Cyclic CMP and cyclic UMP mediate bacterial immunity against phages

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Sequence heterogeneity and anomalous electrophoretic mobility of kinetoplast minicircle DNA from Leishmania tarentolae

Several unit-length minicircles from the kinetoplast DNA of Leishmania tarentolae were cloned into pBR322 and into M13 phage vectors. The complete nucleotide sequences of three different partially homologous minicircles were obtained. The molecules contained a region of approx. 80% sequence homology extending for 160–270 bp and a region unique to each minicircle. A 14-mer was found to be conserved in all kinetoplast minicircle sequences reported to date. The frequency distributions of various minicircle sequence classes in L. tarentolae were obtained by quantitative gel electrophoresis and by examination of the “T ladder” patterns of minicircles randomly cloned into M13 at several sites. By these methods we could assign approx. 50% of the total minicircle DNA into a minimum of five sequence classes. A sequence-dependent polyacrylamide gel migration abnormality was observed with several minicircle fragments both cloned and uncloned. The abnormality was dependent on the presence of a portion of the conserved region of the minicircle.     

肿瘤特异性蛋白B7-H4纳米抗体的筛选和鉴定

羊驼体内存在天然缺少轻链的重链抗体,克隆重链抗体可变区(VHH),即可构建单域抗体(single-domain antibodies,sdAbs),又称纳米抗体(nanobody,Nb)。利用非免疫羊驼噬菌体文库筛选肿瘤特异性蛋白B7-H4的纳米抗体,经过4轮淘选,ELASE鉴定阳性克隆噬菌体,测序获得其DNA序列后体外转录为mRNA,将修饰纯化后的mRNA转染到肿瘤细胞,利用细胞免疫荧光检测mRNA在肿瘤细胞内是否表达,Western印迹进一步验证其表达情况;通过CCK-8法鉴定其对肿瘤细胞的增殖抑制能力;划痕实验鉴定其对肿瘤细胞迁移能力的影响;Transwell法鉴定其对肿瘤细胞的侵袭能力的影响;裸鼠荷瘤模型瘤旁注射mRNA,鉴定其在体内实验对肿瘤组织的作用。结果显示,通过淘选获得1个高亲和性的噬菌体株菌H6;DNA测序并导出的氨基酸序列符合羊驼纳米抗体结构;将其mRNA导入肿瘤细胞,能有效表达出纳米抗体H6;转染H6-mRNA的肿瘤细胞(0.84±0.08)与未转染H6-mRNA的对照组(1.83±0.04)相比,其增殖能力明显受到抑制,P<0.01,其迁移和侵袭能力(78.60±5.36)明显低于空白对照组(197.80±21.04),效果优于B7-H4 mRNA的siRNA(95.40±16.56);在裸鼠乳腺癌模型中能有效抑制肿瘤生长,效果优于紫杉醇和B7-H4 mRNA的siRNA。这说明筛选所得抗B7-H4纳米抗体H6能特异结合B7-H4蛋白并封闭其功能,导致肿瘤细胞的增殖、迁移和侵袭受到抑制。该结果为利用B7-H4作为治疗癌症的靶点提供了实验基础。     

Cloning of aroG, the gene coding for phospho-2-keto-3-deoxy-heptonate aldolase(phe), in Escherichia coli K-12, and subcloning of the aroG promoter and operator in a promoter-detecting plasmid

Defective transducing phages carrying aroG, the structural gene for phenylalanine (phe)-inhibitable phospho-2-keto-heptonate aldolase (EC 4.1.2.15; previously known as 3-deoxy-D-arabinoheptulosonate-7-phosphate synthetase[phe]), have been isolated, and DNA from two of these phages has been used to construct a restriction map of the region from att lambda to aroG. A 7.6-kb PstI-HindIII fragment from one of these phages was cloned into pBR322 and shown to contain aroG. The location of aroG within the 7.6 kb was established by subcloning and Tn3 transpositional mutagenesis. A fragment carrying the aroG promoter and operator has been cloned into a high copy number promoter-cloning vector (pMC489), and the resulting aroGpo-LacZ' (alpha) fusion subcloned in a low copy number vector. Strains with this fusion on the low copy number vector exhibit negative regulation of beta-galactosidase expression by both phenylalanine and tryptophan and positive regulation by tyrosine in a tyrR+ background.     

Bacteriophage Ø105clz induces the GroEL-homologue protein inBacillus subtilis

Using two-dimensional polyacrylamide gel electrophoresis, the GroEL homologue ofBacillus subtilis was shown to be induced upon infection with Ø105clz, a clear plaque mutant of the temperate bacteriophage Ø105. Western blotting of one dimensional polyacrylamide gels also showed the induction of the GroEL homologue when cells were infected with Ø105clz.     

Drugs derived from phage display: From candidate identification to clinical practice

Phage display, one of today’s fundamental drug discovery technologies, allows identification of a broad range of biological drugs, including peptides, antibodies and other proteins, with the ability to tailor critical characteristics such as potency, specificity and cross-species binding. Further, unlike in vivo technologies, generating phage display-derived antibodies is not restricted by immunological tolerance. Although more than 20 phage display-derived antibody and peptides are currently in late-stage clinical trials or approved, there is little literature addressing the specific challenges and successes in the clinical development of phage-derived drugs. This review uses case studies, from candidate identification through clinical development, to illustrate the utility of phage display as a drug discovery tool, and offers a perspective for future developments of phage display technology.     

Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning

Antibodies provide a comprehensive record of the encounters with threats and insults to the immune system. The ability to examine the repertoire of antibodies in serum and discover those that best represent “discriminating features” characteristic of various clinical situations, is potentially very useful. Recently, phage display technologies combined with Next-Generation Sequencing (NGS) produced a powerful experimental methodology, coined “Deep-Panning”, in which the spectrum of serum antibodies is probed. In order to extract meaningful biological insights from the tens of millions of affinity-selected peptides generated by Deep-Panning, advanced bioinformatics algorithms are a must. In this study, we describe Motifier, a computational pipeline comprised of a set of algorithms that systematically generates discriminatory peptide motifs based on the affinity-selected peptides identified by Deep-Panning. These motifs are shown to effectively characterize antibody binding activities and through the implementation of machine-learning protocols are shown to accurately classify complex antibody mixtures representing various biological conditions.