摘要：The eukaryotic genome is packaged into a complex nucleoprotein structure named chromatin, balancing the compactness of genome and the accessibility of regulatory proteins and RNA polymerases to DNA. The mechanisms of the regulation of chromatin dynamics include the post-translational modification of histones, alteration of nucleosome positions by chromatin remodelers, replacement of canonical histones by histone variants with the aid of histone chaperones, and dynamic organization of the three-dimensional genome in the small nucleus. Histone variants are different from canonical histones by substitution of several amino acid residues or changes in amino acid sequence. Histone variants perform specialized functions such as altering nucleosome stability, dynamics, structure, as well as playing critical roles in a range of biological processes like transcriptional regulation, DNA repair and recombination, development and immune responses. Here we discuss how histone variants, their modification and specific loading to chromatin are involved in transcriptional regulation, DNA repair and plant development.

摘要：The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system.

摘要：The cis-acting regulatory elements, e.g., promoters and ribosome binding sites （RBSs） with various desired properties, are building blocks widely used in synthetic biology for fine tuning gene expression. In the last decade, acquisition of a controllable regulatory element from a random library has been established and applied to control the protein expression and metabolic flux in different chassis cells. However, more rational strategies are still urgently needed to improve the efficiency and reduce the laborious screening and multifaceted characterizations. Building precise computational models that can predict the activity of regulatory elements and quantitatively design elements with desired strength have been demonstrated tremendous potentiality. Here, recent progress on construction of cis- acting regulatory element library and the quantitative predicting models for design of such elements are reviewed and discussed in detail.

摘要：Overproduction of small-molecule chemicals using engineered microbial cells has greatly reduced the production cost and promoted environmental protection. Notably, the rapid and sensitive evaluation of the in vivo concentrations of the desired products greatly facilitates the optimization process of cell factories. For this purpose, many genetic components have been adapted into in vivo biosensors of small molecules, which couple the intracel- lular concentrations of small molecules to easily detectable readouts such as fluorescence, absorbance, and cell growth. Such biosensors allow a high-throughput screen- ing of the small-molecule products, and can be roughly classified as protein-based and RNA-based biosensors. This review summarizes the recent developments in the design and applications of biosensors for small-molecule products.

摘要：Ginsenosides, the main pharmacologically active natural compounds in ginseng （Panax ginseng）, are mostly the glycosylated products of protopanaxadiol （PPD） and protopanaxatriol （PPT）. No uridine diphosphate glycosyltransferase （UGT）, which catalyzes PPT to produce PPT-type ginsenosides, has yet been reported. Here, we show that UGTPgl, which has been demonstrated to regio-specifically glycosylate the C20-OH of PPD, also specifically glycosylates the C20-OH of PPT to produce bioactive ginsenoside FI. We report the characterization of four novel UGT genes isolated from P. ginseng, sharing high deduced amino acid identity （〉84%） with UGTPgl. We demonstrate that UGTPgl00 specifically glycosylates the C6-OH of PPT to produce bioactive ginsenoside Rhl, and UGTPgl01 catalyzes PPT to produce F1, followed by the generation of ginsenoside Rgl from FI. However, UGTPgl02 and UGTPgl03 were found to have no detectable activity on PPT. Through structural modeling and site-directed mutagenesis, we identified several key amino acids of these UGTs that may play important roles in determining their activities and substrate regio-specificities. Moreover, we constructed yeast recombinants to biosynthesize F1 and Rhl by introducing the genetically engineered PPT-producing pathway and UGTPgl or UGTPgl00. Our study reveals the possible biosynthetic pathways of PPT-type ginsenosides in Panax plants, and provides a sound manufacturing approach for bioactive PPT-type ginsenosides in yeast via synthetic biology strategies.

摘要：The emerging plant synthetic metabolic engineering has been exhibiting great promise to produce either value-added metabolitesor therapeutic proteins. However, promoters for plant pathway engineering are generally selected empirically. The quantitativecharacterization of plant-based promoters is essential for optimal control of gene expression in plant chassis. Here, we used *** leaves and BY2 suspension cells to quantitatively characterize a library of plant promoters by transient expressionof firefly/Renilla luciferase. We validated the dual-luciferase reporter system by examining the correlation between reporterprotein and mRNA levels. In addition, we investigated the effects of terminator–promoter combinations on gene expressionand found that the combinations of promoters and terminators resulted in a 326-fold difference between the strongest andweakest performance, as reflected in reporter gene expression. As a proof of concept, we used the quantitatively characterizedpromoters to engineer the betalain pathway in N. benthamiana. Seven selected plant promoters with different expressionstrengths were used orthogonally to express CYP76AD1 and DODA, resulting in a final betalain production range of 6.0–362.4 μg/g fresh weight. Our systematic approach not only demonstrates the various intensities of multiple promoter sequencesin N. benthamiana and BY2 cells but also adds to the toolbox of plant promoters for plant engineering.