As the first member of the family with sequence similarity 3 (FAM3), FAM3A promotes synthesis of ATP in mitochondria of hepatic cells and cells from other organs. Dysregulations of FAM3A are involved in the development of diabetes and nonalcoholic fatty liver disease (NAFLD). So far, the molecule mechanism under the physiological and pathological functions of FAM3A is largely unexplored. Here, we determined the crystal structure of FAM3A at high resolution of 1.38Å, complexed with an unknown-source compound which was characterized through metabolomics and confirmed as methacholine by thermal shift assay and surface plasmon resonance (SPR). Exploration for natural ligands of FAM3A was conducted through the same molecular interaction assays. The observed binding of acyl-L-carnitine molecules indicated FAM3A participating in fatty acid beta-oxidation. Knockdown and rescue assays coupled with fatty acid oxidation determination confirmed the role of FAM3A in beta-oxidation. This investigation reveals the molecular mechanism for the biological function of FAM3A and would provide basis for identifying drug target for treatment of diabetes and NAFLD.

目的:初步探讨hit基因对变异链球菌生长和致龋力的影响.方法:通过同源重组构建变异链球菌hit基因缺陷株(Δhit)、hit基因回补株(ΔhitC、ΔhitC-eGFP);观察不同pH下Smu.Δhit、Smu.ΔhitC和ATCC25175模式菌株生长曲线;通过结晶紫染色、蒽酮染色、扫描电镜等实验,比较生长、生物膜形成、粘附、菌体形态差异及耐酸特性;通过人工龋实验,在体外模拟菌株对牙釉产生龋样损坏的差异.结果:成功构建Smu.Δhit、Sum.ΔhitC和Smu.ΔhitC-eGFP菌株;观察发现Smu.Δhit较ATCC25175菌株生长迅速,随着pH值降低,Smu.Δhit生长受到部分抑制,ATCC25175则完全被抑制;Smu.Δhit菌体呈"椭圆球状平铺附着"分散在牙釉面上,胞外生物膜量较少;Smu.Δhit造成的龋样损坏明显强于ATCC25175.结论:hit基因调控变异链球菌生长繁殖,Smu.Δhit缺陷株生长速率显著高于亲本株,更耐受酸性环境,对人牙釉面破坏性更强.

To study the effect of miR-153-3p on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) in a high glucose environment and its potential mechanism. The results showed that high glucose inhibited the osteogenic differentiation of BMSCs, and the expression of miR-153-3p increased during osteogenic differentiation. Further experiments found that in BMSCs induced by high glucose, overexpression of miR-1533p inhibited the osteogenic differentiation of BMSCs, and the expressions of osteogenesis-related genes bone sialoprotein, Collagen I and alkaline phosphatase were down-regulated, while silencing of miR-153-3p alleviated the inhibition effect. The dual-luciferase reporter gene assay confirmed that the 3'-untranslated region (3'-UTR) of runt related transcription factor 2 (RUNX2) had a targeted binding site with miR-153-3p and a negative regulatory effect. Molecular studies further confirmed that miR-153-3p inhibited the osteogenic differentiation of BMSCs by targeting the 3'-UTR of RUNX2. In conclusion, our study found that as one key regulator of high glucose affecting the osteogenic differentiation of BMSCs, miR-153-3p may play a negative regulatory role by inhibiting the expression of RUNX2.

Opsin3 (OPN3) is a photoreceptor membrane protein with a typical seven-alpha helical transmembrane structure that belongs to the G-protein-coupled receptor (GPCR) superfamily and is widely expressed in brain. In recent years, it has been reported that OPN3 is also highly expressed in adipose tissue, and the protein is associated with the production of skin melanin. We found that the N82 site is the glycosylation site of OPN3. SNAP-tagTM has diverse functions and can be applied to a variety of different studies. By constructing a SNAP-tagged OPN3 recombinant protein, the distribution position of SNAP-OPN3 in cells can be clearly observed by fluorescence confocal microscopy using SNAP-Surface® 549 and SNAP-Cell® OregonGreen®, which provides a new method for studying the function of OPN3. It also shows that SNAP-tag does not affect the function of OPN3. Using the SNAP tag we found that OPN3 cannot be taken up to the cell membrane after glycosylation site mutation.

The influence of enamel matrix derivative (EMD) on proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) was explored in high glucose (HG) microenvironment with interaction of Wnt/β-catenin pathway. Extraction of BMSCs from Sprague–Dawley rats, culture, and identification were manifested. The cells were treated with different concentration of EMD in HG to figure out the most available concentration for proliferation and osteogenic differentiation. Then, observation of cell growth curve and cell cycle changes, and detection of Osterix, runt-related transcription factor 2 (Runx2), COL-I, early osteogenic indexes, Calcium salt deposition, and β-catenin protein in Wnt/β-catenin pathway were assured. After adding Wnt/β-catenin pathway inhibitor (XAV-939) in the cells with osteogenesis induction, detection of binding of β-catenin to Osterix was clarified. Via identification BMSCs cultured in vitro was qualified. Different concentrations of EMD could accelerate cell proliferation in HG and osteogenesis induction, and 75 μg/mL EMD had the best effect. The HG augmented BMSCs proliferation and the propidium iodide index of flow cytometry cycle was elevated in HG, which were strengthened via the EMD. After BMSCs’ osteogenesis induction, Osterix, Runx2, CoL-1, early osteogenic indexes, and calcium salt deposition were reduced, but elevated via EMD. β-Catenin was the lowest in the HG, but elevated after EMD. After addition of XAV-939, reduction of β-catenin and the downstream (Osterix and Runx2) were manifested. Detection of binding protein bands was in β-catenin and Osterix of the HG after EMD treatment. EMD may facilitate the osteogenic differentiation of BMSCs via activating the Wnt/β-catenin pathway in HG.

Objective To construct a hit-deficient mutant strain of S. mutans ATCC25175 and verify its cell cycle regulatory function. Method Genomic DNA was extracted from S. mutans ATCC25175 strains, and then the upstream and downstream DNA fragments of the hit gene were cloned into the pFW5 vector (spectinomycin resistant) to construct recombinant plasmids using PCR amplification. Third, employed by natural genetic transformation in S. mutans ATCC25175 strains, the linearized recombinant plasmids were transformed into their genetic competence, induced by the synthesized competence-stimulating peptide (CSP), and then, homologous recombination was utilized to produce crossover and noncrossover products. Fourth, the hit-deficient mutant strains of S. mutans ATCC25175 were screened through the spectinomycin-resistance marker and identified by the electrophoresis of PCR products and PCR Sanger sequencing. Finally, its growth rate in vegetative BHI medium was also investigated. Results The upstream (856 bp) and downstream (519 bp) DNA fragments of the hit gene from the genomic DNA materials of S. mutans ATCC25175 were cloned into two multiple cloning sites (MCS-I and MCS-II) of the pFW5 vector, respectively, and the recombinant plasmid pFW5_hit_Up_Down was constructed and identified by double-emzyme digestion and PCR Sanger sequencing. The linearized recombinant plasmids were transformed into their genetic competence, induced by the synthetic CSP, and then, homologous recombination was utilized to produce various products. The hit-deficient mutant strains of S. mutans ATCC25175 were screened through the spectinomycin resistance marker and identified by the electrophoresis of PCR products and Sanger sequencing. The growth rate of the hit-deficient mutant strains versus their parental S. mutans ATCC25175 strains was increased greatly (P<0.001). Conclusion The hit-deficient mutant strains of S. mutans ATCC25175, having heritable traits, were successfully constructed, and the encoding Hit protein is growth-phase regulated in the cell cycle.

To investigate the EMD’s capacity in BMSCs osteogenic differentiation. In vivo and in vitro, BMSCs were treated with EMD, scanning electron microscopy, and Alizarin Red staining were used to detect the changes in the osteogenic ability of BMSCs, and the proliferation ability of BMSCs was evaluated by CCK8. In addition, by adding xav939, a typical inhibitor of Wnt/β-catenin signaling pathway, the regulatory function of Wnt/β-catenin signaling was clarified. The results showed that EMD promote cell proliferation and 25 μg/ml EMD had the most significant effect. Cells inducing osteogenesis for 2 and 3 even 4 weeks, the cell staining is deeper in EMD treated group than that of the control (P < 0.05) by alizarin Red staining, suggesting more mineralization of BMSCs. In vivo implanting the titanium plate wrapped with 25 μg/ml EMD treated-BMSC film into nude mice for 8 weeks, more nodules were formed on the surface of the titanium plate than that the control (P < 0.05). HE showed that there is a little blue-violet immature bone-like tissue block. Besides, the expression of RUNX Family Transcription Factor 2 (Runx2), Osterix, Osteocalcin (OCN), collagen I (COLI), alkaline phosphatase (ALP) and β-catenin were inhibited in xav939 group (P < 0.05); Inversely, all were activated in EMD group (P < 0.05). In conclusion, EMD promoted the proliferation and osteogenic differentiation of BMSCs. EMD’s function on BMSCs might be associated with the Wnt/β-catenin signaling pathway.

It’s not clear whether the drop well surface can induce heterogeneous nucleation to increase the probability of screening success, although a medium-throughput 48-well SBS (the Society for Biomolecular Screening, USA) polystyrene microplate has been widely used for protein crystallization screening. Here, our accumulating data suggested that this 48-well SBS microplate with rough surface is beneficial for protein crystallization. It was observed that some protein crystals were only formed on the rough edges and/or walls of the drop well, but not on the flat bottom or in the crystallization drop. It was further demonstrated with two standard test proteins. The protuberances, grooves and cavities with varied sizes and shapes at micrometer-scale in the rough drop well wall can serve as nucleants and induce heterogeneous nucleation of protein crystals. The rough wall microplate provides a potent tool for protein crystallographers embarking on crystallization trials.

3′3′-cyclic GMP–AMP (3′3′-cGAMP) belongs to a family of the bacterial secondary messenger cyclic dinucleotides. It was first discovered in the Vibrio cholerae seventh pandemic strains and is involved in efficient intestinal colonization and chemotaxis regulation. Phosphodiesterases (PDEs) that degrade 3′3′-cGAMP play important regulatory roles in the relevant signaling pathways, and a previous study has identified three PDEs in V. cholerae, namely, V-cGAP1, V-cGAP2, and V-cGAP3, functioning in 3′3′-cGAMP degradation. We report the crystal structure, biochemical, and structural analyses of V-cGAP3, providing a foundation for understanding the mechanism of 3′3′-cGAMP degradation and regulation in general. Our crystal and molecular dynamic (MD)-simulated structures revealed that V-cGAP3 contains tandem HD-GYP domains within its N- and C-terminal domains, with similar three-dimensional topologies despite their low-sequence identity. Biochemical and structural analyses showed that the N-terminal domain plays a mechanism of positive regulation for the catalytic C-terminal domain. We also demonstrated that the other homologous Vibrio PDEs, V-cGAP1/2, likely function via a similar mechanism.

Subtle changes in protein sequences are able to alter ligand-protein interactions. Unraveling the mechanism of such phenomena is important for understanding ligand-protein interactions, including the DMXAA-STING interaction. DMXAA specifically binds to mouse STING instead of human STING. However, the S162A mutation and a newly discovered E260I mutation endow human STINGAQ with DMXAA sensitivity. Through molecular dynamics simulations, we revealed how these single mutations alter the DMXAA-STING interaction. Compared to mutated systems, structural correlations in the interaction of STINGAQ with DMXAA are stronger, and the correlations are cross-protomers in the dimeric protein. Analyses on correlation coefficients lead to the identification of two key interactions that mediate the strong cross-protomer correlation in the DMXAA-STINGAQ interaction network: DMXAA-267T-162S* and 238R-260E*. These two interactions are partially and totally interrupted by the S162A and E260I mutations, respectively. Moreover, a smaller number of water molecules are displaced upon DMXAA binding to STINGAQ than that on binding to its mutants, leading to a larger entropic penalty for the former. Considering the sensitivity of STINGAQ and two of its mutants to DMXAA, a strong structural correlation appears to discourage DMXAA-STING binding. Such an observation suggests that DMXAA derivatives, which are deprived of hydrogen-bond interaction with both 162S* and 267T, are potential agonists of human STING.

STING (Stimulator of Interferon Genes, also known as ERIS, MITA and MPYS) is an important adaptor protein in innate immunity. It plays a key role in cytosolic DNA mediated IFN production. STING is the direct sensor of cyclic dinucleotides(CDN) in cytosol, including c-di-GMP from pathogen and cGAMP synthesized by cGAS after DNA stimulating. After binding to and activated by CDNs, STING recruits and activates TBK1 and IRF3 by its C terminal tail. IRF3 is phosphorylated and then dimerize to enter nucleus, resulting in type I interferon (IFN) production.

STING (Stimulator of Interferon Genes, also known as ERIS, MITA and MPYS) is an important adaptor protein in innate immunity.It plays a key role in cytosolic DNA mediated IFN production.STING is the direct sensor of cyclic dinucleotides(CDN) in cytosol, including c-di-GMP from pathogen and cGAMP synthesized by cGAS after DNA stimulating.After binding to and activated by CDNs, STING recruits and activates TBK1 and IRF3 by its C terminal tail.IRF3 is phosphorylated and then dimerize to enter nucleus, resulting in type I interferon (IFN) production.5,6-dimethylxanthenone-4-acetic acid (DMXAA) and 10-carboxymethyl-9-acridanone (CMA) were identified as antitumor/antiviral compounds which acted very well in mouse model but failed in human clinical trial.Further research showed that DMXAA and CMA bind to and activate mouse STING, but not human STING.To further investigate the mechanism of ligands' species selectivity, we studied on human STING(hSTING), rat STING(rSTING) and mouse STING(mSTING) by functional and structural analysis.We found that human and rat STINGs display more similar signaling profiles toward DMXAA and CMA than that of human and mouse STINGs, suggesting that rat is more suitable for preclinical testing of STING-targeted drugs.Previous research showed that a single point mutation in hSTING S162A renders hSTING sensitive to DMXAA.Through molecular dynamics simulations, we revealed how this single mutation alter the DMXAA-STING interaction.Compared to mutated systems, structural correlations in the interaction of STING with DMXAA are stronger, and the correlations are cross-protomers in the dimeric protein.Analyses on correlation coefficients lead to the identification of two key interactions that mediate the strong cross-protomer correlation in the DMXAA-STING interaction network: DMXAA-267T-162S* and 238R-260E*.These two interactions are partially and totally interrupted by the S162A and E260I mutations, respectively.Moreover, a smaller number of water molecules are displaced upon DMXAA binding to STING than that on binding to its mutants, leading to a larger entropic penalty for the former.Considering the sensitivity of STING and two of its mutants to DMXAA, a strong structural correlation appears to discourage DMXAA-STING binding.Such an observation suggests that DMXAA derivatives, which are deprived of hydrogen-bond interaction with both 162S* and 267T, are potential agonists of human STING.Taken together, our findings suggest better animal model for STING-targeted drugs and shed light on optimization of hSTING agonist.

Cyclic dinucleotides (CDNs) and antitumor/antiviral agents (DMXAA and CMA) trigger STING-dependent innate immunity activation. Accumulative evidences have showed that DMXAA and CMA selectively activate mouse, but not human STING signaling. The mechanism underlying this species selectivity remains poorly understood. In this report, we have shown that human and rat STINGs display more similar signaling profiles toward DMXAA and CMA than that of human and mouse STINGs, suggesting that rat is more suitable for preclinical testing of STING-targeted drugs. We have also determined the crystal structures of both apo rat STING and its complex with cyclic GMP-AMP with 2′5′ and 3′5′ phosphodiester linkage (2′3′-cGAMP), a human endogenous CDN. Structure-guided biochemical analysis also revealed the functional importance of the connecting loop (A140-N152) between membrane and cytosolic domains in STING activation. Taken together, these findings reveal that rat STING is more closely related to human STING in terms of substrate preference, serving as a foundation for the development of STING-targeted drugs.

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.

The smu.412c gene encodes a putative histidine triad-like protein (SMU.412c) with 139 residues that is involved in cell-cycle regulation in Streptococcus mutans. The gene was cloned into the expression vector pET28a and subsequently expressed in Escherichia coli strain BL21 (DE3) to give a substantially soluble form of SMU.412c with a His(6) tag at its N-terminus. The recombinant protein was purified to homogeneity in a two-step procedure involving Ni(2+)-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained using the sitting-drop vapour-diffusion method and diffracted to 1.8 A resolution on beamline BL6A at Photon Factory, Tsukuba, Japan. The crystal belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 53.5, c = 141.1 A.