Chromatin maturation depends on continued DNA-replication

The structure of [3H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [3H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. We conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation.     

Comparative structure-function analysis of cytolethal distending toxins

Cytolethal distending toxins (CDTs) constitute a family of bacterial proteins that enter eukaryotic cells with genotoxic activity leading to cell cycle arrest and apoptosis. CDTs are widespread, having been found in a variety of Gram-negative pathogens with a broad tissue tropism. The recently determined crystal structure of the Haemophilus ducreyi CDT provides a powerful starting point for analysis of the structure and function in this toxin family. In this study, we apply comparative modeling and structural analysis to extend the experimental structural information to multiple CDT toxins from a diverse species. Analysis of structurally and functionally important residues in the active subunit, CdtB, and putative cell delivery elements, CdtA and CdtC, begins to establish the fundamental, mechanistic elements of this unique holotoxin. The results reveal that key structural features with important functional consequences are highly conserved across different CDTs, providing a blueprint for directed examination of functional hypotheses in a variety of pathogenic contexts.     

X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior

We have used crystallography and thermodynamic analysis to study nuclease variants I92E and I92K, in which an ionizable side-chain is placed in the hydrophobic core of nuclease. We find that the energetic cost of burying ionizable groups is rather modest. The X-ray determinations show water molecules solvating the buried glutamic acid under cryo conditions, but not at room temperature. The lysine side-chain does not appear solvated in either case. Guanidine hydrochloride (GnHCl) denaturation of I92E and I92K, done as a function of pH and monitored by tryptophan fluorescence, showed that I92E and I92K are folded in the pH range pH 3.5-9.0 and pH 5.5-9.5, respectively. The stability of the parental protein is independent of pH over a broad range. In contrast, the stabilities of I92E and I92K exhibit a pH dependence, which is quantitatively explained by thermodynamic analysis: the PK(a) value of the buried K92 is 5.6, while that of the buried E92 is 8.65. The free energy difference between burying the uncharged and charged forms of the groups is modest, about 6 kcal/mol. We also found that epsilon(app) for I92K and I92E is in the range approximately 10-12, instead of 2-4 commonly used to represent the protein interior. Side-chains 92E and 92K were uncharged under the conditions of the X-ray experiment. Both are buried completely inside the well-defined hydrophobic core of the variant proteins without forming salt-bridges or hydrogen bonds to other functional groups of the proteins. Under cryo conditions 92E shows a chain of four water molecules, which hydrate one oxygen atom of the carboxyl group of the glutamic acid. Two other water molecules, which are present in the wild-type at all temperatures, are also connected to the water ring observed inside the hydrophobic core. The ready burial of water with an uncharged E92 raises the possibility that solvent excursions into the interior also take place in the wild-type protein, but in a random, dynamic way not detectable by crystallography. Such transient excursions could increase the average polarity, and thus epsilon(app), of the protein interior.     

基因前定点敲入FLAG标签表达的FLAG-SND1蛋白参与胞内应激颗粒的形成

CRISPR/ Cas9 (clustered regular interspaced short palindromic repeats-Cas9 nuclease) gene editing technology is an emerging technology for gene-specific knock-out and knock-in in recent years. In this experiment, the CRISPR/ Cas9 gene editing system was used to insert 3×FLAG tags into the front of SND1 gene in HeLa cells, so that the endogenous expression of SND1 protein in cells was equipped with 3×FLAG tags, and the localization of SND1 with stress granules and processing bodies was observed. A sgRNA near the start codon ATG of the SND1 gene was designed, and a recombinant eukaryotic expression plasmid was constructed using px459 as an expression vector. A sequence containing 3×FLAG and a 150 bp homologous arm upstream and downstream of the position to be inserted was designed, and the recombinant plasmid was synthesized by the company. Two plasmids were co-transfected into HeLa cells, and positive cells were screened by puromycin. Western blotting indicated that the cells expressed the 3×FLAG-SND1 fusion protein. Genomic DNA was extracted and sequenced. Cell cycle and apoptosis were detected by flow cytometry after sequencing and the stable strain was obtained without error. It was found that there was no significant difference compared with WT cells. At the same time, the treatment with 0. 5 mmol / L sodium arsenite resulted in oxidative stress in cells, increased phosphorylation of eIF2α protein, and the presence of stress particles in the cytoplasm. There was co-localization between SND1 and stress particle marker protein TIAR, but no co-localization with processed body protein DCP1α. © 2019 The authors.     

In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus

Clustered regularly interspaced short palindromic repeats (CRISPR)‐encoded immunity in Type I systems relies on the Cascade (CRISPR‐associated complex for antiviral defence) ribonucleoprotein complex, which triggers foreign DNA degradation by an accessory Cas3 protein. To establish the mechanism for adaptive immunity provided by the Streptococcus thermophilus CRISPR4‐Cas (CRISPR‐associated) system (St‐CRISPR4‐Cas), we isolated an effector complex (St‐Cascade) containing 61‐nucleotide CRISPR RNA (crRNA). We show that St‐Cascade, guided by crRNA, binds in vitro to a matching proto‐spacer if a proto‐spacer adjacent motif (PAM) is present. Surprisingly, the PAM sequence determined from binding analysis is promiscuous and limited to a single nucleotide (A or T) immediately upstream (?1 position) of the proto‐spacer. In the presence of a correct PAM, St‐Cascade binding to the target DNA generates an R‐loop that serves as a landing site for the Cas3 ATPase/nuclease. We show that Cas3 binding to the displaced strand in the R‐loop triggers DNA cleavage, and if ATP is present, Cas3 further degrades DNA in a unidirectional manner. These findings establish a molecular basis for CRISPR immunity in St‐CRISPR4‐Cas and other Type I systems.     

植物基因打靶效率的研究进展

基因打靶技术是将外源DNA定向整合入基因组中对特定基因进行精确修饰,从而改变生物遗传性状的技术。它在特定基因功能研究、遗传育种和生理机制的理解方面有着重要意义,但植物中较低的基因打靶效率制约着它的进一步推广和应用。本文着重从载体构建、筛选策略、受体细胞状态等方面对打靶效率的提高进行分析,并介绍同源重组酶系、锌指核酶和寡核苷酸技术在基因打靶中的应用。     

破菌时可自动降解宿主核酸的大肠杆菌BL21(DE3)的lpxM突变株构建

研究利用Red同源重组技术对常用大肠杆菌表达宿主菌BL21(DE3)进行改良, 构建破菌时可自动降解宿主核酸的大肠杆菌表达宿主菌, 该菌株可望有助于解决因破菌时宿主菌染色体核酸释放给后续纯化重组蛋白工作带来的困难。将N端连有OmpA的信号肽的S. aureus nucleaseB(nucB)表达框整合至E. coli BL21(DE3)的lpxM位点, 改造后菌株(称为BLN)经诱导能表达nucB、并分泌至周质空间, 这样可使宿主核酸免受该酶“毒性”影响, 菌体裂解后, nucB释放,能自动降解宿主核酸。BLN菌体生长状态以及表达外源重组蛋白的能力与出发菌基本一致。     

安徽不同地区奶站牛奶中金黄色葡萄球菌及其肠毒素污染状况评估

目的评定安徽地区各奶站牛奶中金黄色葡萄球菌以及肠毒素的污染情况。方法通过从安徽省不同地区30所奶站采集乳样,进行乳源性金黄色葡萄球菌的分离与生化鉴定,并采用PCR技术对分离出的菌株进行金黄色葡萄球菌肠毒素血清型鉴定。结果安徽省30个奶站中有4个地区奶站的牛奶中污染金黄色葡萄球菌;从污染牛奶中共分离出5株金黄色葡萄球菌,检出率为16.7%。经鉴定,所分离出的金黄色葡萄球菌中2株为肠毒素A型,1株为肠毒素C型,2株为同时产肠毒素A和肠毒素C。结论安徽省不同地区奶站中的牛奶污染的金黄色葡萄球菌产肠毒素类型以肠毒素A为主。     

金黄色葡萄球菌A型肠毒素双抗体夹心ELISA检测方法的建立及应用

【目的】建立一种快速、灵敏、特异的金黄色葡萄球菌A型肠毒素(Staphylococcal enterotoxin A,SEA)检测方法。【方法】以原核表达的可溶性重组SEA蛋白为免疫原,获得特异性强、亲和力高的单克隆抗体作为捕获抗体,同时制备抗SEA兔多抗血清作为检测抗体建立双抗体夹心ELISA(Double antibody sandwich ELISA,DAS-ELISA)检测方法。【结果】该方法对SEA的线性检测区间为2-128μg/L(y=1.102x-0.07,R2=0.994),检测下限为1.89μg/L,与SEB、SEC2和SED之间无交叉反应;鲜奶SEA人工污染试验测定回收率为94%-114%,变异系数小于10%。应用该方法对46株金黄色葡萄球菌水产品分离株和164株奶牛乳腺炎金黄色葡萄球菌分离株的体外培养上清进行检测,阳性率分别为4.4%和50.6%,表明SEA污染普遍存在。【结论】建立的DAS-ELISA方法特异性、灵敏度和稳定性好,为检测SEA的食源性污染提供了有效手段。     

Thermal unfolding of staphylococcal nuclease and several mutant forms thereof studied by differential scanning calorimetry.

The effects of eight mutations on the thermodynamics of the reversible thermal unfolding of staphylococcal nuclease have been determined over a range of pH and protein concentration by means of differential scanning calorimetry. Variation of the protein concentration was included in our study because we found a significant dependence of the thermodynamics of protein unfolding on concentration. Values for the change in the standard free energy of unfolding, delta delta G0d, produced by the mutations in the pH range 5.0-7.0 varied from 1.9 kcal mol-1 (apparent stabilization) for H124L to -2.8 kcal mol-1 (apparent destabilization) for L25A. As has been observed in numerous other cases, there is no correlation in magnitude or sign between delta delta G0d and the corresponding values for delta delta Hd and T delta delta S0d, the latter quantities being in most cases much larger in magnitude than delta delta G0d. This fact emphasizes the difficulty in attempting to correlate the thermodynamic changes with structural changes observed by X-ray crystallography.