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.     

Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod

Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the ‘out’ state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod’s binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins.

Communicated by Ramaswamy H. Sarma     

Tribolium castaneum as a whole‐animal screening system for the detection and characterization of neuroprotective substances

Parkinson's disease (PD) is a movement disorder caused by the progressive loss of dopaminergic neurons. Natural antioxidants and plant extracts with neuroprotective properties offer a promising new therapeutic approach for PD patients, but a suitable large‐scale screening system is required for their discovery and preclinical analysis. Here we used the red flour beetle (Tribolium castaneum ) as a whole‐animal screening system for the detection and characterization of neuroprotective substances. Paraquat was added to the diet of adult beetles to induce PD‐like symptoms, which were quantified using a novel positive geotaxis behavioral assay. These paraquat‐induced behavioral changes were reduced in beetles fed on diets supplemented with l‐ dihydroxyphenylalanine, ascorbic acid, curcumin, hempseed flour, or the Chinese herb gou‐teng. T. castaneum is, therefore, a valuable model for the screening of neuroprotective substances in chemical libraries and plant extracts and could be developed as a model for the preclinical testing of therapeutic candidates for the treatment of neurodegenerative diseases, such as PD.     

Exploratory algorithm to devise multi-epitope subunit vaccine by investigating Leishmania donovani membrane proteins

Visceral leishmaniasis (VL) is a deadly parasitic infection which affects poorest to poor population living in the endemic countries. Increasing resistant to existing drugs, disease burden and a significant number of deaths, necessitates the need for an effective vaccine to prevent the VL infection. This study employed a combinatorial approach to develop a multi-epitope subunit vaccine by exploiting Leishmania donovani membrane proteins. Cytotoxic T- and helper T-lymphocyte binding epitopes along with suitable adjuvant and linkers were joined together in a sequential manner to design the subunit vaccine. The occurrence of B-cell and IFN-γ inducing epitopes approves the ability of subunit vaccine to develop humoral and cell-mediated immune response. Physiochemical parameters of vaccine protein were also assessed followed by homology modeling, model refinement and validation. Moreover, disulfide engineering was performed for the increasing stability of the designed vaccine and molecular dynamics simulation was performed for the comparative stability purposes and to conform the geometric conformations. Further, molecular docking and molecular dynamics simulation study of a mutated and non-mutated subunit vaccine against TLR-4 immune receptor were performed and respective complex stability was determined. In silico cloning ensures the expression of designed vaccine in pET28a(+) expression vector. This study offers a cost-effective and time-saving way to design a novel immunogenic vaccine that could be used to prevent VL infection.

Communicated by Ramaswamy H. Sarma     

In silico identification and in vitro validation of nogalamycin N-oxide (NSC116555) as a potent anticancer compound against non–small-cell lung cancer cells

The epidermal growth factor receptor (EGFR) was found to be overexpressed in several cancers, especially in lung cancers. Finding new effective drug against EGFR is the key to cancer treatment. In this study, the GOLD docking algorithm was used to virtually screen for novel human EGFR inhibitors from the NCI database. Thirty-four hit compounds were tested for EGFR-tyrosine kinase (TK) inhibition. Two potent compounds, 1-amino-4-(4-[4-amino-2-sulfophenyl]anilino)-9,10-dioxoanthracene-2-sulfonic acid (NSC125910), and nogalamycin N-oxide (NSC116555) were identified with IC₅₀ values against EGFR-TK comparable to gefitinib; 16.14 and 37.71 nM, respectively. However, only NSC116555 demonstrated cytotoxic effects against non–small-cell lung cancer, A549, shown in the cell cytotoxicity assay with an IC₅₀ of 0.19 + 0.01 µM, which was more potent than gefitinib. Furthermore, NSC116555 showed cytotoxicity against A549 via apoptosis in a dose-dependent manner.     

昆虫与植物关系的研究进展和前景

本文综述昆虫与植物之间关系的研究概况，包括历史渊源、昆虫选择寄主植物的生理机制，植物对虫害的反应、用抗虫基因在作物中移植以防治害虫和展望。着重叙述昆虫神经中枢对于植物理化特性所产生的感觉内导的综合作用，植物蒙受虫害后的补偿作用及由此诱导所产生的化学防御作用。讨论了以抗虫基因移植于农林作物来防治害虫是否会引起昆虫对这种新育成的植物产生适应或抗性。昆虫与植物之间的关系是一个重要的科研领域，对其发展前景     

Complete inhibition of in vivo glioma growth by oncostatin M

We describe here the oncostatin M (OSM)-dependent inhibition of in vivo tumour formation after intracerebral inoculation of glioblastoma cells in mice. We generated human glioblastoma cells transfected with the OSM gene under the control of a tetracycline-response promoter. Upon removal of tetracycline from the medium, cells exhibited a differentiated cell morphology, while proliferation was significantly inhibited. After implantation of these cells into nude mice brains, large tumours developed in animals lacking OSM expression, whereas no tumour formation was observed in mice with induced OSM expression. Our results suggest that OSM exerts pronounced antitumorigenic effects on glioblastoma cells in vivo and provide arguments for a therapeutic application of OSM in humans.     

Bile and bile salts and exsheathment of the intestinal nematodes Trichostrongylus colubriformis and Nematodirus battus

1972. Bile and bile salts and exsheathment of the intestinal nematodes Trichostrongylus colubriformis and Nematodirus battus. International Journal for Parasitology, 2: 433–438. Exsheathment of T. colubriformis was potentiated at physiological levels of CO₂ by bile and bile salts. Lamb bile and crude sodium taurocholate preparations produced the greatest increase in exsheathment while rabbit bile, sodium glycocholate and deoxycholate had less pronounced effects. Exsheathment in bile and taurocholate occurred at a pH above 4 and it is therefore suggested that infective larvae which fail to exsheath in the abomasum could well do so in the proximal part of the small intestine. Pure sodium taurocholate was found to greatly potentiate exsheathment of N. battus in vitro but this occurred at a pH below 3 and thus the action of this bile salt could not affect exsheathment in the host.     

鳜鱼口咽腔味蕾和行为反应特性及其对捕食习性的适应

用扫描电镜观察和行为学实验研究鳜鱼口咽腔味蕾形态和分布及吞食行为反应特性，结果表明，鳜鱼口咽腔味蕾丰富，几乎都是Ｉ型和Ⅱ型味蕾，着生于表皮乳突上，主要分布于上颌骨齿周围及内侧，下颌齿周围及外侧，舌前中区，下鳃骨细齿内侧等部位，其它区域分布较少，鳜鱼口咽腔味蕾对食物味道和软硬均非常敏感，鳜鱼仅吞食同时具有一定味道和软硬度的食物，本文探讨了鳜鱼口咽腔味蕾的结构功能关系及其对捕食习性的适应意义。