Intramolecular Carboxyamidation of Alkyne-Tethered O-Acylhydroxamates through Formation of Fe(III)-Nitrenoids.

We developed intramolecular carboxyamidations of alkyne-tethered O-acylhydroxamates followed by either thermally induced spontaneous or 4-(dimethylamino)pyridine-catalyzed O→O or O→N acyl group migration. Under iron-catalyzed conditions, the carboxyamidation products were generated in high yield from both Z-alkene and arene-tethered substrates. DFT calculations indicate that the iron-catalyzed carboxyamidation proceeds via a stepwise mechanism involving iron-imidyl radical cyclization followed by intramolecular acyloxy transfer from the iron center to the alkenyl radical center to furnish the cis-carboxyamidation product. Upon treatment with 4-(dimethylamino)pyridine, the Z-alkene-tethered carboxyamidation products underwent selective O→O acyl migration to generate 2-acyloxy-5-acyl pyrroles. Thermal O→N acyl migration occurs during carboxyamidation if the Z-alkene linker contains an alkyl or an aryl substituent at the ß-position of the carbonyl group. On the other hand, the arene linker-containing compounds selectively undergo O→N acyl migration to generate N-acyl-3-acylisoindolinones, and the corresponding O→O acyl migration forming isoindole derivatives was not observed.

Soluble expression of hMYDGF was improved by strain engineering and optimizations of fermentation strategies in Escherichia coli.

Myeloid-derived growth factor (MYDGF) is a cytokine that exhibits a variety of biological functions. This study focused on utilizing BL21(DE3) strain engineering and fermentation strategies to achieve high-level expression of soluble human MYDGF (hMYDGF) in Escherichia coli. Initially, the E. coli expressing strain BL21(DE3) was engineered by deleting the IpxM gene and inserting the GROEL/S and Trigger factor genes. The engineered E. coli strain BL21(TG)/pT-MYDGF accumulated 3557.3 ± 185.6 µg/g and 45.7 ± 6.7 mg/L of soluble hMYDGF in shake flask fermentation, representing a 15.6-fold increase compared to the control strain BL21(DE3)/pT-MYDGF. Furthermore, the yield of hMYDGF was significantly enhanced by optimizing the fermentation conditions. Under optimized conditions, the 5L bioreactor yielded up to 2665.8 ± 164.3 µg/g and 407.6 ± 42.9 mg/L of soluble hMYDGF. The results indicate that the implementation of these optimization strategies could enhance the ratio and yield of soluble proteins expressed by E.coli, thereby meeting the demands of industrial production. This study employed sophisticated strategies to lay a solid foundation for the industrial application of hMYDGF.

Cycloisomerization of Alkyne-Tethered N-Acyloxycarbamates to 2-(3H)Oxazolones through Nitrenoid-Mediated Carboxyamidation.

The cycloisomerization of alkyne-tethered N-benzoyloxycarbamates to 2-(3H)oxazolones is described. Two catalytic systems are tailored for intramolecular 5-exo-alkyne carboxyamidation and concomitant alkene isomerization. PtCl2 /CO (5 mol%, toluene, 100 °C) promotes both carboxyamidation and alkene isomerization but has a limited substrate scope. On the other hand, FeCl3 (5 mol%, CH3 CN, 100 °C) promotes carboxyamidation effectively but a cocatalyst is required for the exocyclic alkene isomerization. Thus, a two-step one-pot protocol has been developed for a broader reaction scope, which involves FeCl3 -catalyzed carboxyamidation and base-induced alkene isomerization. Crossover experiments suggest that these reactions proceed mainly through a mechanism involving acylnitrenoid intermediates rather than carbenoid intermediates.

Turbulent-like velocity fluctuations in two-dimensional granular materials subject to cyclic shear.

We perform a systematic experimental study to investigate the velocity fluctuations in the two-dimensional granular matter of low and high friction coefficients subjected to cyclic shear of a range of shear amplitudes, whose velocity fields are strikingly turbulent-like with vortices of different scales. The scaling behaviors of both the transverse velocity power spectra ET(k) ∝ k-αT and, more severely, the longitudinal velocity power spectra EL(k) ∝ k-αL are affected by the prominent peak centered around k ≈ 2π of the inter-particle distance due to the static structure factor of the hard-particle nature in contrast to the real turbulence. To reduce the strong peak effect to the actual values of αν (the subscript 'ν' refers to either T or L), we subsequently analyze the second-order velocity structure functions of S(2)ν(r) in real space, which show the power-law scalings of S(2)ν(r) ∝ rßν for both modes. From the values of ßν, we deduce the corresponding αν from the scaling relations of αν = ßν + 2. The deduced values of αν increase continuously with the shear amplitude γm, showing no signature of yielding transition, and are slightly larger than αν = 2.0 at the limit of γm → 0, which corresponds to the elastic limit of the system, for all γm. The inter-particle friction coefficients show no significant effect on the turbulent-like velocity fluctuations. Our findings suggest that the turbulent-like collective particle motions are governed by both the elasticity and plasticity in cyclically sheared granular materials.

The Edwards volume ensemble in cyclically sheared granular experiments.

We experimentally investigate the Edwards volume ensemble in cyclically sheared bidisperse disks of two friction coefficients (µ ≈ 0.3 and µ → ∞) subjected to a range of shear amplitudes γm. Despite the local and global anisotropy, hysteresis, and the potential long-range correlation of the free volume, the Edwards volume ensemble surprisingly provides an excellent statistical description of disk packings in cyclically sheared systems. Our finding can be better understood from the comprehensive analysis of the geometric and statistical properties of Voronoi cells of individual particles. First, the average degrees of anisotropy of Voronoi cells are weak at both the microscopic and macroscopic scales within a range of shear amplitudes γm of up to γm = 12% regardless of the inter-particle friction coefficients µ even though the azimuthal distributions of the Voronoi cell depend on µ. Second, there is only negligible hysteresis of global compactivity and volume fluctuations. Finally, the spatial correlations of the free volume and the orientation are weakly anisotropic and short ranged for practical purposes. Both results are independent of µ. Interestingly, our free-volume statistical results are consistent with the simple physical picture that the free volume is directly proportional to the compactivity.

Ruthenabenzene: A Robust Precatalyst.

Metallaaromatics constitute a unique class of aromatic compounds where one or more transition metal elements are incorporated into the aromatic system, the parent of which is metallabenzene. One of the main concerns about metallabenzenes generally deals with the structural characterization related to their relative aromaticity compared to the carbon archetype. Transition metal-containing metallabenzenes are also implicated in certain catalytic processes such as alkyne metathesis polymerization; however, these transition metal-based metallaaromatic compounds have not been developed as a catalyst. Herein, we describe an effective strategy to generate diverse arrays of ruthenabenzenes and demonstrated them as an aromatic equivalent of the Grubbs-type ruthenium alkylidene catalysts. These ruthenabenzenes can be prepared via an enyne metathesis and metallotropic [1,3]-shift cascade process to form alkyne-chelated ruthenium alkylidene intermediates followed by spontaneous cycloaromatization. The aromatic nature of these complexes was confirmed by spectroscopic and X-ray crystallographic data, and the mechanistic pathways for the cycloaromatization process were studied by DFT calculations. These ruthenabenzenes display robust catalytic activity for metathesis and other transformations, which illustrates that metallabenzenes are not only compounds of structural and theoretical interests but also are a novel platform for new catalyst development.

Roles of Ubiquitination and SUMOylation in DNA Damage Response.

Ubiquitin and ubiquitin-like modifiers, such as SUMO, exert distinct physiological functions by conjugating to protein substrates. Ubiquitination or SUMOylation of protein substrates determine the fate of modified proteins, including proteasomal degradation, cellular re-localization, alternations in binding partners and serving as a protein-binding platform, in a ubiquitin or SUMO linkage-dependent manner. DNA damage occurs constantly in living organisms but is also repaired by distinct tightly controlled mechanisms including homologous recombination, non-homologous end joining, inter-strand crosslink repair, nucleotide excision repair and base excision repair. On sensing damaged DNA, a ubiquitination/SUMOylation landscape is established to recruit DNA damage repair factors. Meanwhile, misloaded and mission-completed repair factors will be turned over by ubiquitin or SUMO modifications as well. These ubiquitination and SUMOylation events are tightly controlled by both E3 ubiquitin/SUMO ligases and deubiquitinases/deSUMOylases. In this review, we will summarize identified ubiquitin and SUMO-related modifications and their function in distinct DNA damage repair pathways, and provide evidence for responsible E3 ligases, deubiquitinases, SUMOylases and deSUMOylases in these processes. Given that genome instability leads to human disorders including cancer, understanding detailed molecular mechanisms for ubiquitin and SUMO-related regulations in DNA damage response may provide novel insights into therapeutic modalities to treat human diseases associated with deregulated DNA damage response.

Lowering Endogenous Cathepsin D Abundance Results in Reactive Oxygen Species Accumulation and Cell Senescence.

Cathepsin D is reportedly to be closely associated with tumor development, migration, and invasion, but its pathological mechanism is not fully elucidated. We aimed to evaluate phenotypic changes and molecular events in response to cathepsin D knockdown. Lowering endogenous cathepsin D abundance (CR) induced senescence in HeLa cells, leading to reduced rate of cell proliferation and impaired tumorigenesis in a mouse model. Quantitative proteomics revealed that compared with control cells (EV), the abundances of several typical lysosomal proteases were decreased in the lysosomal fraction in CR cells. We further showed that cathepsin D knockdown caused increased permeability of lysosomal membrane and reactive oxygen species accumulation in CR cells, and the scavenging of reactive oxygen species by antioxidant was able to rescue cell senescence. Despite the increased reactive oxygen species, the proteomic data suggested a global reduction of redox-related proteins in CR cells. Subsequent analysis indicated that the transcriptional activity of nuclear factor erythroid-related factor 2 (Nrf2), which regulates the expression of groups of antioxidant enzymes, was down-regulated by cathepsin D knockdown. Importantly, Nrf2 overexpression significantly reduced cell senescence. Although transient oxidative stress promoted the accumulation of Nrf2 in the nucleus, we showed that the Nrf2 protein exited nucleus if oxidative stress persisted. In addition, when cathepsin D was transiently knocked down, the cathepsin-related events followed a sequential order, including lysosomal leakage during the early stage, followed by oxidative stress augmentation, and ultimately Nrf2 down-regulation and senescence. Our results suggest the roles of cathepsin D in cancer cells in maintaining lysosomal integrity, redox balance, and Nrf2 activity, thus promoting tumorigenesis. The MS Data are available via ProteomeXchange with identifier PXD002844.

A Comprehensive Proteomics Analysis Reveals a Secretory Path- and Status-Dependent Signature of Exosomes Released from Tumor-Associated Macrophages.

Exosomes are 30-120 nm-sized membrane vesicles of endocytic origin that are released into the extracellular environment and play roles in cell-cell communication. Tumor-associated macrophages (TAMs) are important constituents of the tumor microenvironment; thus, it is critical to study the features and complex biological functions of TAM-derived exosomes. Here, we constructed a TAM cell model from a mouse macrophage cell line, Ana-1, and performed comparative proteomics on exosomes, exosome-free media, and cells between TAMs and Ana-1. Proteomic analysis between exosome and exosome-free fractions indicated that the functions of exosome dominant proteins were mainly enriched in RNA processing and proteolysis. TAM status dramatically affected the abundances of 20S proteasome subunits and ribosomal proteins in their exosomes. The 20S proteasome activity assay strongly indicated that TAM exosomes possessed higher proteolytic activity. In addition, Ana-1- and TAM-derived exosomes have different RNA profiles, which may result from differential RNA processing proteins. Taken together, our comprehensive proteomics study provides novel views for understanding the complicated roles of macrophage-derived exosomes in the tumor microenvironment.

Ubiquitination of inositol-requiring enzyme 1 (IRE1) by the E3 ligase CHIP mediates the IRE1/TRAF2/JNK pathway.

Deciphering the inositol-requiring enzyme 1 (IRE1) signaling pathway is fundamentally important for understanding the unfolded protein response (UPR). The ubiquitination of proteins residing on the endoplasmic reticulum (ER) membrane has been reported to be involved in the UPR, although the mechanism has yet to be fully elucidated. Using immunoprecipitation and mass spectrometry, IRE1 was identified as a substrate of the E3 ligase CHIP (carboxyl terminus of HSC70-interacting protein) in HEK293 cells under geldanamycin-induced ER stress. Two residues of IRE1, Lys(545) and Lys(828), were targeted for Lys(63)-linked ubiquitination. Moreover, in CHIP knockdown cells, IRE1 phosphorylation and the IRE1-TRAF2 interaction were nearly abolished under ER stress, which may be due to lacking ubiquitination of IRE1 on Lys(545) and Lys(828), respectively. The cellular responses were evaluated, and the data indicated that CHIP-regulated IRE1/TRAF2/JNK signaling antagonized the senescence process. Therefore, our findings suggest that CHIP-mediated ubiquitination of IRE1 contributes to the dynamic regulation of the UPR.

Reactivity of Enyne-Allenes Generated via an Alder-Ene Reaction.

Tandem transformations of 1,3-diynyl propiolate derivatives are described. The Alder-ene reaction generates an enyne-allene, which undergoes a formal 1,7-H shift or a Diels-Alder reaction, depending on the substituent on the alkyne. A terminal or aryl-substituted alkyne promotes a 1,7-H shift to generate a new enyne-allene, which undergoes a Myers-Saito cycloaromatization followed by a 1,5-H transfer-mediated cyclization to form highly functionalized benzo-fused 6-membered cycles. The reactivity of the preformed enyne-allene shows comparable reactivity profiles.

Amino Acid-Dependent Material Properties of Tetrapeptide Condensates.

Condensates formed by intrinsically disordered proteins mediate a myriad of cellular processes and are linked to pathological conditions including neurodegeneration. Rules of how different types of amino acids (e.g., π-π pairs) dictate the physical properties of biomolecular condensates are emerging, but our understanding of the roles of different amino acids is far from complete. Here we studied condensates formed by tetrapeptides of the form XXssXX, where X is an amino acid and ss represents a disulfide bond along the backbone. Eight peptides form four types of condensates at different concentrations and pH values: droplets (X = F, L, M, P, V, A); amorphous dense liquids (X = L, M, P, V, A); amorphous aggregates (X = W), and gels (X = I, V, A). The peptides exhibit enormous differences in phase equilibrium and material properties, including a 368-fold range in the threshold concentration for phase separation and a 3856-fold range in viscosity. All-atom molecular dynamics simulations provide physical explanations of these results. The present work also reveals widespread critical behaviors, including critical slowing down manifested by the formation of amorphous dense liquids and critical scaling obeyed by fusion speed, with broad implications for condensate function.

The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.

Background: Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective: To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods: We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results: We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions: This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.

Trisomy 8 Defines a Distinct Subtype of Myeloproliferative Neoplasms Driven by the MYC-Alarmin Axis.

Despite advances in understanding the genetic abnormalities in myeloproliferative neoplasms (MPN) and the development of JAK2 inhibitors, there is an urgent need to devise new treatment strategies, particularly for patients with triple-negative (TN) myelofibrosis (MF) who lack mutations in the JAK2 kinase pathway and have very poor clinical outcomes. Here we report that MYC copy number gain and increased MYC expression frequently occur in TN-MF and that MYC-directed activation of S100A9, an alarmin protein that plays pivotal roles in inflammation and innate immunity, is necessary and sufficient to drive development and progression of MF. Notably, the MYC-S100A9 circuit provokes a complex network of inflammatory signaling that involves numerous hematopoietic cell types in the bone marrow microenvironment. Accordingly, genetic ablation of S100A9 or treatment with small molecules targeting the MYC-S100A9 pathway effectively ameliorates MF phenotypes, highlighting the MYC-alarmin axis as a novel therapeutic vulnerability for this subgroup of MPNs. Significance: This study establishes that MYC expression is increased in TN-MPNs via trisomy 8, that a MYC-S100A9 circuit manifest in these cases is sufficient to provoke myelofibrosis and inflammation in diverse hematopoietic cell types in the BM niche, and that the MYC-S100A9 circuit is targetable in TN-MPNs.

DOG1 as a novel antibody-drug conjugate target for the treatment of multiple gastrointestinal tumors and liver metastasis.

Discovered On Gastrointestinal stromal tumors protein 1 (DOG1), a major calcium-activated chloride channel, has been used as a common diagnostic marker for gastrointestinal stromal tumors. However, the therapeutic application of DOG1 was not well defined. Here, we aim to investigate its potential as a therapeutic target for an antibody-drug conjugate (ADC) in various cancers of the alimentary tract and metastasis. The DOG1 expression profile was determined among TCGA samples and tissue microarrays. High levels of DOG1 expression were ubiquitously observed in multiple cancer samples from the alimentary tract determined by TCGA samples and tissue microarrays. Circulating tumor cells isolated from metastatic colon cancer patients were also positive for DOG1 expression. The mechanisms of anti-DOG1 antibody were investigated by dual-luciferase reporter assay. The anti-DOG1 antibody could inhibit proliferation and metastasis via p53 signaling in limited cancer cell lines. The anti-DOG1 antibody was conjugated with a microtubule inhibitor DM4, to construct a new anti-DOG1-DM4-ADC to strengthen its activity. The anti-DOG1-DM4-ADC showed cytotoxicity at the nanomolar level in vitro. In the murine xenograft tumor models, treatment of anti-DOG1-DM4-ADC achieved a significant tumor growth inhibition rate. Our study indicates that anti-DOG1-DM4-ADC may be promising therapeutic molecules for DOG1-positive alimentary tract tumors and may be effective in inhibiting recurrence after curative resection of liver metastases of colorectal origin.

Reservoir quality and its controlling diagenetic factors in the Bentiu Formation, Northeastern Muglad Basin, Sudan.

The Abu Gabra and Bentiu formations are widely distributed within the interior Muglad Basin. Recently, much attention has been paid to study, evaluate and characterize the Abu Gabra Formation as a proven reservoir in Muglad Basin. However, few studies have been documented on the Bentiu Formation which is the main oil/gas reservoir within the basin. Therefore, 33 core samples of the Great Moga and Keyi oilfields (NE Muglad Basin) were selected to characterize the Bentiu Formation reservoir using sedimentological and petrophysical analyses. The aim of the study is to de-risk exploration activities and improve success rate. Compositional and textural analyses revealed two main facies groups: coarse to-medium grained sandstone (braided channel deposits) and fine grained sandstone (floodplain and crevasse splay channel deposits). The coarse to-medium grained sandstone has porosity and permeability values within the range of 19.6% to 32.0% and 1825.6 mD to 8358.0 mD respectively. On the other hand, the fine grained clay-rich facies displays poor reservoir quality as indicated by porosity and permeability ranging from 1.0 to 6.0% and 2.5 to 10.0 mD respectively. A number of varied processes were identified controlling the reservoir quality of the studies samples. Porosity and permeability were enhanced by the dissolution of feldspars and micas, while presence of detrital clays, kaolinite precipitation, iron oxides precipitation, siderite, quartz overgrowths and pyrite cement played negative role on the reservoir quality. Intensity of the observed quartz overgrowth increases with burial depth. At great depths, a variability in grain contact types are recorded suggesting conditions of moderate to-high compactions. Furthermore, scanning electron microscopy revealed presence of micropores which have the tendency of affecting the fluid flow properties in the Bentiu Formation sandstone. These evidences indicate that the Bentiu Formation petroleum reservoir quality is primarily inhibited by grain size, total clay content, compaction and cementation. Thus, special attention should be paid to these inhibiting factors to reduce risk in petroleum exploration within the area.

Response of a continental fault basin to the global OAE1a during the Aptian: Hongmiaozi Basin, Northeast China.

This paper presents new research on a lacustrine anoxic event (LAE). These data include stable carbon isotope (δ13Corg), pyrite sulfur isotope (δ34Spy), trace element and biomarker ratios from the Hongmiaozi Basin (North China) and unravel the response of continental lakes under the influence of early Aptian extreme climate conditions. According to the stratigraphic chronology (122-118 Ma) and carbon isotope correlations, terrestrial sediment was influenced by the early Aptian Oceanic Anoxic Event (OAE1a). The results show that the Xiahuapidianzi Group experienced a significant warming process under negative excursions in carbon isotopes due to the influence of increased carbon dioxide partial pressure (pCO2). The climate varied from warm and humid to hot and arid (high Sr/Cu, low Rb/Sr, calcareous mudstone), the evaporation and salinity increased (high Sr/Ba and B/Ga), and land input sources decreased (low Zr, Ti and Th). Moreover, high total organic carbon (TOC) content was source from bacteria, algae (n-alkanes), and euxinic depositional environments (Pr/Ph, Cu/Zn and U V Mo). In the stage of continuous carbon isotopes positive excursion, organic matter accumulated rapidly. A paleolake environment model has provided a better understanding of current global climate issues under global warming caused by increased carbon dioxide concentrations.

SPOP and OTUD7A Control EWS-FLI1 Protein Stability to Govern Ewing Sarcoma Growth.

Chromosomal translocation results in development of an Ewing sarcoma breakpoint region 1-Friend leukemia integration 1 (EWS-FLI1) fusion oncogene in the majority of Ewing sarcoma. The persistent dependence of the tumor for this oncoprotein points to EWS-FLI1 as an ideal drug target. Although EWS-FLI1 transcriptional targets and binding partners are evaluated, the mechanisms regulating EWS-FLI1 protein stability remain elusive. Speckle-type POZ protein (SPOP) and OTU domain-containing protein 7A (OTUD7A) are identified as the bona fide E3 ligase and deubiquitinase, respectively, that control EWS-FLI1 protein turnover in Ewing sarcoma. Casein kinase 1-mediated phosphorylation of the VTSSS degron in the FLI1 domain enhances SPOP activity to degrade EWS-FLI1. Opposing this process, OTUD7A deubiquitinates and stabilizes EWS-FLI1. Depletion of OTUD7A in Ewing sarcoma cell lines reduces EWS-FLI1 protein abundance and impedes Ewing sarcoma growth in vitro and in mice. Performing an artificial-intelligence-based virtual drug screen of a 4-million small molecule library, 7Ai is identified as a potential OTUD7A catalytic inhibitor. 7Ai reduces EWS-FLI1 protein levels and decreases Ewing sarcoma growth in vitro and in a xenograft mouse model. This study supports the therapeutic targeting of OTUD7A as a novel strategy for Ewing sarcoma bearing EWS-FLI1 and related fusions, and may also be applicable to other cancers dependent on aberrant FLI1 expression.

Experimental Approaches in Delineating mTOR Signaling.

The mTOR signaling controls essential biological functions including proliferation, growth, metabolism, autophagy, ageing, and others. Hyperactivation of mTOR signaling leads to a plethora of human disorders; thus, mTOR is an attractive drug target. The discovery of mTOR signaling started from isolation of rapamycin in 1975 and cloning of TOR genes in 1993. In the past 27 years, numerous research groups have contributed significantly to advancing our understanding of mTOR signaling and mTOR biology. Notably, a variety of experimental approaches have been employed in these studies to identify key mTOR pathway members that shape up the mTOR signaling we know today. Technique development drives mTOR research, while canonical biochemical and yeast genetics lay the foundation for mTOR studies. Here in this review, we summarize major experimental approaches used in the past in delineating mTOR signaling, including biochemical immunoprecipitation approaches, genetic approaches, immunofluorescence microscopic approaches, hypothesis-driven studies, protein sequence or motif search driven approaches, and bioinformatic approaches. We hope that revisiting these distinct types of experimental approaches will provide a blueprint for major techniques driving mTOR research. More importantly, we hope that thinking and reasonings behind these experimental designs will inspire future mTOR research as well as studies of other protein kinases beyond mTOR.

Streptavidin Promotes DNA Binding and Activation of cGAS to Enhance Innate Immunity.

cGAS/STING signaling plays an essential role in sensing cytosolic DNA. cGAS activity is regulated by posttranslational modifications and binding partners. cGAS interactome largely includes mammalian or viral proteins. Whether and how bacterial proteins bind cGAS to modulate innate immunity remain elusive. Here, we found streptavidin, a secreted bacterial protein, selectively bound cGAS to promote DNA-induced cGAS activation and interferon-ß production. Mechanistically, streptavidin enhanced DNA binding and cGAS phase separation, therefore facilitating cGAS activation. Using an HSV-1-infected mouse model, we found streptavidin nanoparticles facilitated HSV-1 clearance through improving innate immunity. Considering the clinical usage of streptavidin as an immune stimulant and drug delivery vehicle and its biotechnological usage for biotin-labeled protein purification and detection, our studies not only provide an example for a bacterial protein regulating cGAS activity but also suggest caution needs to be taken when using streptavidin in various applications given to its ability to induce innate immunity.