The carboxy-terminus,a key regulator of protein function

All proteins end with a carboxyl terminus that has unique biophysical properties and is often disordered. Although there are examples of important C-termini functions, a more global role for the C-terminus is not yet established. In this review, we summarize research on C-termini, a unique region in proteins that cells exploit. Alternative splicing and proteolysis increase the diversity of proteins and peptides in cells with unique C-termini. The C-termini of proteins contain minimotifs, short peptides with an encoded function generally characterized as binding, posttranslational modifications, and trafficking. Many of these activities are specific to minimotifs on the C-terminus. Approximately 13% of C-termini in the human proteome have a known minimotif, and the majority, if not all of the remaining termini have conserved motifs inferring a function that remains to be discovered. C-termini, their predictions, and their functions are collated in the C-terminome, Proteus, and Terminus Oriented Protein Function INferred Database (TopFIND) database/web systems. Many C-termini are well conserved, and some have a known role in health and disease. We envision that this summary of C-termini will guide future investigation of their biochemical and physiological significance.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Aryl Hetaryl Ketones and Thioketones as Efficient Inhibitors of Peptidyl‐Prolyl cis‐trans Isomerases

A series of 18 differently substituted new aryl hetaryl ketones and thioketones were synthesized in four to six steps from commercial starting materials. The new ketones were evaluated as inhibitors of the peptidyl‐prolyl cis‐trans isomerase hPin1 with K_i values ranging in the one‐digit micromolar to sub‐micromolar numbers. A crystal structure revealed the non‐planar arrangement of the aryl residues at the carbonyl compound and supports the hypothesis that the new compounds might mimic the transition state of the enzymatic conversion.     

Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants

Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants’ increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti‐aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains.     

玉米DEAD-box RNA解旋酶基因的克隆及分析

DEAD-box RNA解旋酶参与RNA转录、前体mRNA剪切、核糖体发生、核质运输、蛋白质翻译、RNA降解等重要的生命活动.根据本室在S-Mo17Rf3Rf3cDNA芯片研究中,检测到花粉发育后期RNA解旋酶上调表达的结果,应用RACE技术从S-Mo17Rf3Rf3花粉中克隆得到该RNA解旋酶基因全长cDNA,命名为ZmRH2并在GenBank注册登记 (DQ327709).序列分析表明：该cDNA全长1 652bp,从第163 bp开始到1 386bp含有一个开放阅读框,编码407个氨基酸.其编码的蛋白质具有DEAD-box RNA解旋酶特有的9个保守模体,与水稻、拟南芥和豌豆中的DEAD-box RNA解旋酶的氨基酸序列存在着很高的同源性.RT-PCR分析表明,该基因在近等基因系S-Mo17Rf3Rf3和S-Mo17rf3rf3的叶、根、和雌穗中的表达没有差异,但在花丝和花粉中有明显差异.     

Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe

The V3 loop on gp120 from human immunodeficiency virus type 1 (HIV-1) is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is a principal target for neutralizing antibodies and a major determinant for cell tropism and syncytium formation. In this study, the nucleotide sequences of the env gene region coding the V3 loop were determined by DNA sequencing methods for four novel HIV-1 strains that circulate in the countries of Eastern Europe, such as Russia, Belarus, Ukraine, etc. Based on the empirical data obtained, the 3D structures of the V3 loops associated with these viral modifications were generated by computer modeling and then compared to discover similarities in the spatial arrangement of this functionally important site of gp120. Despite the HIV-1 genetic variety, several regions of the V3 loop that contain residues critical for cell tropism were shown to be structurally invariant, which may explain its exceptional role in a co-receptor usage. These data together with those on the biological activity of the V3 individual residues clearly show that these conserved structural motifs of gp120 represent potential HIV-1 weak points most suitable for therapeutic intervention.     

橡胶延伸因子基因及3'端非编码区的克隆与序列分析

橡胶延伸因子ＲＥＦ（Ｒｕｂｂｅｒ Ｅｌｏｎｇａｔｉｏｎ Ｆａｃｔｏｒ）是橡胶生物合成中最重要的酶之一．作者利用ＲＥＦ基因序列设计并合成引物． 通过提取胶乳总ＲＮＡ 用ＲＴ法合成ｃＤＮＡ 后,通过ＰＣＲ技术扩增并克隆了ＲＥＦ基因和３端非编码区． 序列测定结果表明,ＲＥＦ基因全长４１４ 个碱基,编码１３８ 个氨基酸,３端非编码区长１１２ ｂｐ． 与Ｇｏｙｖａｅｒｔｓ Ｅ 等人发表的序列比较：ＲＥＦ基因同源率为１００％ ,３端非编码区有２ ｂｐ 的差异,同源率为９８％ ． 将所克隆的ＲＥＦ基因及３非编码区进行地高辛标记, 对胶乳和叶片总ＲＮＡ 进行点杂交分析,结果表明,胶乳总ＲＮＡ 呈阳性反应,叶片总ＲＮＡ 则呈阴性反应．