Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes.

RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.

High harmonic generation in solids: particle and wave perspectives.

High harmonic generation (HHG) from gas-phase atoms (or molecules) has opened up a new frontier in ultrafast optics, where attosecond time resolution and angstrom spatial resolution are accessible. The fundamental physical pictures of HHG are always explained by the laser-induced recollision of particle-like electron motion, which lay the foundation of attosecond spectroscopy. In recent years, HHG has also been observed in solids. One can expect the extension of attosecond spectroscopy to the condensed matter if a description capable of resolving the ultrafast dynamics is provided. Thus, a large number of theoretical studies have been proposed to understand the underlying physics of solid HHG. Here, we revisit the recollision picture in solid HHG and show some challenges of current particle-perspective methods, and present the recently developed wave-perspective Huygens-Fresnel picture for understanding dynamical systems within the ambit of strong-field physics.

m6Aminer: Predicting the m6Am Sites on mRNA by Fusing Multiple Sequence-Derived Features into a CatBoost-Based Classifier.

As one of the most important post-transcriptional modifications, m6Am plays a fairly important role in conferring mRNA stability and in the progression of cancers. The accurate identification of the m6Am sites is critical for explaining its biological significance and developing its application in the medical field. However, conventional experimental approaches are time-consuming and expensive, making them unsuitable for the large-scale identification of the m6Am sites. To address this challenge, we exploit a CatBoost-based method, m6Aminer, to identify the m6Am sites on mRNA. For feature extraction, nine different feature-encoding schemes (pseudo electron-ion interaction potential, hash decimal conversion method, dinucleotide binary encoding, nucleotide chemical properties, pseudo k-tuple composition, dinucleotide numerical mapping, K monomeric units, series correlation pseudo trinucleotide composition, and K-spaced nucleotide pair frequency) were utilized to form the initial feature space. To obtain the optimized feature subset, the ExtraTreesClassifier algorithm was adopted to perform feature importance ranking, and the top 300 features were selected as the optimal feature subset. With different performance assessment methods, 10-fold cross-validation and independent test, m6Aminer achieved average AUC of 0.913 and 0.754, demonstrating a competitive performance with the state-of-the-art models m6AmPred (0.905 and 0.735) and DLm6Am (0.897 and 0.730). The prediction model developed in this study can be used to identify the m6Am sites in the whole transcriptome, laying a foundation for the functional research of m6Am.

Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.

Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in multiple diseases, PC has been regarded as a potential therapeutic target for obesity, diabetes, and cancer. Albeit acetyl-CoA has been recognized as the allosteric regulator of PC for over 60 years, the underlying mechanism of how acetyl-CoA induces PC activation remains enigmatic. Herein, by using time-resolved cryo-electron microscopy, we have captured the snapshots of PC transitional states during its catalytic cycle. These structures and the biochemical studies reveal that acetyl-CoA stabilizes PC in a catalytically competent conformation, which triggers a cascade of events, including ATP hydrolysis and the long-distance communication between the two reactive centers. These findings provide an integrated picture for PC catalysis and unveil the unique allosteric mechanism of acetyl-CoA in an essential biochemical reaction in all kingdoms of life.

Filming movies of attosecond charge migration in single molecules with high harmonic spectroscopy.

Electron migration in molecules is the progenitor of chemical reactions and biological functions after light-matter interaction. Following this ultrafast dynamics, however, has been an enduring endeavor. Here we demonstrate that, by using machine learning algorithm to analyze high-order harmonics generated by two-color laser pulses, we are able to retrieve the complex amplitudes and phases of harmonics of single fixed-in-space molecules. These complex dipoles enable us to construct movies of laser-driven electron migration after tunnel ionization of N2 and CO2 molecules at time steps of 50 attoseconds. Moreover, the angular dependence of the migration dynamics is fully resolved. By examining the movies, we observe that electron holes do not just migrate along the laser polarization direction, but may swirl around the atom centers. Our result establishes a general scheme for studying ultrafast electron dynamics in molecules, paving a way for further advance in tracing and controlling photochemical reactions by femtosecond lasers.

Full experimental determination of tunneling time with attosecond-scale streaking method.

Tunneling is one of the most fundamental and ubiquitous processes in the quantum world. The question of how long a particle takes to tunnel through a potential barrier has sparked a long-standing debate since the early days of quantum mechanics. Here, we propose and demonstrate a novel scheme to accurately determine the tunneling time of an electron. In this scheme, a weak laser field is used to streak the tunneling current produced by a strong elliptically polarized laser field in an attoclock configuration, allowing us to retrieve the tunneling ionization time relative to the field maximum with a precision of a few attoseconds. This overcomes the difficulties in previous attoclock measurements wherein the Coulomb effect on the photoelectron momentum distribution has to be removed with theoretical models and it requires accurate information of the driving laser fields. We demonstrate that the tunneling time of an electron from an atom is close to zero within our experimental accuracy. Our study represents a straightforward approach toward attosecond time-resolved imaging of electron motion in atoms and molecules.

Rotational echo spectroscopy for accurate measurement of molecular alignment.

We measure the molecular alignment induced in gas using molecular rotational echo spectroscopy. Our results show that the echo intensity and the time interval between the local extremas of the echo responses depend sensitively on the pump intensities and the initial molecular rotational temperature, respectively. This allows us to accurately extract these experimental parameters from the echo signals and then further determine the molecular alignment in experiments. The accuracy of our method has been verified by comparing the simulation with the extracted parameters from the molecular alignment experiment performed with a femtosecond pump pulse.

Fingerprint of the Interbond Electron Hopping in Second-Order Harmonic Generation.

We experimentally explore the fingerprint of the microscopic electron dynamics in second-order harmonic generation (SHG). It is shown that the interbond electron hopping induces a novel source of nonlinear polarization and plays an important role even when the driving laser intensity is 2 orders of magnitude lower than the characteristic atomic field. Our model predicts anomalous anisotropic structures of the SHG yield contributed by the interbond electron hopping, which is identified in our experiments with ZnO crystals. Moreover, a generalized second-order susceptibility with an explicit form is proposed, which provides a unified description in both the weak and strong field regimes. Our work reveals the nonlinear responses of materials at the electron scale and extends the nonlinear optics to a previously unexplored regime, where the nonlinearity related to the interbond electron hopping becomes dominant. It paves the way for realizing controllable nonlinearity on an ultrafast time scale.

All-optical attosecond time domain interferometry.

Interferometry, a key technique in modern precision measurements, has been used for length measurement in engineering metrology and astronomy. An analogous time-domain interferometric technique would represent a significant complement to spatial domain applications and require the manipulation of interference on extreme time and energy scales. Here, we report an all-optical interferometer using laser-driven high order harmonics as attosecond temporal slits. By controlling the phase of the temporal slits with an external field, a time domain interferometer that preserves both attosecond temporal resolution and hundreds of meV energy resolution is implemented. We apply this exceptional temporal resolution to reconstruct the waveform of an arbitrarily polarized optical pulse, and utilize the provided energy resolution to interrogate the abnormal character of the transition dipole near the Cooper minimum in argon. This novel attosecond interferometry paves the way for high precision measurements in the time-energy domain using all-optical approaches.

Huygens-Fresnel Picture for High Harmonic Generation in Solids.

High harmonic generation (HHG) is usually described by the laser-induced recollision of particlelike electrons, which lies at the heart of attosecond physics and also inspires numerous attosecond spectroscopic methods. Here, we demonstrate that the wavelike behavior of electrons plays an important role in solid HHG. By taking an analogy to the Huygens-Fresnel principle, an electron wave perspective on solid HHG is proposed by using the wavelet stationary-phase method. From this perspective, we have explained the deviation between the cutoff law predicted by the particlelike recollision model and the numerical simulation of semiconductor Bloch equations. Moreover, the emission times of HHG can be well predicted with our method involving the wave property of electrons. However, in contrast, the prediction with the particlelike recollision model shows obvious deviations compared to the semiconductor Bloch equations simulation. The wavelike properties of the electron motion can also be revealed by the HHG in a two-color field.

Zipper head mechanism of telomere synthesis by human telomerase.

Telomerase, a multi-subunit ribonucleoprotein complex, is a unique reverse transcriptase that catalyzes the processive addition of a repeat sequence to extend the telomere end using a short fragment of its own RNA component as the template. Despite recent structural characterizations of human and Tetrahymena telomerase, it is still a mystery how telomerase repeatedly uses its RNA template to synthesize telomeric DNA. Here, we report the cryo-EM structure of human telomerase holoenzyme bound with telomeric DNA at resolutions of 3.5 Å and 3.9 Å for the catalytic core and biogenesis module, respectively. The structure reveals that a leucine residue Leu980 in telomerase reverse transcriptase (TERT) catalytic subunit functions as a zipper head to limit the length of the short primer-template duplex in the active center. Moreover, our structural and computational analyses suggest that TERT and telomerase RNA (hTR) are organized to harbor a preformed active site that can accommodate short primer-template duplex substrates for catalysis. Furthermore, our findings unveil a double-fingers architecture in TERT that ensures nucleotide addition processivity of human telomerase. We propose that the zipper head Leu980 is a structural determinant for the sequence-based pausing signal of DNA synthesis that coincides with the RNA element-based physical template boundary. Functional analyses unveil that the non-glycine zipper head plays an essential role in both telomerase repeat addition processivity and telomere length homeostasis. In addition, we also demonstrate that this zipper head mechanism is conserved in all eukaryotic telomerases. Together, our study provides an integrated model for telomerase-mediated telomere synthesis.

Enhancement of the photocurrents injected in gapped graphene by the orthogonally polarized two-color laser field.

We theoretically investigate the photocurrents injected in gapped graphene by the orthogonally polarized two-color laser field. Depending on the relative phase, the photocurrents can be coherently controlled by deforming the electron trajectory in the reciprocal space. Under the same field strength, the peak photocurrent in the orthogonally polarized two-color field is about 20 times larger than that for linearly polarized light, and about 3.6 times for elliptically polarized light. The enhancement of the photocurrent can be attributed to an obvious asymmetric distribution of the real population in the reciprocal space, which is sensitive to the waveform of the laser field and related to the quantum interference between the electron trajectories. Our work provides a noncontact method to effectively enhance the injected current in graphene.

Dynamic Core Polarization in High Harmonic Generation from Solids: The Example of MgO Crystals.

Previously, the strong field processes in solids have always been explained by the single-active-electron (SAE) model with a frozen core excluding the fluctuation of background electrons. In this work, we demonstrate the strong field induced dynamic core polarization effect and propose a model for revealing its role in high harmonic generation (HHG) from solids. We show that the polarized core induces an additional polarization current beyond the SAE model based on the frozen cores. It gives a new mechanism for HHG and leads to new anisotropic structures, which are experimentally observed with MgO. Our experiments indicate that the influences of dynamic core polarization on HHG are obvious for both linearly and elliptically polarized laser fields. Our work establishes the bridge between the HHG and the dynamic changes of the effective many-electron interaction in solids, which paves the way to probe the ultrafast electron dynamics.

Multilevel quantum interference in the formation of high-order fractional molecular alignment echoes.

We theoretically investigate the formation of the high-order fractional alignment echo in OCS molecule and systematically study the dependence of echo intensity on the intensities and time delay of the two excitation pulses. Our simulations reveal an intricate dependence of the intensity of high-order fractional alignment echo on the laser conditions. Based on the analysis with rotational density matrix, this intricate dependence is further demonstrated to arise from the interference of multiple quantum pathways that involve multilevel rotational transitions. Our result provides a comprehensive multilevel picture of the quantum dynamics of high-order fractional alignment echo in molecular ensembles, which will facilitate the development of "rotational echo spectroscopy."

Structural insights into transcriptional regulation of human RNA polymerase III.

RNA polymerase III (Pol III) synthesizes structured, essential small RNAs, such as transfer RNA, 5S ribosomal RNA and U6 small nuclear RNA. Pol III, the largest nuclear RNA polymerase, is composed of a conserved core region and eight constitutive regulatory subunits, but how these factors jointly regulate Pol III transcription remains unclear. Here, we present cryo-EM structures of human Pol III in both apo and elongating states, which unveil both an orchestrated movement during the apo-to-elongating transition and an unexpected apo state in which the RPC7 subunit tail occupies the DNA-RNA-binding cleft of Pol III, suggesting that RPC7 plays important roles in both autoinhibition and transcription initiation. The structures also reveal a proofreading mechanism for the TFIIS-like subunit RPC10, which stably retains its catalytic position in the secondary channel, explaining the high fidelity of Pol III transcription. Our work provides an integrated picture of the mechanism of Pol III transcription regulation.

Measuring the rotational temperature and pump intensity in molecular alignment experiments via high harmonic generation.

We demonstrate a method to simultaneously measure the rotational temperature and pump intensity in laser-induced molecular alignment by the time-resolved high harmonic spectroscopy (HHS). It relies on the sensitive dependence of the arising times of the local minima and maxima of the harmonic yields at the rotational revivals on the pump intensity and rotational temperature. By measuring the arising times of these local extrema from the time-resolved harmonic signals, the rotational temperature and pump intensity can be accurately measured. We have demonstrated our method using N2 molecules. The validity and robustness of our method are tested with different harmonic orders and by changing the gas pressures as well as the distance between the gas exit and the optical axis. Moreover, we have also demonstrated the versatility of our method by applying it to CO2 molecules.

Fully stabilized multi-TW optical waveform synthesizer: Toward gigawatt isolated attosecond pulses.

A stable 50-mJ three-channel optical waveform synthesizer is demonstrated and used to reproducibly generate a high-order harmonic supercontinuum in the soft x-ray region. This synthesizer is composed of pump pulses from a 10-Hz repetition-rate Ti:sapphire pump laser and signal and idler pulses from an infrared two-stage optical parametric amplifier driven by this pump laser. With full active stabilization of all relative time delays, relative phases, and the carrier-envelope phase, a shot-to-shot stable intense continuum harmonic spectrum is obtained around 60 eV with pulse energy above 0.24 µJ. The peak power of the soft x-ray continuum is evaluated to be beyond 1 GW with a 170-as transform limit duration. We found a characteristic delay dependence of the multicycle waveform synthesizer and established its control scheme. Compared with the one-color case, we experimentally observe an enhancement of the cutoff spectrum intensity by one to two orders of magnitude using three-color waveform synthesis.

Structural insight into precursor ribosomal RNA processing by ribonuclease MRP.

Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to RNase P, which selectively cleaves transfer RNA-like substrates, it has remained a mystery how RNase MRP recognizes its diverse substrates. To address this question, we determined cryo-electron microscopy structures of Saccharomyces cerevisiae RNase MRP alone and in complex with a fragment of pre-rRNA. These structures and the results of biochemical studies reveal that coevolution of both protein and RNA subunits has transformed RNase MRP into a distinct ribonuclease that processes single-stranded RNAs by recognizing a short, loosely defined consensus sequence. This broad substrate specificity suggests that RNase MRP may have myriad yet unrecognized substrates that could play important roles in various cellular contexts.

Generation of isolated circularly polarized attosecond pulses by three-color laser field mixing.

We propose and theoretically demonstrate a method to generate the circularly polarized supercontinuum with three-color electric fields. The three-color field is synthesized from an orthogonally polarized two-color (OTC) laser field and an infrared gating field. All driving pulse durations are extended to 40 fs. We demonstrate that the three-color field imposes curved trajectories for ionized electrons and extends the time interval between each harmonic emitting. Through adjusting intensity ratios among three components of the driving field, a nearly circular isolated attosecond pulse can be generated.

Determination of Electron Band Structure using Temporal Interferometry.

We propose an all-optical method to directly reconstruct the band structure of semiconductors. Our scheme is based on the temporal Young's interferometer realized by high harmonic generation with a few-cycle laser pulse. As a time-energy domain interferometer, temporal interference encodes the band structure into the fringe in the energy domain. The relation between the band structure and the emitted harmonic frequencies is established. This enables us to retrieve the band structure from the spectrum of high harmonic generation with a single-shot measurement. Our scheme paves the way to study matters under ambient conditions and to track the ultrafast modification of band structures.