Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators.

NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. Bacterial NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and coordinating ρ-dependent termination and translation. The NusG paralog RfaH engages the EC only at operon polarity suppressor (ops) sites and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryoelectron microscopy (cryo-EM) to determine structures of ECs at ops with NusG or RfaH. Both factors chaperone base-pairing of the upstream duplex DNA to suppress backtracking, explaining stimulation of elongation genome-wide. The RfaH-opsEC structure reveals how RfaH confers operon specificity through specific recognition of an ops hairpin in the single-stranded nontemplate DNA and tighter binding to the EC to exclude NusG. Tight EC binding by RfaH sterically blocks the swiveled RNAP conformation necessary for hairpin-stabilized pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.

Structural biology of the Toll-like receptor family.

Innate immune receptors respond to common structural patterns in microbial molecules and are called pattern recognition receptors. Toll-like receptors (TLRs) play critical roles in the innate immune system by recognizing microbial lipids, carbohydrates, nucleic acids, and proteins. Precise definition of the ligand "pattern" of TLRs has been difficult to determine primarily owing to a lack of high-resolution structures. Recently, the structures of several TLR-ligand complexes and the intracellular signaling domains have been determined by X-ray crystallography. This new structural information, combined with extensive biochemical and immunological data accumulated over decades, sheds new light on ligand-recognition and -activation mechanisms. In this review, we summarize the TLR structures and discuss proposed ligand-recognition and -activation mechanisms.

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.

Sequence-specific pausing by RNA polymerase (RNAP) during transcription plays crucial and diverse roles in gene expression. In bacteria, RNA structures are thought to fold within the RNA exit channel of the RNAP and can increase pause lifetimes significantly. The biophysical mechanism of pausing is uncertain. We used single-particle cryo-EM to determine structures of paused complexes, including a 3.8-Å structure of an RNA hairpin-stabilized, paused RNAP that coordinates RNA folding in the his operon attenuation control region of E. coli. The structures revealed a half-translocated pause state (RNA post-translocated, DNA pre-translocated) that can explain transcriptional pausing and a global conformational change of RNAP that allosterically inhibits trigger loop folding and can explain pause hairpin action. Pause hairpin interactions with the RNAP RNA exit channel suggest how RNAP guides the formation of nascent RNA structures.

An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.

Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA-DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA-DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation.

Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors.

The R-loops forming around DNA double-strand breaks (DSBs) within actively transcribed genes play a critical role in the DSB repair process. However, the mechanisms underlying R-loop formation at DSBs remain poorly understood, with diverse proposed models involving protein factors associated with RNA polymerase (RNAP) loading, pausing/backtracking or preexisting transcript RNA invasion. In this single-molecule study using Escherichia coli RNAP, we discovered that transcribing RNAP alone acts as a highly effective DSB sensor, responsible for generation of R-loops upon encountering downstream DSBs, without requiring any additional factors. The R-loop formation efficiency is greatly influenced by DNA end structures, ranging here from 2.8% to 73%, and notably higher on sticky ends with 3' or 5' single-stranded overhangs compared to blunt ends without any overhangs. The R-loops extend unidirectionally upstream from the DSB sites and can reach the transcription start site, interfering with ongoing-round transcription. Furthermore, the extended R-loops can persist and maintain their structures, effectively preventing the efficient initiation of subsequent transcription rounds. Our results are consistent with the bubble extension model rather than the 5'-end invasion model or the middle insertion model. These discoveries provide valuable insights into the initiation of DSB repair on transcription templates across bacteria, archaea and eukaryotes.

Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination.

Transcriptional pause is essential for all types of termination. In this single-molecule study on bacterial Rho factor-dependent terminators, we confirm that the three Rho-dependent termination routes operate compatibly together in a single terminator, and discover that their termination efficiencies depend on the terminational pauses in unexpected ways. Evidently, the most abundant route is that Rho binds nascent RNA first and catches up with paused RNA polymerase (RNAP) and this catch-up Rho mediates simultaneous releases of transcript RNA and template DNA from RNAP. The fastest route is that the catch-up Rho effects RNA-only release and leads to 1D recycling of RNAP on DNA. The slowest route is that the RNAP-prebound stand-by Rho facilitates only the simultaneous rather than sequential releases. Among the three routes, only the stand-by Rho's termination efficiency positively correlates with pause duration, contrary to a long-standing speculation, invariably in the absence or presence of NusA/NusG factors, competitor RNAs or a crowding agent. Accordingly, the essential terminational pause does not need to be long for the catch-up Rho's terminations, and long pauses benefit only the stand-by Rho's terminations. Furthermore, the Rho-dependent termination of mgtA and ribB riboswitches is controlled mainly by modulation of the stand-by rather than catch-up termination.

Health Care Utilization for Common Shoulder Disorders: Analysis of the 2010-2019 National Patient Sample Data from the Health Insurance Review and Assessment Service in Korea.

Background and Objective: The aim of this study was to analyze trends in surgical and non-surgical service utilization for common shoulder disorders in Korea from 2010 to 2019. Methods and Materials: This retrospective, cross-sectional, descriptive study utilized National Patient Sample data from the Health Insurance and Review Assessment Service (HIRA) of Korea. These data constitute a 2% sample out of the entire Korean population and include data for a variety of parameters instrumental for health care research. Patients with at least one medical service use for rotator cuff syndrome or tear, impingement syndrome, or adhesive capsulitis between January 2010 and December 2019 were included. Trends in healthcare utilization by disorder type, patient demographics, seasonal service use, and treatment details were examined. Results: There was an upward trend in the total number of patients and costs for shoulder disorders, from 35,798 patients and USD 5,485,196 in 2010 to 42,558 and USD 11,522,543 in 2019, respectively. The number of patients aged ≥60 and hospital visits increased. March had the highest number of claims. Physical therapy was the most common non-surgical procedure, while nerve block claims more than doubled. Opioid prescription rates also tripled. Surgical treatments were dominated by shoulder rotator cuff repair and acromioplasty. Conclusions: There was a significant increase in healthcare utilization for shoulder disorders, marked by rising costs and patient numbers. The use of nerve blocks and opioids notably increased. These data are valuable for clinicians, researchers, and policymakers.

Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription.

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene.

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs.

Retinoic acid-inducible gene I (RIG-I) is responsible for innate immunity via the recognition of short double-stranded RNAs in the cytosol. With the clue that G-U wobble base pairs in the influenza A virus's RNA promoter region are responsible for RIG-I activation, we determined the complex structure of RIG-I ΔCARD and a short hairpin RNA with G-U wobble base pairs by X-ray crystallography. Interestingly, the overall helical backbone trace was not affected by the presence of the wobble base pairs; however, the base pair inclination and helical axis angle changed upon RIG-I binding. NMR spectroscopy revealed that RIG-I binding renders the flexible base pair of the influenza A virus's RNA promoter region between the two G-U wobble base pairs even more flexible. Binding to RNA with wobble base pairs resulted in a more flexible RIG-I complex. This flexible complex formation correlates with the entropy-favoured binding of RIG-I and RNA, which results in tighter binding affinity and RIG-I activation. This study suggests that the structure and dynamics of RIG-I are tailored to the binding of specific RNA sequences with different flexibility.

Comparison of Clinical Findings of Congenital Muscular Torticollis Between Patients With and Without Sternocleidomastoid Lesions as Determined by Ultrasonography.

AIM: To compare clinical findings for patients with congenital muscular torticollis (CMT) between those with and without a sternocleidomastoid (SCM) lesion. METHODS: Medical records of 182 patients with CMT were retrospectively reviewed and the patients were divided into SCM lesion and nonlesion groups by ultrasonographic results. Intrauterine position, age, duration of therapy, rotation/tilting side, and the passive range of motion and angle of the neck were compared. RESULTS: There were 74 SCM lesion and 108 nonlesion cases. The mean age at the first visit was 55.3 days in the SCM lesion group and 146.6 days in the nonlesion group. The mean therapy time in the nonlesion group was 66.5 days, significantly shorter than for the SCM lesion group (117.5 d). Tilting and rotation of the head in the same direction was observed only in the nonlesion group (n=9, 8.3%). Rotational limitation of the affected muscle side was 22.6 degree in the SCM lesion and 3.6 degree in the nonlesion group, and the tilting limitation was 19.2 degree in the SCM lesion and 10.4 degree in the nonlesion group. CONCLUSIONS: The nonlesion group had a better prognosis with shorter treatment duration. This group was more limited in head tilting than in head rotation, and the pattern of head rotation/tilting in the same direction was observed only in this group. These findings suggest that pathophysiological mechanisms and clinical characteristics may differ between CMT patients with and without SCM lesions. LEVEL OF EVIDENCE: Level II-prognostic studies, retrospective study.

Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer.

Toll-like receptor 2 (TLR2) initiates potent immune responses by recognizing diacylated and triacylated lipopeptides. Its ligand specificity is controlled by whether it heterodimerizes with TLR1 or TLR6. We have determined the crystal structures of TLR2-TLR6-diacylated lipopeptide, TLR2-lipoteichoic acid, and TLR2-PE-DTPA complexes. PE-DTPA, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid, is a synthetic phospholipid derivative. Two major factors contribute to the ligand specificity of TLR2-TLR1 or TLR2-TLR6 heterodimers. First, the lipid channel of TLR6 is blocked by two phenylalanines. Simultaneous mutation of these phenylalanines made TLR2-TLR6 fully responsive not only to diacylated but also to triacylated lipopeptides. Second, the hydrophobic dimerization interface of TLR2-TLR6 is increased by 80%, which compensates for the lack of amide lipid interaction between the lipopeptide and TLR2-TLR6. The structures of the TLR2-lipoteichoic acid and the TLR2-PE-DTPA complexes demonstrate that a precise interaction pattern of the head group is essential for a robust immune response by TLR2 heterodimers.

Relationship between starting age of cranial-remolding-orthosis therapy and effectiveness of treatment in children with deformational plagiocephaly.

PURPOSE: The aim of this study was to investigate the optimal age for starting cranial-remolding-orthosis therapy in children with deformational plagiocephaly. METHODS: Medical records of 310 patients with deformational plagiocephaly were retrospectively reviewed and the initial and final cranial vault asymmetry index (CVAI), age when starting therapy, duration of therapy, mean change of CVAI, improvement rate, and treatment success were analyzed. We compared outcomes according to the groups divided by ages starting therapy. RESULTS: There were no significant differences in improvement rate and duration of cranial-remolding-orthosis therapy among patients starting therapy at the age of 3, 4, and 5 months. However, when starting therapy after the age of 6 months, the rates of CVAI improvement were significantly lower and the duration of therapy was significantly increased. CONCLUSION: Considering the spontaneous resolution effect according to the head growth nature, the age 5 month is the optimal period to start cranial-remolding-orthosis therapy for deformational plagiocephaly.

Inflammatory burden interacts with conventional cardiovascular risk factors for carotid plaque formation in rheumatoid arthritis.

OBJECTIVE: Patients with RA have an increased risk of atherosclerosis and cardiovascular (CV) diseases compared with the general population. The aim of this study was to evaluate the role of inflammatory burden in the formation of carotid plaques in patients with RA. METHODS: We performed carotid artery US to measure the carotid intima-media thickness (IMT) and plaques in 406 patients with RA and 209 age- and sex-matched healthy controls. To assess the inflammatory burden, the area under the curve (AUC) of ESR over time was calculated. RESULTS: The carotid plaque frequency and mean IMT were significantly increased in patients with RA relative to controls. After adjustment for age and gender, the presence of carotid plaques in patients with RA was associated with HAQ score, tender joint count (TJC), swollen joint count (SJC), 28-joint DAS, ESR, CRP, LEF use, current corticosteroid dose and the number of conventional CV risk factors. After multivariate regression analysis, the factors significantly associated with plaque formation were TJC (P = 0.002), ESR (P = 0.002) and the number of conventional CV risk factors (P = 0.041). Among 194 RA patients with ESR AUC data, the presence of carotid plaque was independently associated with both the ESR AUC and number of conventional CV risk factors, which showed a synergistic interaction. CONCLUSION: Cumulative inflammatory burden contributes to the development of carotid atherosclerosis through a synergistic interaction with conventional CV risk factors in patients with RA.

Umbilical cord blood therapy potentiated with erythropoietin for children with cerebral palsy: a double-blind, randomized, placebo-controlled trial.

Allogeneic umbilical cord blood (UCB) has therapeutic potential for cerebral palsy (CP). Concomitant administration of recombinant human erythropoietin (rhEPO) may boost the efficacy of UCB, as it has neurotrophic effects. The objectives of this study were to assess the safety and efficacy of allogeneic UCB potentiated with rhEPO in children with CP. Children with CP were randomly assigned to one of three parallel groups: the pUCB group, which received allogeneic UCB potentiated with rhEPO; the EPO group, which received rhEPO and placebo UCB; and the Control group, which received placebo UCB and placebo rhEPO. All participants received rehabilitation therapy. The main outcomes were changes in scores on the following measures during the 6 months treatment period: the gross motor performance measure (GMPM), gross motor function measure, and Bayley scales of infant development-II (BSID-II) Mental and Motor scales (18). F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET/CT) and diffusion tensor images (DTI) were acquired at baseline and followed up to detect changes in the brain. In total, 96 subjects completed the study. Compared with the EPO (n = 33) and Control (n = 32) groups, the pUCB (n = 31) group had significantly higher scores on the GMPM and BSID-II Mental and Motor scales at 6 months. DTI revealed significant correlations between the GMPM increment and changes in fractional anisotropy in the pUCB group. 18F-FDG-PET/CT showed differential activation and deactivation patterns between the three groups. The incidence of serious adverse events did not differ between groups. In conclusion, UCB treatment ameliorated motor and cognitive dysfunction in children with CP undergoing active rehabilitation, accompanied by structural and metabolic changes in the brain.

Discovery of novel disease-causing mutation in SSBP1 and its correction using adenine base editor to improve mitochondrial function.

Mutations in nuclear genes regulating mitochondrial DNA (mtDNA) replication are associated with mtDNA depletion syndromes. Using whole-genome sequencing, we identified a heterozygous mutation (c.272G>A:p.Arg91Gln) in single-stranded DNA-binding protein 1 (SSBP1), a crucial protein involved in mtDNA replisome. The proband manifested symptoms including sensorineural deafness, congenital cataract, optic atrophy, macular dystrophy, and myopathy. This mutation impeded multimer formation and DNA-binding affinity, leading to reduced efficiency of mtDNA replication, altered mitochondria dynamics, and compromised mitochondrial function. To correct this mutation, we tested two adenine base editor (ABE) variants on patient-derived fibroblasts. One variant, NG-Cas9-based ABE8e (NG-ABE8e), showed higher editing efficacy (≤30%) and enhanced mitochondrial replication and function, despite off-target editing frequencies; however, risks from bystander editing were limited due to silent mutations and off-target sites in non-translated regions. The other variant, NG-Cas9-based ABE8eWQ (NG-ABE8eWQ), had a safer therapeutic profile with very few off-target effects, but this came at the cost of lower editing efficacy (≤10% editing). Despite this, NG-ABE8eWQ-edited cells still restored replication and improved mtDNA copy number, which in turn recovery of compromised mitochondrial function. Taken together, base editing-based gene therapies may be a promising treatment for mitochondrial diseases, including those associated with SSBP1 mutations.

To burst or hide.

The transcription activator of the λ phage, CII, determines whether the phage will undergo the lytic or the lysogenic pathway. In a report by Zhao et al. in this issue of Structure, the cryo-EM structure of the λCII-dependent transcription activation complex reveals how λCII activates the PRE promoter to turn on the lysogenic pathway.

Does removal of tracheostomy affect dysphagia? A kinematic analysis.

Tracheostomy tubes are thought to increase the incidence of aspiration and several mechanisms that might cause this have been suggested. Some studies reported alterations in laryngeal elevation during swallowing, which they attributed to an anchoring effect of the tracheostomy tube resulting in dysphagia. The purpose of the present study was to kinematically investigate the effect of tracheostomy on the swallowing process in dysphagic patients. Thirteen patients (7 males, 6 females; mean age = 61.4 years) were prospectively enrolled between August 2008 and December 2009. The inclusion criteria for a patient who had undergone tracheostomy were an ability to tolerate tube plugging for 48 h and the capacity to expectorate without assistance. All patients underwent two videofluoroscopic swallow studies (VFSS), before and after decannulation. We measured 21 time interval variables during swallowing in the pharyngeal phase and the extent of laryngeal elevation. No patient exhibited any change in swallowing function status [Penetration - Aspiration Scale (PAS) (median value = 1)] in the interval between the two VFSS tests. Upon kinematic analysis, no significant difference in any variable pertaining to laryngeal elevation or pharyngeal constriction was found when pre- and post-decannulation VFSS test data were compared (p > 0.05). The present study thus showed that removal of a tracheostomy tube does not affect the kinematics of swallowing. Our results support previous findings that indicated no relationship between tracheostomy tube placement and dysphagia.

Evaluation of dysphagia after cervical surgery using laryngeal electromyography.

The purpose of this study was to investigate the causes of dysphagia after cervical surgery using laryngeal electromyography (LEMG), and the effect of laryngeal neuropathy on the severity of dysphagia. Seventeen patients with dysphagia evident after cervical surgery were included. Video fluoroscopic swallow study (VFSS) parameters evaluated included the volume of residue in the vallecular pouch and the pyriform sinus, the Rosenbek penetration-aspiration scale (PAS), and the swallowing function scoring system (SFSS). By VFSS findings, patients were classified into a mild or severe dysphagia group. Nine of 17 patients showed voice change. SFSS scores were 0 in 2 patients, 3 in 1 patient, 4 in 1 patient, 5 in 1 patient, and 6 in 12 patients. PAS scores were 1 in 8 patients, 2 in 5 patients, 7 in 3 patients, and 8 in 1 patient. Laryngeal neuropathy was evident in seven patients (41.2%). Of these, all patients exhibited recurrent laryngeal neuropathy and 28.6% had superior laryngeal neuropathy. When we evaluated LEMG findings with respect to the severity of dysphagia, the severe dysphagia group showed significant association with the presence of laryngeal neuropathy (p = 0.006). Although the level of residue in the vallecular pouch was not associated with the presence of laryngeal neuropathy (p = 0.442), the amount of residue in the pyriform sinus did show a significant association (p = 0.020).

Protein Cages Engineered for Interaction-Driven Selective Encapsulation of Biomolecules.

Hollow protein cages have become attractive drug delivery vehicles with high biocompatibility and precise functional/structural manipulability. However, difficulties in effective cargo loading inside the cages have been limiting further development of protein cage-based drug carriers. Here, we developed a specific interaction-driven encapsulation and cellular delivery strategy for various biomolecules by engineering a porous protein cage. The computationally designed hyperstable mi3 protein cage was circularly permuted to fuse the cancer targeting RGD tripeptide to the cage surface and SpyTag (ST), which forms a covalent bond with SpyCatcher (SC), to the cage inner cavity. SC-fused proteins with different sizes and charges could be stably and actively encapsulated in the engineered nanocage via the ST/SC reaction. Cargo protein encapsulation inside the cage was directly confirmed by cryo-electron microscopy (EM) structure determination. In addition, SC-fused monomeric avidin was added to the nanocage to encapsulate various biotinylated (nonprotein) cargos such as oligonucleotides and the anticancer drug doxorubicin. All cargo molecules loaded onto the engineered mi3 were effectively delivered to cells. This work introduces a highly versatile cargo loading/delivery strategy, where loading/delivery interactions, cargo molecules, and cell targeting moieties can be further varied for optimal cellular drug delivery.