAs, but increases lncRNA translation.

Post-transcriptional gene regulation is an important step in eukaryotic gene expression. The last step to govern production of nascent peptides is during the process of mRNA translation. mRNA translation is controlled by many translation initiation factors that are susceptible to post-translational modifications. Here we report that one of the translation initiation factors, eIF4E, is phosphorylated by Mammalian Ste20-like kinase (MST1). Upon phosphorylation, eIF4E weakly interacts with the 5' CAP to inhibit mRNA translation. Simultaneously, active polyribosome is more associated with long noncoding RNAs (lncRNAs). Moreover, the linc00689-derived micropeptide, STORM (Stress- and TNF-α-activated ORF Micropeptide), is triggered by TNF-α-induced and MST1-mediated eIF4E phosphorylation, which exhibits molecular mimicry of SRP19 and, thus, competes for 7SL RNA. Our findings have uncovered a novel function of MST1 in mRNA and lncRNA translation by direct phosphorylation of eIF4E. This novel signaling pathway will provide new platforms for regulation of mRNA translation via post-translational protein modification.