Mechanistic Insights Research Articles

Cross-Frequency Coupling as a Biomarker for Early Stroke Recovery

Background The application of neuroimaging-based biomarkers in stroke has enriched our understanding of post-stroke recovery mechanisms, including alterations in functional connectivity based on synchronous oscillatory activity across various cortical regions. Phase-amplitude coupling, a type of cross-frequency coupling, may provide additional mechanistic insight. Objective To determine how the phase of prefrontal cortex delta (1-3 Hz) oscillatory activity mediates the amplitude of motor cortex beta (13-20 Hz) oscillations in individual’s early post-stroke. Methods Participants admitted to an inpatient rehabilitation facility completed resting and task-based EEG recordings and motor assessments around the time of admission and discharge along with structural neuroimaging. Unimpaired controls completed EEG procedures during a single visit. Mixed-effects linear models were performed to assess within- and between-group differences in delta-beta prefrontomotor coupling. Associations between coupling and motor status and injury were also determined. Results Thirty individuals with stroke and 17 unimpaired controls participated. Coupling was greater during task versus rest conditions for all participants. Though coupling during affected extremity task performance decreased during hospitalization, coupling remained elevated at discharge compared to controls. Greater baseline coupling was associated with better motor status at admission and discharge and positively related to motor recovery. Coupling demonstrated both positive and negative associations with injury involving measures of lesion volume and overlap injury to anterior thalamic radiation, respectively. Conclusions This work highlights the utility of prefrontomotor cross-frequency coupling as a potential motor status and recovery biomarker in stroke. The frequency- and region-specific neurocircuitry featured in this work may also facilitate novel treatment strategies in stroke.

High Prevalence of F2 20210G > A in Splanchnic Vein Thrombosis and Cerebral Venous Sinus Thrombosis: A Retrospective Cohort Study of Patients with Thrombosis in Atypical Sites.

Atypical sites for thrombosis include deep vein thrombosis (DVT) of the upper extremity (UE-DVT), splanchnic vein thrombosis (SVT), and cerebral venous sinus thrombosis (CVST). In addition to specific pathogenic factors, their underlying mechanisms share similarities with typical venous thromboembolism (VTE), namely, DVT of the lower extremity and/or pulmonary embolism, but are less understood. Records of unselected patients with a history of typical VTE (n = 2,011), UE-DVT (n = 117), SVT (n = 83), and CVST (n = 82), who were referred to the Institute in Bonn for ambulatory thrombophilia testing, were retrospectively analyzed. Acquired and hereditary thrombosis risk factors were comparatively assessed. UE-DVT was characterized by a high rate (50.4%) of site-specific acquired risk factors. Compared with typical VTE, SVT was more frequently associated with systemic inflammation, infection, or malignancy (2.2 vs. 12.0%, p = 3·10-8) and the JAK2 V617F mutation was present in 16.9%. In CVST compared with typical VTE, demographics and higher rates of oral contraception (43.2 vs. 57.6%, p = 0.011) and pregnancy (4.2 vs. 10.9%, p = 0.012) suggest a significant hormonal influence on etiology. While the prevalence of inhibitor deficiencies and factor V Leiden mutation did not differ between cohorts, the prevalence of F2 20210G > A was higher in SVT (15.7%, p = 0.003) and CVST (15.9%, p = 0.003) than in typical VTE (7.0%). The cohorts with thrombosis in atypical sites showed distinctive patterns of acquired risk factors. Further studies are warranted to provide additional mechanistic insight into the role of hormonal influence in CVST and the contribution of F2 20210G > A to the development of SVT and CVST.

Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome

Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Mutations of HGSNAT cause HS accumulation and consequently mucopolysaccharidosis IIIC, a devastating lysosomal storage disease characterized by progressive neurological deterioration and early death where no treatment is available. HGSNAT catalyzes a unique transmembrane acetylation reaction where the acetyl group of cytosolic acetyl-CoA is transported across the lysosomal membrane and attached to HS in one reaction. However, the reaction mechanism remains elusive. Here we report six cryo-EM structures of HGSNAT along the reaction pathway. These structures reveal a dimer arrangement and a unique structural fold, which enables the elucidation of the reaction mechanism. We find that a central pore within each monomer traverses the membrane and controls access of cytosolic acetyl-CoA to the active site at its luminal mouth where glucosamine binds. A histidine-aspartic acid catalytic dyad catalyzes the transfer reaction via a ternary complex mechanism. Furthermore, the structures allow the mapping of disease-causing variants and reveal their potential impact on the function, thus creating a framework to guide structure-based drug discovery efforts.

Purinyl N-directed aroylation of 6-arylpurine ribo- and 2'-deoxyribonucleosides, and mechanistic insights.

The purinyl ring contains four embedded nitrogen atoms of varying basicities. Selective utilization of these ring nitrogen atoms can lead to relatively facile remote functionalization, yielding modified purinyl motifs that are otherwise not easily obtained. Herein, we report previously undescribed N-directed aroylation of 6-arylpurine ribo and the more labile 2'-deoxyribonucleosides. Kinetic isotope analysis as well as reaction with a well-defined dimeric, palladated 9-benzyl 6-arylpurine provided evidence for N-directed cyclometallation as a key step, with a plausible rate-limiting C-H bond cleavage. Radical inhibition experiments indicate the likely intermediacy of aroyl radicals. The chemistry surmounts difficulties often posed in the functionalization of polynitrogenated and polyoxygenated nucleosidic structures that possess complex reactivities and a labile glycosidic bond that is more sensitive in the 2'-deoxy substrates.

Allosteric effects of EF-G domain I mutations inducing ribosome frameshifting revealed by multiplexed force spectroscopy.

Ribosome translocation catalyzed by elongation factor G (EF-G) is a critical step in protein synthesis where the ribosome typically moves along the mRNA by three nucleotides at each step. To investigate the mechanism of EF-G catalysis, it is essential to precisely resolve the ribosome motion at both ends of the mRNA, which, to our best knowledge, is only achieved with the magnetic-based force spectroscopy developed by our groups. Here, we introduce a novel multiplexed force spectroscopy technique that, for the first time, offers single-nucleotide resolution for multiple samples. This technique combines multiple acoustic force generators with the smallest atomic magnetometer designed for biological research. Utilizing this technique, we demonstrate that mutating EF-G at the GTP binding pocket results in the ribosome moving only two nucleotides on both ends of the mRNA, thereby compromising ribosome translocation. This finding suggests a direct link between GTP hydrolysis and ribosome translocation. Our results not only provide mechanistic insights into the role of GTP binding pocket but also illuminate how allosteric mutations can manipulate translocation. We anticipate broader applications of our technique in the ribosome field, leveraging its high efficiency and single-nucleotide resolution.

Prefrontal coding of learned and inferred knowledge during REM and NREM sleep

Idling brain activity has been proposed to facilitate inference, insight, and innovative problem-solving. However, it remains unclear how and when the idling brain can create novel ideas. Here, we show that cortical offline activity is both necessary and sufficient for building unlearned inferential knowledge from previously acquired information. In a transitive inference paradigm, male C57BL/6J mice gained the inference 1 day after, but not shortly after, complete training. Inhibiting the neuronal computations in the anterior cingulate cortex (ACC) during post-learning either non-rapid eye movement (NREM) or rapid eye movement (REM) sleep, but not wakefulness, disrupted the inference without affecting the learned knowledge. In vivo Ca2+ imaging suggests that NREM sleep organizes the scattered learned knowledge in a complete hierarchy, while REM sleep computes the inferential information from the organized hierarchy. Furthermore, after insufficient learning, artificial activation of medial entorhinal cortex-ACC dialog during only REM sleep created inferential knowledge. Collectively, our study provides a mechanistic insight on NREM and REM coordination in weaving inferential knowledge, thus highlighting the power of idling brain in cognitive flexibility.

Mechanistic and kinetic insights of the formation of allene and propyne from the C3H3 reaction with water.

Allene (H2C = C = CH2) and propyne (CH3-C≡CH) are important compounds in the combustion chemistry. They can be created from the reaction of proparyl radicals with water. In this study, therefore, a computational study into the C3H3 + H2O potential energy landscape has been carefully conducted. The computed results indicate that the reaction paths forming the products (allene: CH2CCH2 + •OH) and (propyne: HCCCH3 + •OH) prevail under the 300-2000K temperature range, where the latter is much more predominant compared to the former. However, these two products are not easily formed under ambient conditions due to the high energy barriers. In the 300 - 2000K temperature range, the branching ratio for the propyne + •OH product declines from 100 to 86%, whereas the allene + •OH product shows an increase, reaching 14% at 2000K. The overall bimolecular rate constant of the title reaction can be presented by the modified Arrhenius expression of ktotal = 1.94 × 10-12 T0.14 exp[(-30.55kcal.mol-1)/RT] cm3 molecule-1s-1. The total rate constant at the ambient conditions in this work, 2.37 × 10-34 cm3 molecule-1s-1, was found to be over five orders of magnitude lower than the total rate constant of the C3H3 + NH3 reaction, 7.98 × 10-29 cm3 molecule-1s-1, calculated by Hue et al. (Int. J. Chem. Kinet. 2020, 4(2), 84-91). The results in this study contribute to elucidating the mechanism of allene and propylene formation from the C3H3 + H2O reaction, and they can be used for modeling C3H3-related systems under atmospheric and combustion conditions. All the geometric structures of the C3H3 + H2O system were optimized by the B3LYP method in conjunction with the 6-311 + + G(3df,2p) basis set. Single-point energies of these species were calculated at the CCSD(T)/6-311 + + G(3df,2p) level of theory. The CCSD(T)/CBS level has also been used to compute single-point energies for the two major reaction channels (C3H3 + H2O → allene + •OH and C3H3 + H2O → propyne + •OH). Rate constants and branching ratios of the key reaction channels were calculated in the 300-2000K temperature interval using the Chemrate software based on the transition state theory (TST) with Eckart tunneling corrections.

Modeling of cell cultivation for monoclonal antibody production processes considering lactate metabolic shifts.

Demand for monoclonal antibodies (mAbs) is rapidly increasing. To achieve higher productivity, there have been improvements to cell lines, operating modes, media, and cultivation conditions. Representative mathematical models are needed to narrow down the growing number of process alternatives. Previous studies have proposed mechanistic models to depict cell metabolic shifts (e.g., lactate production to consumption). However, the impacts of variations of some operating conditions have not yet been fully incorporated in such models. This paper offers a new mechanistic model considering variations in dissolved oxygen and glutamine depletion on cell metabolism applied to a novel Chinese hamster ovary (CHO) cell line. Expressions for the specific rates of lactate production, glutamine consumption, and mAb production were formulated for stirred and shaken-tank reactors. A deeper understanding of lactate metabolic shifts was obtained under different combinations of experimental conditions. Lactate consumption was more pronounced in conditions with higher DO and low glutamine concentrations. The model offers mechanistic insights that are useful for designing advanced operation strategies. It can be used in design space generation and process optimization for better productivity and product quality.

Enhanced degradation of methanethiol via operational pH regulation in biofilm reactor: Insight of sulfur metabolism pathways and microbial adaptation mechanism

Methanethiol (CH3SH), a typical organic sulfur pollutant, poses significant risks to both human health and ecological stability due to its high toxicity and corrosive properties. Membrane aerated biofilm reactor (MABR) has been regarded as a promising and eco-friendly solution for removing organic sulfur from wastewater. However, the oxidation of CH3SH might lead to spontaneous acidification, which might affect microbial metabolic activities to influence the CH3SH biotransformation in MABR system. This work demonstrated that operational pH regulation could effectively promote the complete conversion of CH3SH to SO42- in MABR, while the transformation efficiency was only 40.6% under uncontrolled pH condition. Meanwhile, operational pH regulation resulted in 35.2% reduction in the excessive secretion of extracellular polymeric substances, thereby building a stable biofilm structure with sufficient oxygen mass transfer to enhance the CH3SH transformation. Additionally, operational pH regulation favored the enrichment of sulfur-oxidizing microorganisms (e.g., Rhodanobacter and Rhodobacter), while the uncontrolled pH favored the proliferation of microorganisms in harsh environment (e.g., Chitinophagaceae sp. and Sphingobacteriales sp.). Moreover, operational pH regulation enhanced the expression of critical genes involved in sulfur metabolism (e.g., SELENBP1 and SoxA), accompanied with glycolysis (e.g., ppgK and pfkB) and pyruvate metabolism (e.g., ackA and aceE), which could provide sufficient energy and electron. Conversely, these gene expressions were down-regulated in pH unregulation reactor, while the microbial adaptation mechanism was activated through the enhancement of DNA replication, quorum sensing, and two-component system, enabling resistance to extreme acidic conditions. This study would provide the in-depth understanding of operational pH regulation on organic sulfur degradation and transformation in MABR system and offer novel guidance for organic sulfur removal.

The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neuropeptide precursor in the Drosophila central nervous system

Numerous roles for the Alk receptor tyrosine kinase have been described in Drosophila, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analyzed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk and scRNA-seq datasets from larval brains in which Alk signaling was manipulated identified a previously uncharacterized Drosophila neuropeptide precursor encoded by CG4577 as an Alk signaling transcriptional target. CG4577, which we named Sparkly (Spar), is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the Drosophila Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the Drosophila CNS.

The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neuropeptide precursor in the Drosophila central nervous system.

Numerous roles for the Alk receptor tyrosine kinase have been described in Drosophila, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analyzed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk and scRNA-seq datasets from larval brains in which Alk signaling was manipulated identified a previously uncharacterized Drosophila neuropeptide precursor encoded by CG4577 as an Alk signaling transcriptional target. CG4577, which we named Sparkly (Spar), is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the Drosophila Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the Drosophila CNS.

Halogen-functionalized covalent organic frameworks for photocatalytic Cr(VI) reduction under visible light

Covalent organic frameworks (COFs) are a type of novel organic catalysts which show great potential in the treatment of environmental contaminations. Herein, we synthesized three isoreticular halogen-functionalized (F, Cl and Br) porphyrin COFs for visible-light (420 nm ≤ λ ≤ 780 nm) photocatalytic reduction of Cr(VI) to Cr(III). Halogen substituents with tunable electronegativity can regulate the band structure and modulate the charge carrier kinetics of COFs. In the absence of any sacrificial reagent, the isoreticular COFs exhibited good photocatalytic reduction activity of Cr(VI). Particularly, the TAPP-2F showed nearly 100 % conversion efficiency and the highest reaction rate constants (k) on account of the strong electronegativity of F substituent. Experimental results and theoretical calculations showed that the conduction band (CB) potentials of COFs became more negative and charge carrier separation increased with the enhancement of electronegativity (Br < Cl < F), which could provide sufficient driving force for the photoreduction of Cr(VI) to Cr(III). The halogen substituents strategy for regulating the electronic structure of COFs can provide opportunities for designing efficient photocatalysts for environmental remediation. Meanwhile, the mechanistic insights reported in this study help to understand the photocatalytic degradation pathways of heavy metals.

Industrial Routes from Sugars and Biomass to CMF and other 5-(Halomethyl)furfurals.

The synthesis of 5-(halomethyl)furfurals (XMFs, X = F, Cl, Br, I), including 5-(chloromethyl)furfural (CMF), 5-(bromomethyl)furfural (BMF), 5-(iodomethyl)furfural (IMF), and 5-(fluoromethyl)furfural (FMF), from biomass represents a pivotal advancement in renewable chemistry and engineering. Harnessing waste biomass as a raw material offers a sustainable alternative to fossil-based resources, mitigating environmental degradation and addressing pressing energy needs. CMF and BMF, characterized by their enhanced stability over the hydroxyl analog, 5-(hydroxymethyl)furfural (HMF), exhibit promise as renewable building blocks for scale-up and commercialization. The surge in research interest, particularly from 2010 to 2024, reflects a growing recognition of XMFs' potential as novel platform chemicals. This review highlights the evolution of XMF synthesis methods, focusing on their transformation from saccharides and lignocellulosic biomass. Mechanistic insights and experimental setups are scrutinized for industrial feasibility and scalability, shedding light on technical challenges and avenues for further research. The analysis underscores the burgeoning significance of XMFs in the transition towards sustainable chemical production, emphasizing the importance of process optimization and mechanistic understanding for commercial deployment.

Coherent photoexcitation of entangled triplet pair states.

The functional properties of organic semiconductors are defined by the interplay between optically bright and dark states. Organic devices require rapid conversion between these bright and dark manifolds for maximum efficiency, and one way to achieve this is through multiexciton generation (S1→1TT). The dark state 1TT is typically generated from bright S1 after optical excitation; however, the mechanistic details are hotly debated. Here we report a 1TT generation pathway in which it can be coherently photoexcited, without any involvement of bright S1. Using <10-fs transient absorption spectroscopy and pumping sub-resonantly, 1TT is directly generated from the ground state. Applying this method to a range of pentacene dimers and thin films of various aggregation types, we determine the critical material properties that enable this forbidden pathway. Through a strikingly simple technique, this result opens the door for new mechanistic insights into 1TT and other dark states in organic materials.

Abstract PO-031: Systematic discovery of chemotherapy response biomarkers in Peripheral T Cell Lymphomas

Abstract Background. Identifying which patients will benefit from individual therapies remains a general challenge in oncology. Predictive biomarkers of drug sensitivity, when known, can increase the rate of success of trials, and allow stratification of patients for targeted combination therapies, as recent shown by the GUIDANCE-01 trial in Large B-Cell Lymphoma. Peripheral T-Cell Lymphomas (PTCL) could particularly benefit from this approach, being heterogeneous diseases against which many therapies are active in unpredictable subsets of patients. A central challenge of biomarker discovery is finding true determinants of drug response, which may be multiple genes, among thousands of molecular features that may accidentally correlate. Here, we aim to mitigate this challenge by combining functional genetic screens and gene expression profiling in diverse PTCL cultures, to enable the systematic discovery of drug sensitivity biomarkers. Methods. To discover genes whose expression directly modifies drug sensitivity, we conducted genome-wide CRISPR screens with PTCL cells under treatment with five therapies with clinical activity in PTCL: Romidepsin, Pralatrexate, Gemcitabine, Oxaliplatin, and Bortezomib. To discover genes whose basal expression significantly correlates with specific drug sensitivities, we measured RNAseq and drug response functions for a diverse panel of 27 PTCL cultures. Genes in the intersection of both experiments are causally related to and correlate with drug responses in PTCL, and have the statistical benefit of detection by independent methods. Results. Functional genetic screens on therapy provided mechanistic insights for each drug of interest, and identified genes whose perturbation affects drug sensitivity. Whereas hundreds of genes nominally correlate with drug sensitivity in cell line panels, for each drug a shortlist of only 5 to 20 genes are both CRISPR hits and correlate with response across PTCL cultures. For each drug tested, multi-gene sensitivity scores constructed from hits stratify PTCL cultures into statistically distinct sensitive and non-sensitive subgroups (Mann Whitney P-Values &amp;lt;0.01). These genes’ relationships to drug mechanisms were often supported by prior studies, including functions in DNA repair, cell cycle regulation, and solute carriers required for cellular entry of specific therapies, such as SLC19A1 for Pralatrexate and SLC43A2 for Oxaliplatin. Conclusions. Combining functional genetic screens and correlative drug sensitivity measurements narrowed the search for predictive biomarkers of drug sensitivity, and may be a general means of refining biomarker hypotheses for validation in clinical datasets. Although chemotherapy sensitivity is commonly polygenic, multi-gene scores based on few mechanistically-related genes were able to significantly distinguish drug sensitive from resistant PTCLs. These approaches provide novel hypotheses for drug-gene relationships that may serve as the basis for molecular subtyping of individual lymphomas for precision regimens. Citation Format: Adam C Palmer, Jacob C Pantazis. Systematic discovery of chemotherapy response biomarkers in Peripheral T Cell Lymphomas [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-031.

Iron Olefin Metathesis: Unlocking Reactivity and Mechanistic Insights.

Olefin metathesis catalyzed by iron complexes has garnered substantial interest due to iron's abundance and nontoxicity relative to ruthenium, yet its full potential remains untapped, largely because of the propensity of iron carbenes to undergo cyclopropanation instead of cycloreversion from a metallacycle intermediate. In this report, we elucidate the reactions of [{PC(sp2)P}Fe(L)(N2)], ([PC(sp2)P] = bis[2-(diisopropylphosphino)phenyl]methylene) with strained olefins, unveiling their capability to yield metathesis-related products. Our investigations led to the isolation of a structurally characterized metallacyclobutane during the reaction with norbornadiene derivatives, ultimately leading to a ring-opened iron alkylidene. These findings provide compelling evidence that iron complexes adhere to the Chauvin olefin metathesis mechanism.

Imidazolidinones Derivatives As Pioneering Anticancer Agents: Unraveling Insights Through synthesis And Structure‐Activity Exploration

AbstractImidazolidinone derivatives have emerged as promising anticancer agents, captivating the attention of researchers in medicinal chemistry. Imidazolidinones, characterized by their unique chemical structure, have demonstrated versatility in synthetic methodologies. Researchers have developed a variety of derivatives, each with distinct modifications, allowing for fine‐tuning of pharmacological properties. This review explores the journey of imidazolidinone compounds, from synthesis to structure‐activity exploration, and investigates their anticancer mechanistic pathways. The synthesis methodologies, including diverse approaches and reaction conditions, were examined. Structural modifications are discussed, showing the versatility sof imidazolidinone scaffolds. Mechanistic insights into their anticancer mechanisms, in vitro, ex‐vivo and in vivo activities, with their challenges in development are critically analyzed. This paper concludes by emphasizing the potential of imidazolidinone derivatives and suggesting future research directions in the pursuit of novel and effective anticancer therapeutics.

Genome-Wide CRISPR Screen Identifies an NF2-Adherens Junction Mechanistic Dependency for Cardiac Lineage.

Cardiomyocyte differentiation involves a stepwise clearance of repressors and fate-restricting regulators through the modulation of BMP (bone morphogenic protein)/Wnt-signaling pathways. However, the mechanisms and how regulatory roadblocks are removed with specific developmental signaling pathways remain unclear. We conducted a genome-wide CRISPR screen to uncover essential regulators of cardiomyocyte specification in human embryonic stem cells using a myosin heavy chain 6 (MYH6)-GFP (green fluorescence protein) reporter system. After an independent secondary single guide ribonucleic acid validation of 25 candidates, we identified NF2 (neurofibromin 2), a moesin-ezrin-radixin like (MERLIN) tumor suppressor, as an upstream driver of early cardiomyocyte lineage specification. Independent monoclonal NF2 knockouts were generated using CRISPR-Cas9, and cell states were inferred through bulk RNA sequencing and protein expression analysis across differentiation time points. Terminal lineage differentiation was assessed by using an in vitro 2-dimensional-micropatterned gastruloid model, trilineage differentiation, and cardiomyocyte differentiation. Protein interaction and post-translation modification of NF2 with its interacting partners were assessed using site-directed mutagenesis, coimmunoprecipitation, and proximity ligation assays. Transcriptional regulation and trajectory inference from NF2-null cells reveal the loss of cardiomyocyte identity and the acquisition of nonmesodermal identity. Sustained elevation of early mesoderm lineage repressor SOX2 and upregulation of late anticardiac regulators CDX2 and MSX1 in NF2 knockout cells reflect a necessary role for NF2 in removing regulatory roadblocks. Furthermore, we found that NF2 and AMOT (angiomotin) cooperatively bind to YAP (yes-associated protein) during mesendoderm formation, thereby preventing YAP activation, independent of canonical MST (mammalian sterile 20-like serine-threonine protein kinase)-LATS (large tumor suppressor serine-threonine protein kinase) signaling. Mechanistically, cardiomyocyte lineage identity was rescued by wild-type and NF2 serine-518 phosphomutants, but not NF2 FERM (ezrin-radixin-meosin homology protein) domain blue-box mutants, demonstrating that the critical FERM domain-dependent formation of the AMOT-NF2-YAP scaffold complex at the adherens junction is required for early cardiomyocyte lineage differentiation. These results provide mechanistic insight into the essential role of NF2 during early epithelial-mesenchymal transition by sequestering the repressive effect of YAP and relieving regulatory roadblocks en route to cardiomyocytes.

Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants.

This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. As part of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was established and refined during the past 15 years. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. Later, this phenomenon was shown to be general. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide more mechanistic insight than traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects.

Evolution of a small phage protein overcomes antiphage defense in Enterococcus faecalis.

The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of new antibiotics needed to combat these infections remains stagnant. MDR enterococci, which are a common cause of hospital-acquired infections, are emerging as one of the major contributors to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which entails the use of lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of phage resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from vancomycin-resistant Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) and we show that this enzyme is sufficient to restrict the replication of lytic phage phi47 in E. faecalis . We further find that phi47 can evolve to overcome restriction by acquiring a missense mutation in a novel TIV-RE inhibitor protein encoded by many enterococcal phages. We show that this inhibitor, which we have named type IV restriction inhibiting factor A ( tifA ), directly binds to and inactivates diverse TIV-REs. Overall, our findings significantly advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages can evolve to overcome antiphage defense systems.