Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease.

Somatic mutations in nonmalignant tissues accumulate with age and injury, but whether these mutations are adaptive on the cellular or organismal levels is unclear. To interrogate genes in human metabolic disease, we performed lineage tracing in mice harboring somatic mosaicism subjected to nonalcoholic steatohepatitis (NASH). Proof-of-concept studies with mosaic loss of Mboat7, a membrane lipid acyltransferase, showed that increased steatosis accelerated clonal disappearance. Next, we induced pooled mosaicism in 63 known NASH genes, allowing us to trace mutant clones side by side. This in vivo tracing platform, which we coined MOSAICS, selected for mutations that ameliorate lipotoxicity, including mutant genes identified in human NASH. To prioritize new genes, additional screening of 472 candidates identified 23 somatic perturbations that promoted clonal expansion. In validation studies, liver-wide deletion of Tbx3, Bcl6, or Smyd2 resulted in protection against hepatic steatosis. Selection for clonal fitness in mouse and human livers identifies pathways that regulate metabolic disease.

Targeting LYPLAL1-mediated cGAS depalmitoylation enhances the response to anti-tumor immunotherapy.

Cyclic GMP-AMP synthase (cGAS) binds pathogenic and other cytoplasmic double-stranded DNA (dsDNA) to catalyze the synthesis of cyclic GMP-AMP (cGAMP), which serves as the secondary messenger to activate the STING pathway and innate immune responses. Emerging evidence suggests that activation of the cGAS pathway is crucial for anti-tumor immunity; however, no effective intervention method targeting cGAS is currently available. Here we report that cGAS is palmitoylated by ZDHHC9 at cysteines 404/405, which promotes the dimerization and activation of cGAS. We further identified that lysophospholipase-like 1 (LYPLAL1) depalmitoylates cGAS to compromise its normal function. As such, inhibition of LYPLAL1 significantly enhances cGAS-mediated innate immune response, elevates PD-L1 expression, and enhances anti-tumor response to PD-1 blockade. Our results therefore reveal that targeting LYPLAL1-mediated cGAS depalmitoylation contributes to cGAS activation, providing a potential strategy to augment the efficacy of anti-tumor immunotherapy.

GOLM1 Promotes Pulmonary Fibrosis through Upregulation of NEAT1.

Idiopathic pulmonary fibrosis (IPF) is a lethal progressive disease with elusive molecular mechanisms and limited therapeutic options. Aberrant activation of fibroblasts is a central hallmark of lung fibrosis. Here, we report that Golgi membrane protein 1 (GOLM1, also known as GP73 or GOLPH2) was increased in the lungs of patients with pulmonary fibrosis and mice with bleomycin (BLM)-induced pulmonary fibrosis. Loss of GOLM1 inhibited proliferation, differentiation, and extracellular matrix deposition of fibroblasts, whereas overexpression of GOLM1 exerted the opposite effects. Similarly, worsening pulmonary fibrosis after BLM treatment was observed in GOLM1-knock-in mice, whereas BLM-treated Golm1-knockout mice exhibited alleviated pulmonary fibrosis and collagen deposition. Furthermore, we identified long noncoding RNA NEAT1 downstream of GOLM1 as a potential mediator of pulmonary fibrosis through increased GOLM1 expression. Depletion of NEAT1 inhibited fibroblast proliferation and extracellular matrix production and reversed the profibrotic effects of GOLM1 overexpression. Additionally, we identified KLF4 as a downstream mediator of GOLM1 signaling to NEAT1. Our findings suggest that GOLM1 plays a pivotal role in promoting pulmonary fibrosis through the GOLM1-KLF4-NEAT1 signaling axis. Targeting GOLM1 and its downstream pathways may represent a novel therapeutic strategy for treating pulmonary fibrosis.

In vivo screening identifies SPP2, a secreted factor that negatively regulates liver regeneration.

BACKGROUND AND AIMS: The liver is remarkably regenerative and can completely recover even when 80% of its mass is surgically removed. Identification of secreted factors that regulate liver growth would help us understand how organ size and regeneration are controlled but also provide candidate targets to promote regeneration or impair cancer growth. APPROACH AND RESULTS: To enrich for secreted factors that regulate growth control, we induced massive liver overgrowth with either YAP or MYC . Differentially expressed secreted factors were identified in these livers using transcriptomic analysis. To rank candidates by functionality, we performed in vivo CRISPR screening using the Fah knockout model of tyrosinemia. We identified secreted phosphoprotein-2 (SPP2) as a secreted factor that negatively regulates regeneration. Spp2 -deficient mice showed increased survival after acetaminophen poisoning and reduced fibrosis after repeated carbon tetrachloride injections. We examined the impact of SPP2 on bone morphogenetic protein signaling in liver cells and found that SPP2 antagonized bone morphogenetic protein signaling in vitro and in vivo. We also identified cell-surface receptors that interact with SPP2 using a proximity biotinylation assay coupled with mass spectrometry. We showed that SPP2's interactions with integrin family members are in part responsible for some of the regeneration phenotypes. CONCLUSIONS: Using an in vivo CRISPR screening system, we identified SPP2 as a secreted factor that negatively regulates liver regeneration. This study provides ways to identify, validate, and characterize secreted factors in vivo.

Efficacy and indications of gamma knife radiosurgery for recurrent low-and high-grade glioma.

PURPOSE: To investigate the indications and efficacy of gamma knife radiosurgery (GKRS) as a salvage treatment for recurrent low-and high-grade glioma. METHODS: This retrospective study of 107 patients with recurrent glioma treated with GKRS between 2009 and 2022, including 68 high-grade glioma (HGG) and 39 low-grade glioma (LGG) cases. The Kaplan-Meier method was used to calculate the overall survival (OS) and progression-free survival (PFS). The log-rank test was used to analyze the multivariate prognosis of the Cox proportional hazards model. Adverse reactions were evaluated according to the Common Terminology Criteria for Adverse Events version 4.03. The prognostic value of main clinical features was estimated, including histopathology, Karnofsky performance status (KPS), recurrence time interval, target location, two or more GKRS, surgery for recurrence, site of recurrence, left or right side of the brain and so on. RESULTS: The median follow-up time was 74.5 months. The median OS and PFS were 17.0 months and 5.5 months for all patients. The median OS and PFS were 11.0 months and 5.0 months for HGG, respectively. The median OS and PFS were 49.0 months and 12.0 months for LGG, respectively. Multivariate analysis showed that two or more GKRS, left or right side of the brain and brainstem significantly affected PFS. Meanwhile, the KPS index, two or more GKRS, pathological grade, and brainstem significantly affected OS. Stratified analysis showed that surgery for recurrence significantly affected OS and PFS for LGG. KPS significantly affected OS and PFS for HGG. No serious adverse events were noted post-GKRS. CONCLUSION: GKRS is a safe and effective salvage treatment for recurrent glioma. Moreover, it can be applied after multiple recurrences with tolerable adverse effects.

Localized Electron Density Regulation Effect for Promoting Solid-Liquid Ion Adsorption to Enhance Areal Capacitance of Micro-Supercapacitors.

The development of flexible microelectronic systems requires the construction of high-energy-output planar micro-supercapacitors (MSCs). Herein, the localized electron density, by introducing graphene quantum dots (GQDs) on the surface of electrodes, is regulated. The enhanced local field intensity promotes ion electrostatic adsorption at the solid-liquid interface, which significantly improves the energy density of MSCs in the confined space. Local electronic structure has been investigated from the perspective of the topological analysis of the electron localization function (ELF) and the electron density. Impressively, the edges of the simulated structure exhibit a higher electron density distribution than the CC skeleton. This finding indicates that the introduced GQDs reinforce the intrinsic electrical double-layer capacitance (EDLC) and the oxygen-bearing functional groups at the edge, further increasing the pseudocapacitance performance. Moreover, the edge electron aggregation effect enables the all-carbon-based symmetric MSCs to exhibit ultra-high areal capacitance (21.78 mF cm-2 ) and excellent cycle stability (86.74% retention after 25 000 cycles). This novel surface local charge regulation strategy is also applied for intensifying ion electrostatic adsorption on Zn-ion hybrid MSCs (polyvalent metal ions) and ion-gel electrolyte MSCs (non-metallic ions). With excellent planar integration, this device demonstrates excellent flexibility and has potential applications in timing and environmental monitoring.

Molecular characterization and immune functions of lipasin in Nile tilapia (Oreochromis niloticus): Involvement in the regulation of tumor necrosis factor-α secretion.

Lipasin, the product of the angiopoietin-like 8 (angptl8) gene, is known as a critical regulator of plasma lipid metabolism. However, its immune function in vertebrates is currently poorly understood. By 5'/3'-rapid amplification of cDNA ends (RACE), we established the structural identity of Nile tilapia (Oreochromis niloticus) angptl8. The transcripts of tilapia angptl8 were widely expressed in various tissues, with the highest levels in the liver. Following lipopolysaccharide in vivo challenges, time-dependent angptl8 gene expression was observed in the head kidney and liver. On the basis of the sequence obtained, we produced recombinant lipasin that inhibited lipoprotein lipase activity. Treatment of head kidney leukocytes with lipasin stimulated tumor necrosis factor-α (TNF-α) secretion and gene expression. In addition, lipasin-induced TNF-α secretion could be prevented by inhibiting the nuclear factor-kappa B (NF-κB) signaling pathway. Furthermore, lipasin enhanced the phosphorylation and degradation of IκBα and promoted translocation of the p65 subunit of NF-κB to the nucleus. Collectively, the current findings suggested that lipasin was involved in the immune response of Nile tilapia and stimulated TNF-α secretion by activating the NF-κB pathway in tilapia head kidney leukocytes.

The mechanisms of multidrug resistance of breast cancer and research progress on related reversal agents.

Chemotherapy is the mainstay in the treatment of breast cancer. However, many drugs that are commonly used in clinical practice have a high incidence of side effects and multidrug resistance (MDR), which is mainly caused by overexpression of drug transporters and related enzymes in breast cancer cells. In recent years, researchers have been working hard to find newer and safer drugs to overcome MDR in breast cancer. In this review, we provide the molecule mechanism of MDR in breast cancer, categorize potential lead compounds that inhibit single or multiple drug transporter proteins, as well as related enzymes. Additionally, we have summarized the structure-activity relationship (SAR) based on potential breast cancer MDR modulators with lower side effects. The development of novel approaches to suppress MDR is also addressed. These lead compounds hold great promise for exploring effective chemotherapy agents to overcome MDR, providing opportunities for curing breast cancer in the future.

Treadmill exercise promotes E3 ubiquitin ligase to remove amyloid ß and P-tau and improve cognitive ability in APP/PS1 transgenic mice.

BACKGROUND: Moderate physical exercise is conducive to the brains of healthy humans and AD patients. Previous reports have suggested that treadmill exercise plays an anti-AD role and improves cognitive ability by promoting amyloid clearance, inhibiting neuronal apoptosis, reducing oxidative stress level, alleviating brain inflammation, and promoting autophagy-lysosome pathway in AD mice. However, few studies have explored the relationships between the ubiquitin-proteasome system and proper exercise in AD. The current study was intended to investigate the mechanism by which the exercise-regulated E3 ubiquitin ligase improves AD. METHODS: Both wild type and APP/PS1 transgenic mice were divided into sedentary (WTC and ADC) and exercise (WTE and ADE) groups (n = 12 for each group). WTE and ADE mice were subjected to treadmill exercise of 12 weeks in order to assess the effect of treadmill running on learning and memory ability, Aß plaque burden, hyperphosphorylated Tau protein and E3 ubiquitin ligase. RESULTS: The results indicated that exercise restored learning and memory ability, reduced Aß plaque areas, inhibited the hyperphosphorylation of Tau protein activated PI3K/Akt/Hsp70 signaling pathway, and improved the function of the ubiquitin-proteasome system (increased UCHL-1 and CHIP levels, decreased BACE1 levels) in APP/PS1 transgenic mice. CONCLUSIONS: These findings suggest that exercise may promote the E3 ubiquitin ligase to clear ß-amyloid and hyperphosphorylated Tau by activating the PI3K/Akt signaling pathway in the hippocampus of AD mice, which is efficient in ameliorating pathological phenotypes and improving learning and memory ability.

An intercomparison of ozone taken from the Copernicus atmosphere monitoring service and the second Modern-Era retrospective analysis for research and applications over China during 2018 and 2019.

Spatiotemporal variations of ozone (O3) taken from the Copernicus Atmosphere Monitoring Service (CAMS) and the second Modern-Era Retrospective Analysis for Research and Applications (MERRA-2) were intercompared and evaluated with ground and ozone-sonde observations over China in 2018 and 2019. Intercomparison of the surface ozone from CAMS and MERRA-2 reanalysis showed significant negative bias (CAMS minus MERRA-2, same below) at Tibetan Plateau of up to 80 µg/m3, and the average R2 was about 0.6 across China. Evaluated with the ground observations from China National Environmental Monitoring Center (CNEMC), we found that CAMS and MERRA-2 reanalysis were capable of capturing the key patterns of monthly and diurnal variations of surface ozone over China except for the western region, and MERRA-2 overestimated the observations compared to CAMS. Vertically, the CAMS profiles overestimated the ozone-sonde from the World Ozone and Ultraviolet Radiation Data Center (WOUDC) above 200 hPa with the magnitude reaching up to 150 µg/m3, while little bias was found between the reanalysis and observations below 200 hPa. Intercomparison drawn from the vertical distribution between CAMS and MERRA-2 reanalysis showed that the negative bias appeared throughout the troposphere over China, while the positive bias emerged in the upper troposphere and lower stratosphere (UTLS) with high order of magnitude exceeding 100 µg/m3, indicating large uncertainties at higher altitudes. In summary, we concluded that CAMS reanalysis showed better agreement with the observations in contrast to MERRA-2, and the large discrepancy especially at higher altitudes between these two reanalysis datasets could not be ignored.

Traditional Chinese medicine for food allergy and eczema.

OBJECTIVE: To summarize the recent evidence of traditional Chinese medicine (TCM) for food allergy and eczema. DATA SOURCES: Published literature from PubMed database and abstract conference presentations. STUDY SELECTIONS: Studies relevant to TCM for food allergy and eczema were included. RESULTS: TCM is the main component of complementary and alternative medicine in the United States. Food Allergy Herbal Formula 2 (FAHF-2) (derived from the classical formula Wu Mei Wan) prevented systemic anaphylaxis in murine models and was found to have safety and preliminary immunomodulatory effects on T cells and basophils. The phase II trial of combined TCM with oral immunotherapy and omalizumab for multiple food allergy is ongoing. Retrospective practice-based evidence study revealed that comprehensive TCM therapy effectively prevented frequent and severe food anaphylaxis triggered by skin contact or protein inhalation. The traditional Japanese herbal medicine Kakkonto suppressed allergic diarrhea and decreased mast cells in intestinal mucosa in a murine model. The active compounds from TCM were found to have potent inhibition of immunoglobulin (Ig) E, mast cell activation, and proinflammatory cytokine or signaling pathway (tumor necrosis factor alpha, interleukin 8, NF-κB) suggesting value for both IgE and non-IgE-mediated food allergy. Triple TCM therapy including ingestion, bath, and cream markedly improved skin lesion, itching, and sleep loss in patients with corticosteroid dependent, recalcitrant, or topical steroid withdrawal. Xiao Feng San and Japanese and Korean formulas were found to have effectiveness in eczema. Furthermore, acupuncture reduced wheal size, skin itching, and basophil activation in atopic dermatitis. Moreover, TCM is generally safe. CONCLUSION: TCM has potential as safe and effective therapy for food allergy and eczema. Further research is needed for botanical drug development and to further define the mechanisms of actions. TRIAL REGISTRATION: FAHF-2: https://ichgcp.net/clinical-trials-registry/NCT00602160; ethyl acetate and butanol purified FAHF-2: https://clinicaltrials.gov/ct2/show/NCT02879006.

6-Gingerol suppresses tumor cell metastasis by increasing YAPser127 phosphorylation in renal cell carcinoma.

According to the World Health Organization, the incidence and mortality rates of renal cell carcinoma (RCC) are rapidly increasing worldwide. Serious side effects caused by immune therapy and resistance to targeted drug therapy are urgent clinical problems facing kidney treatment. There is increasing global interest in developing natural products with a reduced number of side effects as adjunctive therapeutic options for RCC. Ginger is a spice and herbal remedy used worldwide, and 6-gingerol is a major pharmacologically active ingredient in ginger. In our study, we found that 6-gingerol suppressed RCC cell migration and metastasis in vitro and in vivo. Moreover, reduction in MMP2, Slug, and Vimentin protein levels was observed following 6-gingerol treatment of 786-O and ACHN cells. Furthermore, we revealed the mechanisms underlying the ability of 6-gingerol to inhibit RCC cell migration and metastasis. 6-Gingerol increased yes-associated protein (YAP)ser127 phosphorylation and reduced YAP levels in cell nuclei. We also used a series of loss-of-function and gain-of-function experiments to support our results. Western blot results showed that MMP2, Slug, and Vimentin protein expression was downregulated in YAP-silenced cells and upregulated in YAP-overexpressing cells. Transwell data demonstrated that YAP suppressed RCC migration ability. Immunofluorescence images showed that 6-gingerol decreased YAP levels, leading to disordered F-actin and a reduction in cell lamellipodia. Overall, our results indicated that 6-gingerol is a potential antimetastatic compound for use in kidney therapy.

Levels of nasal exhaled hydrogen sulfide in the general population and allergic rhinitis patients.

BACKGROUND: Objective measures used for the differential diagnosis and severity assessment of allergic rhinitis (AR) are still lacking. The involvement of hydrogen sulfide (H2 S) in the development of AR indicates that nasal exhaled H2 S (NeH2 S) has potential as a biomarker to be used in AR patients. This study aimed to evaluate the application value of NeH2 S measurement in the diagnosis and assessment of AR. METHODS: This study was a multi-center cross-sectional survey conducted in Northwestern China. Demographic information collection and rhinitis assessment were completed through questionnaires. The level of NeH2 S and serum immunoglobulin E were measured. RESULTS: The level of NeH2 S in general population ranged from 0 to 35 ppb, with a median value of 2 ppb. The NeH2 S levels in seasonal allergic rhinitis (SAR) patients were significantly lower than those in general population (2 [1, 2.75] vs. 2 [2, 3] ppb; p = .023), and the NeH2 S value of the SAR group tended to be lower than that of the non-allergic rhinitis (NAR) group (2 [1, 2.75] vs. 2 [2, 3] ppb; p = .094). The subgroup of AR patients with symptoms lasting longer than 2 weeks per month had a lower NeH2 S level compared with the subgroup of patients with symptoms lasting less than 2 weeks per month (2 [1, 2] vs. 2 [2, 3] ppb; p = .015). CONCLUSION: This study described the distribution range of NeH2 S levels in the general population. Further study with larger sample size was needed to clarify the relationship between NeH2 S level and AR.

Reducing Oxygen Evolution Reaction Overpotential in Cobalt-Based Electrocatalysts via Optimizing the "Microparticles-in-Spider Web" Electrode Configurations.

Sluggish kinetics of the multielectron transfer process is still a bottleneck for efficient oxygen evolution reaction (OER) activity, and the reduction of reaction overpotential is crucial to boost reaction kinetics. Herein, a correlation between the OER overpotential and the cobalt-based electrode composition in a "Microparticles-in-Spider Web" (MSW) superstructure electrode is revealed. The overpotential is dramatically decreased first and then slightly increased with the continuous increase ratio of Co/Co3 O4 in the cobalt-based composite electrode, corresponding to the dynamic change of electrochemically active surface area and charge-transfer resistance with the electrode composition. As a proof-of-concept, the optimized electrode displays a low overpotential of 260 mV at 10.0 mA cm-2 in alkaline conditions with a long-time stability. This electrochemical performance is comparable and even superior to the most currently reported Co-based OER electrocatalysts. The remarkable electrocatalytic activity is attributed to the optimization of the electrochemically active sites and electron transfer in the MSW superstructure. Theoretical calculations identify that the metallic Co and Co3 O4 surface catalytic sites play a vital role in improving electron transport and reaction Gibbs free energies for reducing overpotential, respectively. A general way of boosting OER kinetics via optimizing the electrode configurations to mitigate reaction overpotential is offered in this study.

High-performance plasmonic refractive index sensors via synergy between annealed nanoparticles and thin films.

Plasmonic nanostructure-based refractive index (RI) sensors are the core component of biosensor systems and play an increasingly important role in the diagnosis of human disease. However, the costs of traditional plasmonic RI sensors are not acceptable to everyone due to their expensive fabrication process. Here, a novel low-cost and high-performance visible-light RI sensor with a particle-on-film configuration was experimentally demonstrated. The sensor was fabricated by transferring annealed Au nanoparticles (NPs) onto a thin gold film with polymethyl methacrylate (PMMA) as a support. RI sensitivities of approximately 209 nm/RIU and 369 nm/RIU were achieved by reflection and transmission spectrum measurements, respectively. The high sensitivity is due to the strong plasmon-mediated energy confinement within the interface between the particles and the film. The possibility of wafer-scale production and high working stability achieved by the transfer process, together with the high sensitivity to the environmental RI, provides an extensive impact on the realization of universal biosensors for biological applications.

Fretting Wear Behavior and Damage Mechanisms of Inconel X-750 Alloy in Dry Contact Condition.

Frictional and fretting wear behaviors of Inconel X-750 alloy against GCr15 steel ball were investigated in dry contact condition with ∼60% air humidity. Fretting tests were run at the high frequency tribosystem SRV 4 in room temperature and ball-on-flat contact configuration were adopted with the relative oscillatory motion of small displacement amplitude (40 µm). Sliding regimes, wear volumes, frictional properties, and material damage mechanisms were studied with regard to different normal loading and test durations. After the tests, the worn surface morphologies were analyzed by three-dimensional (3D) optical surface profiler, scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS) to distinguish fretting running conditions and material responses for different test cases. It was found that the material removals by abrasive and adhesive wear, debris formation and oxidization, and wear delamination were the main damage mechanisms under the lower normal load where the full slide or gross slip regime (GSR) was dominant between the contact surfaces. On the other hand, fretting regime was found to be a stick-slip or a partial slip at greater loads where damage mechanisms were correlated with deformed asperities, fatigue cracks, and thick layer removal due to highly concentrated cyclic stresses. Time dependence was crucial during GSR where the wear volume increased substantially; however, the wear volumes and scars sizes were consistent over time because of stick-slip effects under the higher normal load.

NEDD4L Protein Catalyzes Ubiquitination of PIK3CA Protein and Regulates PI3K-AKT Signaling.

Oncogenic PIK3CA (p110α), the catalytic subunit of class IA PI3K, plays a major role in PI3K-related cancer progression. The mechanisms underlying the dynamic regulation of PIK3CA protein levels remain unknown. Here we demonstrated that PIK3CA is regulated by polyubiquitination. We identified NEDD4L as the E3 ligase that catalyzes PIK3CA polyubiquitination, leading to its proteasome-dependent degradation. NEDD4L ubiquitinates both the free and regulatory subunit-bound PIK3CA but does not ubiquitinate the regulatory subunit of PI3K. Overexpression of NEDD4L accelerates the turnover rate of PIK3CA, whereas suppression of NEDD4L results in not only the accumulation of PIK3CA but also a paradoxical decrease of AKT activation. Thus, we propose that NEDD4L negatively regulates PIK3CA protein levels via ubiquitination and is required for the maintenance of PI3K-AKT signaling pathway.

Acetylation of p53 Protein at Lysine 120 Up-regulates Apaf-1 Protein and Sensitizes the Mitochondrial Apoptotic Pathway.

The p53 tumor suppressor controls cell growth, metabolism, and death by regulating the transcription of various target genes. The target-specific transcriptional activity of p53 is highly regulated. Here we demonstrate that acetylation of p53 at Lys-120 up-regulates its transcriptional activity toward Apaf-1, a core component in the mitochondrial apoptotic pathway, and thus sensitizes caspase activation and apoptosis. We found that histone deacetylase (HDAC) inhibitors, including butyrate, augment Lys-120 acetylation of p53 and thus Apaf-1 expression by inhibiting HDAC1. In p53-null cells, transfection of wild-type but not K120R mutant p53 can restore the p53-dependent sensitivity to butyrate. Strikingly, transfection of acetylation-mimicking K120Q mutant p53 is sufficient to up-regulates Apaf-1 in a manner independent of butyrate treatment. Therefore, HDAC inhibitors can induce p53 acetylation at lysine 120, which in turn enhances mitochondrion-mediated apoptosis through transcriptional up-regulation of Apaf-1.

Structural genomics studies of human caries pathogen Streptococcus mutans.

Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.

Structural and functional characterization of a novel α/ß hydrolase from cariogenic pathogen Streptococcus mutans.

The protein Smu.1393c from Streptococcus mutans is annotated as a putative α/ß hydrolase, but it has low sequence identity to the structure-known α/ß hydrolases. Here we present the crystal structure of Smu.1393c at 2.0 Å resolution. Smu.1393c has a fully open alkaline substrate pocket, whose conformation is unique among other similar hydrolase structures. Three residues, Ser101, His251, and Glu125, were identified as the active center of Smu.1393c. By screening a series of artificial hydrolase substrates, we demonstrated Smu.1393c had low carboxylesterase activity towards short-chain carboxyl esters, which provided a clue for exploring the in vivo function of Smu.1393c.