The non-cell-autonomous function of ID1 promotes AML progression via ANGPTL7 from the microenvironment.

The bone marrow microenvironment (BMM) can regulate leukemia stem cells (LSCs) via secreted factors. Increasing evidence suggests that dissecting the mechanisms by which the BMM maintains LSCs may lead to the development of effective therapies for the eradication of leukemia. Inhibitor of DNA binding 1 (ID1), a key transcriptional regulator in LSCs, previously identified by us, controls cytokine production in the BMM, but the role of ID1 in acute myeloid leukemia (AML) BMM remains obscure. Here, we report that ID1 is highly expressed in the BMM of patients with AML, especially in BM mesenchymal stem cells, and that the high expression of ID1 in the AML BMM is induced by BMP6, secreted from AML cells. Knocking out ID1 in mesenchymal cells significantly suppresses the proliferation of cocultured AML cells. Loss of Id1 in the BMM results in impaired AML progression in AML mouse models. Mechanistically, we found that Id1 deficiency significantly reduces SP1 protein levels in mesenchymal cells cocultured with AML cells. Using ID1-interactome analysis, we found that ID1 interacts with RNF4, an E3 ubiquitin ligase, and causes a decrease in SP1 ubiquitination. Disrupting the ID1-RNF4 interaction via truncation in mesenchymal cells significantly reduces SP1 protein levels and delays AML cell proliferation. We identify that the target of Sp1, Angptl7, is the primary differentially expression protein factor in Id1-deficient BM supernatant fluid to regulate AML progression in mice. Our study highlights the critical role of ID1 in the AML BMM and aids the development of therapeutic strategies for AML.

An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.

Tryptophanyl-tRNA synthetase (TrpRS) links tryptophan to tRNATrp, thereby playing an indispensable role in protein translation. Unlike most class I aminoacyl-tRNA synthetases (AARSs), TrpRS functions as a homodimer. Herein, we captured an 'open-closed' asymmetric structure of Escherichia coli TrpRS (EcTrpRS) with one active site occupied by a copurified intermediate product and the other remaining empty, providing structural evidence for the long-discussed half-of-the-sites reactivity of bacterial TrpRS. In contrast to its human counterpart, bacterial TrpRS may rely on this asymmetric conformation to functionally bind with substrate tRNA. As this asymmetric conformation is probably a dominant form of TrpRS purified from bacterial cells, we performed fragment screening against asymmetric EcTrpRS to support antibacterial discovery. Nineteen fragment hits were identified, and 8 of them were successfully cocrystallized with EcTrpRS. While a fragment named niraparib bound to the L-Trp binding site of the 'open' subunit, the other 7 fragments all bound to an unprecedented pocket at the interface between two TrpRS subunits. Binding of these fragments relies on residues specific to bacterial TrpRS, avoiding undesired interactions with human TrpRS. These findings improve our understanding of the catalytic mechanism of this important enzyme and will also facilitate the discovery of bacterial TrpRS inhibitors with therapeutic potential.

The Inhibition of γ-Aminobutyric Acid B1 Receptor Regulates Angiogenesis via the Hippo/YAP Signaling Pathway.

Promoting the establishment of collateral circulation is essential for chronic lower extremity ischemia. However, no effective therapeutic drugs have yet been developed. Recent studies discovered that in the peripheral arteries, there are γ-aminobutyric acid B1 (GABAB1) receptors expressed in endothelial cells and smooth muscle cells, these receptors may have some effects in regulating vascular functions, but the precise mechanism is not yet clear. This study explores the effect of GABAB1 receptor inhibition on angiogenesis and its regulatory mechanism. The expression of GABAB1 in human umbilical vein endothelial cells (HUVECs) was knocked down using shRNA transfection, and effects on HUVECs' proliferation, migration, and tube formation ability were detected. Western blot and RT-PCR were used to verify the signal pathway. The murine hind limb ischemia model was used to verify the effect of CGP35348, an antagonist of GABAB1R, on the recovery of blood flow perfusion and angiogenesis in ischemic tissues. Cell proliferation, migration, and tube formation ability were improved after GABAB1 receptor knockdown in HUVECs. The phosphorylation of the HIPPO/Yes-associated protein (YAP) pathway decreased, while the effect of promoting angiogenesis increased. After treating the ischemic hindlimbs of mice with GABAB1 receptor antagonists, the blood flow perfusion recovered and the angiogenesis increased. These findings demonstrate the effect of GABAB1 receptor inhibition on the HIPPO/YAP pathway in regulating angiogenesis, suggesting that inhibiting GABAB1 receptor levels might be a novel approach for chronic lower extremity ischemia diseases.

Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.

Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.

Predicting and Analyzing Restenosis Risk after Endovascular Treatment in Lower Extremity Arterial Disease: Development and Assessment of a Predictive Nomogram.

PURPOSE: This study aimed to develop and internally validate nomograms for predicting restenosis after endovascular treatment of lower extremity arterial diseases. MATERIALS AND METHODS: A total of 181 hospitalized patients with lower extremity arterial disease diagnosed for the first time between 2018 and 2019 were retrospectively collected. Patients were randomly divided into a primary cohort (n=127) and a validation cohort (n=54) at a ratio of 7:3. The least absolute shrinkage and selection operator (LASSO) regression was used to optimize the feature selection of the prediction model. Combined with the best characteristics of LASSO regression, the prediction model was established by multivariate Cox regression analysis. The predictive models' identification, calibration, and clinical practicability were evaluated by the C index, calibration curve, and decision curve. The prognosis of patients with different grades was compared by survival analysis. Internal validation of the model used data from the validation cohort. RESULTS: The predictive factors included in the nomogram were lesion site, use of antiplatelet drugs, application of drug coating technology, calibration, coronary heart disease, and international normalized ratio (INR). The prediction model demonstrated good calibration ability, and the C index was 0.762 (95% confidence interval: 0.691-0.823). The C index of the validation cohort was 0.864 (95% confidence interval: 0.801-0.927), which also showed good calibration ability. The decision curve shows that when the threshold probability of the prediction model is more significant than 2.5%, the patients benefit significantly from our prediction model, and the maximum net benefit rate is 30.9%. Patients were graded according to the nomogram. Survival analysis found that there was a significant difference in the postoperative primary patency rate between patients of different classifications (log-rank p<0.001) in both the primary cohort and the validation cohort. CONCLUSION: We developed a nomogram to predict the risk of target vessel restenosis after endovascular treatment by considering information on lesion site, postoperative antiplatelet drugs, calcification, coronary heart disease, drug coating technology, and INR. CLINICAL IMPACT: Clinicians can grade patients after endovascular procedure according to the scores of the nomograms and apply intervention measures of different intensities for people at different risk levels. During the follow-up process, an individualized follow-up plan can be further formulated according to the risk classification. Identifying and analyzing risk factors is essential for making appropriate clinical decisions to prevent restenosis.

X-shaped structure of bacterial heterotetrameric tRNA synthetase suggests cryptic prokaryote functions and a rationale for synthetase classifications.

AaRSs (aminoacyl-tRNA synthetases) group into two ten-member classes throughout evolution, with unique active site architectures defining each class. Most are monomers or homodimers but, for no apparent reason, many bacterial GlyRSs are heterotetramers consisting of two catalytic α-subunits and two tRNA-binding ß-subunits. The heterotetrameric GlyRS from Escherichia coli (EcGlyRS) was historically tested whether its α- and ß-polypeptides, which are encoded by a single mRNA with a gap of three in-frame codons, are replaceable by a single chain. Here, an unprecedented X-shaped structure of EcGlyRS shows wide separation of the abutting chain termini seen in the coding sequences, suggesting strong pressure to avoid a single polypeptide format. The structure of the five-domain ß-subunit is unique across all aaRSs in current databases, and structural analyses suggest these domains play different functions on α-subunit binding, ATP coordination and tRNA recognition. Moreover, the X-shaped architecture of EcGlyRS largely fits with a model for how two classes of tRNA synthetases arose, according to whether enzymes from opposite classes can simultaneously co-dock onto separate faces of the same tRNA acceptor stem. While heterotetrameric GlyRS remains the last structurally uncharacterized member of aaRSs, our study contributes to a better understanding of this ancient and essential enzyme family.

Tourniquet Use Improves Intraoperative Parameters, Leading to Similar Postoperative Outcomes Compared With No Tourniquet Use in Anterior Cruciate Ligament Reconstruction: A Prospective, Double-Blind, Randomized Clinical Trial.

PURPOSE: To examine the effect of tourniquet use in arthroscopic anterior cruciate ligament reconstruction in terms of: (1) intraoperative visualization with operative time and consumption of sterile saline, and (2) intra- and postoperative blood loss, postoperative pain, opioid consumption, swelling, serum creatine phosphokinase (CPK) and hemoglobin (Hb) concentrations, clinical outcomes, and graft healing. METHODS: In this prospective randomized clinical trial, patients were assigned to tourniquet inflation (tourniquet-up) or tourniquet deflation (tourniquet-down) groups. Primary outcomes were intraoperative visualization with operative time and sterile saline consumption. Secondary outcomes were intra- and postoperative blood loss, postoperative pain, opioid consumption, swelling, serum CPK, Hb concentration, subjective and objective functional scores, and graft healing. RESULTS: Intraoperative visualization was satisfactory in 100 of 100 cases in the tourniquet-up group and 64 of 100 cases in the tourniquet-down group (P < .05). The mean operative time was 58.4 ± 5.7 minutes in the tourniquet-up group and 72.5 ± 8.6 minutes in the tourniquet-down group (P < .05). The mean sterile saline consumption was 6.4 ± 2.5 L in the tourniquet-up group and 8.7 ± 4.6 L in the tourniquet-down group (P < .05). The respective amounts of estimated intraoperative and postoperative blood loss were 95.3 ± 25.1 mL and 240.3 ± 44.5 mL in the tourniquet-up group and 230.2 ± 22.3 mL and 75.6 ± 15.3 mL in the tourniquet-down group (P < .05). Our results showed no significant difference in postoperative pain, opioid consumption, percentage of patients using opioids, swelling, mean serum CPK and Hb levels, subjective and objective functional scores, or graft healing (P > .05) between the 2 groups. CONCLUSIONS: Tourniquet use during anterior cruciate ligament reconstruction significantly improves intraoperative visualization, shortens operative time, and decreases intraoperative sterile saline consumption and blood loss without serious adverse events or greater complication rates based on early postoperative outcomes. LEVEL OF EVIDENCE: Level I, randomized controlled trial.

SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS.

SETD2, the histone H3 lysine 36 methyltransferase, previously identified by us, plays an important role in the pathogenesis of hematologic malignancies, but its role in myelodysplastic syndromes (MDSs) has been unclear. In this study, low expression of SETD2 correlated with shortened survival in patients with MDS, and the SETD2 levels in CD34+ bone marrow cells of those patients were increased by decitabine. We knocked out Setd2 in NUP98-HOXD13 (NHD13) transgenic mice, which phenocopies human MDS, and found that loss of Setd2 accelerated the transformation of MDS into acute myeloid leukemia (AML). Loss of Setd2 enhanced the ability of NHD13+ hematopoietic stem and progenitor cells (HSPCs) to self-renew, with increased symmetric self-renewal division and decreased differentiation and cell death. The growth of MDS-associated leukemia cells was inhibited though increasing the H3K36me3 level by using epigenetic modifying drugs. Furthermore, Setd2 deficiency upregulated hematopoietic stem cell signaling and downregulated myeloid differentiation pathways in the NHD13+ HSPCs. Our RNA-seq and chromatin immunoprecipitation-seq analysis indicated that S100a9, the S100 calcium-binding protein, is a target gene of Setd2 and that the addition of recombinant S100a9 weakens the effect of Setd2 deficiency in the NHD13+ HSPCs. In contrast, downregulation of S100a9 leads to decreases of its downstream targets, including Ikba and Jnk, which influence the self-renewal and differentiation of HSPCs. Therefore, our results demonstrated that SETD2 deficiency predicts poor prognosis in MDS and promotes the transformation of MDS into AML, which provides a potential therapeutic target for MDS-associated acute leukemia.

Small extracellular vesicles of hypoxic endothelial cells regulate the therapeutic potential of adipose-derived mesenchymal stem cells via miR-486-5p/PTEN in a limb ischemia model.

BACKGROUND: Patients with critical limb ischemia (CLI) are at great risk of major amputation and cardiovascular events. Adipose-derived mesenchymal stem cell (ADSC) therapy is a promising therapeutic strategy for CLI, but the poor engraftment and insufficient angiogenic ability of ADSCs limit their regenerative potential. Herein, we explored the potential of human umbilical vein endothelial cells (HUVECs)-derived small extracellular vesicles (sEVs) for enhancing the therapeutic efficacy of ADSCs in CLI. RESULTS: sEVs derived from hypoxic HUVECs enhanced the resistance of ADSCs to reactive oxygen species (ROS) and further improved the proangiogenic ability of ADSCs in vitro. We found that the hypoxic environment altered the composition of sEVs from HUVECs and that hypoxia increased the level of miR-486-5p in sEVs. Compared to normoxic sEVs (nsEVs), hypoxic sEVs (hsEVs) of HUVECs significantly downregulated the phosphatase and tensin homolog (PTEN) via direct targeting of miR-486-5p, therefore activating the AKT/MTOR/HIF-1α pathway and influencing the survival and pro-angiogenesis ability of ADSCs. In a hindlimb ischemia model, we discovered that hsEVs-primed ADSCs exhibited superior cell engraftment, and resulted in better angiogenesis and tissue repair. CONCLUSION: hsEVs could be used as a therapeutic booster to improve the curative potential of ADSCs in a limb ischemia model. This finding offers new insight for CLI treatment.

Patients With Right Lower Extremity Deep Vein Thrombosis Have a Higher Risk of Symptomatic Pulmonary Embolism: A Retrospective Study of 1585 Patients.

OBJECTIVE: To determine the risk for pulmonary embolism (PE) and explore the relationship between the site of thrombosis and PE in patients with acute lower extremity deep vein thrombosis (DVT). METHODS: A total of 1585 hospitalized patients first diagnosed with acute lower extremity DVT were investigated retrospectively. The patients were divided into two groups: the non-PE group (Group 1) and the PE group (Group 2). Then, Group 2 was divided into two subgroups: asymptomatic pulmonary embolism (asPE, Group 2a) and symptomatic pulmonary embolism (sPE, Group 2b). Kaplan-Meier curves and logistic regression analysis were used to explore the relevant risk factors for PE. RESULTS: Among 1585 patients, 458 patients suffered from PE, accounting for 28.9%. 102 (22.3%) of them had the typical clinical manifestations of PE and were defined as sPE, and the remaining 356 (77.7%) patients were classified as asPE. Patients with proximal lower extremity DVT were significantly more predominant in the PE group than in the non-PE group (92.8% vs. 86.2%, P<0.001). Moreover, in Group 2, patients with typical PE manifestations showed a higher proportion of patients with right lower extremity DVT than left lower extremity DVT (26.7% vs. 17.7%, P = 0.035), and bilateral lower extremity DVT than unilateral DVT (44.1% vs. 20.5%, P<0.001). By multivariate analysis, alcohol consumption (OR, 1.824; 95% CI, 1.194-2.787; P = 0.005), heart failure (OR, 2.345; 95% CI, 1.560-3.526; P<0.001), proximal DVT (OR, 2.096; 95% CI,1.407-3.123; P<0.001) were independent risk factors for PE. CONCLUSIONS: Patients with proximal acute lower extremity DVT were more likely to suffer from PE than those with distal DVT. Patients with right acute lower extremity DVT had a higher risk of sPE than patients with left acute lower extremity DVT. Alcohol consumption and heart failure were associated with the occurrence of PE in patients with acute lower extremity DVT.

Effects of molecular weight of polyaspartic acid on nitrogen use efficiency and crop yield.

BACKGROUND: In the past decades, ever-increasing fertilizer use has led to a continuous increase in agricultural output. However, serious waste of resources occurs because of the low utilization of fertilizers. Polyaspartic acid (PASP) is a biodegradable polymer that can be used as a fertilizer synergist in agricultural production to improve the nutrient utilization capacity of plants. For polymers, the molecular weight (MW) often affects their effectiveness. However, little information is available on the effects of PASP MW in agriculture, especially on nitrogen leaching and plant element uptake. RESULTS: This work was conducted to identify the effect of PASPs with three different MWs - PASP-1 (MW: 5517), PASP-2 (MW: 6934), and PASP-3 (MW: 7568) - on nitrogen leaching, lettuce growth, and wheat cultivation. The results revealed that PASP favored plant growth and nitrogen accumulation in the soil, independent of crop species. PASP with a higher MW improved yields and the agronomic characteristics of lettuce and wheat. Furthermore, apparent amelioration of nitrogen use efficiency for lettuce (7.6%, 12.8%, and 15.0%) and wheat (4.6%, 8.1%, and 9.2%) was observed in the treatments with PASP addition. The effects and merits of PASPs on preventing ammonium nitrogen leaching and improving lettuce and wheat productivity were as follows: PASP-3 > PASP-2 > PASP-1. CONCLUSION: The MW of PASP is an essential factor affecting inorganic nitrogen leaching and crop productivity, and PASP with a higher MW (7568) is recommended for application in agriculture. © 2022 Society of Chemical Industry.

Caspase-3 controls AML1-ETO-driven leukemogenesis via autophagy modulation in a ULK1-dependent manner.

AML1-ETO (AE), a fusion oncoprotein generated by t(8;21), can trigger acute myeloid leukemia (AML) in collaboration with mutations including c-Kit, ASXL1/2, FLT3, N-RAS, and K-RAS. Caspase-3, a key executor among its family, plays multiple roles in cellular processes, including hematopoietic development and leukemia progression. Caspase-3 was revealed to directly cleave AE in vitro, suggesting that AE may accumulate in a Caspase-3-compromised background and thereby accelerate leukemogenesis. Therefore, we developed a Caspase-3 knockout genetic mouse model of AML and found that loss of Caspase-3 actually delayed AML1-ETO9a (AE9a)-driven leukemogenesis, indicating that Caspase-3 may play distinct roles in the initiation and/or progression of AML. We report here that loss of Caspase-3 triggers a conserved, adaptive mechanism, namely autophagy (or macroautophagy), which acts to limit AE9a-driven leukemia. Furthermore, we identify ULK1 as a novel substrate of Caspase-3 and show that upregulation of ULK1 drives autophagy initiation in leukemia cells and that inhibition of ULK1 can rescue the phenotype induced by Caspase-3 deletion in vitro and in vivo. Collectively, these data highlight Caspase-3 as an important regulator of autophagy in AML and demonstrate that the balance and selectivity between its substrates can dictate the pace of disease.

Perioperative duloxetine improves postoperative outcomes after anterior talofibular ligament repair for chronic lateral ankle instability for patients with depression: A prospective randomized clinical trial.

BACKGROUND: Recent studies have indicated that depression is associated with persistent postoperative pain and decreased satisfaction following foot and ankle surgery. This study aimed to evaluate the effect of perioperative duloxetine on postoperative outcomes of anterior talofibular ligament (ATFL) surgical repair for chronic ankle instability (CAI) in patients with depression. We further sought to evaluate patients' satisfaction and side effects related to duloxetine. MATERIAL AND METHODS: Patients undergoing ATFL repair were screened for depression preoperatively with the Patient Health Questionnaire (PHQ-9). Among 249 patients who underwent arthroscopic or open surgical Brostrom repair of the ATFL, 120 patients were identified as being "possibly depressed" and were included in the study. Sixty patients were randomly assigned to the duloxetine group (one day preoperatively and for 6 weeks postoperatively), and the other sixty were randomized to the placebo group. Painkillers and opioid consumption, pain scores, and patient satisfaction were recorded at 12, 24, 48, and 72hours postoperatively and at follow-up visits 1, 3, and 6 months after surgery. Patient-reported outcome measures (PROMs) were assessed preoperatively and at 3, 6, 12 and 24 months postoperatively. Duloxetine-related side effects such as nausea/vomiting and fatigue were also recorded. RESULTS: The patients in the duloxetine group reported a significantly longer time to rescue analgesic and reduced opioid requirements (including celecoxib, pregabalin, acetaminophen, and tramadol). The patients experienced decreased pain intensity and greater satisfaction with their pain management at 24, 48, 72h and 1 and 3 months after surgery (p<0.05). The duloxetine group also had significantly better clinical and functional outcomes at 3 and 6 months of follow-up compared to the placebo group (p<0.05). The occurrence and rate of symptoms of duloxetine side effects were not significant. DISCUSSION: Depression is an important factor to consider and address because its presence before surgery can predict poor postoperative outcomes, including more severe postoperative pain, persistent postoperative pain, and increased consumption of painkillers and opioids. CONCLUSION: Perioperative administration of duloxetine following ATFL repair for CAI in patients with depression increased the time to first postoperative rescue analgesic request and reduced both opioid consumption and postoperative pain. This approach also led to a high level of patient satisfaction. In addition, duloxetine improved the quality of recovery without leading to significant side effects. LEVEL OF EVIDENCE: I; prospective randomized controlled trial.

Structure-guided inhibitor design targeting CntL provides the first chemical validation of the staphylopine metallophore system in bacterial metal acquisition.

To survive in the metal-scarce environment within the host, pathogens synthesize various small molecular metallophores to facilitate the acquisition of transition metals. The cobalt and nickel transporter (Cnt) system synthesizes and transports staphylopine, a nicotianamine-like metallophore, and serves as a primary transition metal uptake system in Gram-positive bacteria including the human pathogen Staphylococcus aureus. In this study, we report the design of the first inhibitor of the Cnt system by targeting the key aminobutanoyltransferase CntL which is involved in the biosynthesis of staphylopine. Through structure-guided fragment linking and optimization, a class of acceptor-adenosine dual-site inhibitors against S. aureus CntL (SaCntL) were designed and synthesized. The most potent inhibitor, compound 9, demonstrated a ΔTm value of 9.4 °C, a Kd value of 0.021 ± 0.004 µM, and an IC50 value of 0.06 µM against SaCntL. The detailed mechanism by which compound 9 inhibits SaCntL has been elucidated through a high-resolution co-crystal structure. Treatment with compound 9 resulted in a moderate downregulation of intracellular concentrations of iron, nickel, and cobalt ions in the S. aureus cells cultured in the metal-scarce medium, providing the first chemical validation of the important role of Cnt system in bacterial metal acquisition. Our findings pave the way for the development of CntL-based antibacterial agents in future.

Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria.

Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 µM (no ATP) to 0.45 µM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.

Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation.

SETD2 is the only enzyme responsible for transcription-coupled histone H3 lysine 36 trimethylation (H3K36me3). Mutations in SETD2 cause human diseases including cancer and developmental defects. In mice, Setd2 is essential for embryonic vascular remodeling. Given that many epigenetic modifiers have recently been found to possess noncatalytic functions, it is unknown whether the major function(s) of Setd2 is dependent on its catalytic activity or not. Here, we established a site-specific knockin mouse model harboring a cancer patient-derived catalytically dead Setd2 (Setd2-CD). We found that the essentiality of Setd2 in mouse development is dependent on its methyltransferase activity, as the Setd2CD/CD and Setd2-/- mice showed similar embryonic lethal phenotypes and largely comparable gene expression patterns. However, compared with Setd2-/-, the Setd2CD/CD mice showed less severe defects in allantois development, and single-cell RNA-seq analysis revealed differentially regulated allantois-specific 5' Hoxa cluster genes in these two models. Collectively, this study clarifies the importance of Setd2 catalytic activity in mouse development and provides a new model for comparative study of previously unrecognized Setd2 functions.

ABIN1 (Q478) is Required to Prevent Hematopoietic Deficiencies through Regulating Type I IFNs Expression.

A20-binding inhibitor of NF-κB activation (ABIN1) is a polyubiquitin-binding protein that regulates cell death and immune responses. Although Abin1 is located on chromosome 5q in the region commonly deleted in patients with 5q minus syndrome, the most distinct of the myelodysplastic syndromes (MDSs), the precise role of ABIN1 in MDSs remains unknown. In this study, mice with a mutation disrupting the polyubiquitin-binding site (Abin1Q478H/Q478H ) is generated. These mice develop MDS-like diseases characterized by anemia, thrombocytopenia, and megakaryocyte dysplasia. Extramedullary hematopoiesis and bone marrow failure are also observed in Abin1Q478H/Q478H mice. Although Abin1Q478H/Q478H cells are sensitive to RIPK1 kinase-RIPK3-MLKL-dependent necroptosis, only anemia and splenomegaly are alleviated by RIPK3 deficiency but not by MLKL deficiency or the RIPK1 kinase-dead mutation. This indicates that the necroptosis-independent function of RIPK3 is critical for anemia development in Abin1Q478H/Q478H mice. Notably, Abin1Q478H/Q478H mice exhibit higher levels of type I interferon (IFN-I) expression in bone marrow cells compared towild-type mice. Consistently, blocking type I IFN signaling through the co-deletion of Ifnar1 greatly ameliorated anemia, thrombocytopenia, and splenomegaly in Abin1Q478H/Q478H mice. Together, these results demonstrates that ABIN1(Q478) prevents the development of hematopoietic deficiencies by regulating type I IFN expression.

SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis.

A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.

The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.

As a class of essential enzymes in protein translation, aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are organized into two classes of 10 enzymes each, based on two conserved active site architectures. The (αß)2 glycyl-tRNA synthetase (GlyRS) in many bacteria is an orphan aaRS whose sequence and unprecedented X-shaped structure are distinct from those of all other aaRSs, including many other bacterial and all eukaryotic GlyRSs. Here, we report a cocrystal structure to elucidate how the orphan GlyRS kingdom specifically recognizes its substrate tRNA. This structure is sharply different from those of other aaRS-tRNA complexes but conforms to the clash-free, cross-class aaRS-tRNA docking found with conventional structures and reinforces the class-reconstruction paradigm. In addition, noteworthy, the X shape of orphan GlyRS is condensed with the largest known spatial rearrangement needed by aaRSs to capture tRNAs, which suggests potential nonactive site targets for aaRS-directed antibiotics, instead of less differentiated hard-to-drug active site locations.