细菌中黄素单核苷酸核糖开关研究进展

核糖开关(Riboswitch)具有RNA结构,是位于mRNA 5′非编码区的RNA传感器。在无任何蛋白质因子参与下,可特异性地直接结合代谢产物,使自身构象发生相应变化,启动或阻断mRNA的转录、翻译、拼接等过程来调控基因的表达。某些Riboswitch可应用于抗菌药物研发。本文综述了Flavin mononucleotide riboswitch(FMN riboswitch)三维结构、基因表达调控的机制及热力学、动力学的研究进展,为基于FMN riboswitch的合理药物设计奠定了基础,并对开发新一代抗菌药物进行了展望。     

MST技术在生命科学中的应用进展

在生命科学领域中,生物分子间的相互作用具有非常重要的作用。通过分子间相互作用分析不仅可阐明细胞生物学事件,而且为疾病发生机制和药物发现提供基础。MST技术是一种基于检测在温度梯度中的生物分子电泳迁移率的变化而检测生物分子间结合、解离过程,获取分子间相互作用的模式和动力学常数等方面信息的新技术,是近年来发展的研究生物分子相互作用的强有力工具,已广泛应用于生命科学领域研究。本文综述了MST的技术原理、分析方法及其在生命科学领域的应用进展。     

核糖开关与基因表达调控

核糖开关(riboswitch)是近几年基因表达调控研究的一个热点.核糖开关位于mRNA的非翻译区(untranslated regions, UTR),能够直接感受胞内外信号并引起自身二级结构的变化,在转录或后转录（翻译和mRNA稳定性）水平实现对下游相关基因的表达调控,该过程不依赖于包括蛋白质在内的其它任何因子的作用. 根据现已发现的核糖开关所能识别的信号因子类型,可以将其分为4类,即小分子代谢物、金属离子、环境因素及空载tRNA敏感的核糖开关;其中,小分子代谢物敏感的核糖开关是发现和研究最多且最深入的一类. 随着研究的深入,将会有更多的核糖开关被发现,这不仅有助于理解生物进化与环境适应性,而且在生物学基础研究,新型药物的开发以及工业生产领域都将发挥重要作用.     

用模块化分子元件调控和编程生物系统

合成生物学的目标包括“通过合成来理解生命”以及用现代工程学方法设计合成复杂生物系统．其工程学目标的实现依赖于可集成、可调控、可重用、功能多样的蛋白质、RNA、DNA等基本分子元件．以分子机制为基础,合理设计与实验室进化相结合,改造和创建生物分子的相互作用特异性、调控方式、定量活性等,是实现生物系统人工调控与编程的重要策略,同时为自下而上设计合成日益复杂的人工生物系统奠定基础．     

促进或抑制α-synuclein蛋白异常聚集的相互作用蛋白质

α-synuclein蛋白的异常聚集在共核蛋白病的发病过程中起到了关键性作用。与α-synuclein相互作用的蛋白质对其异常聚集起着不同的调节作用,有的蛋白质(如:蛋白synphilin-1、微管蛋白、A-β肽等)会促进α-synuclein蛋白的异常聚集,而另外一些蛋白质(如:膜联蛋白A5、基于自识别元素设计的小肽等)却能够抑制α-synuclein蛋白的异常聚集。认识与α-synuclein相互作用的蛋白,并研究其作用位点,是从分子水平上理解α-synuclein蛋白质异常聚集、揭示共核蛋白病致病机制,以及设计新药物的基础。分子动力学模拟为开展这方面研究开辟了新的途径。文章对该领域的研究进展进行了综述。     

WRKY转录因子与植物逆境响应

WRKY转录因子是高等植物特有的一类转录调控因子,也是植物生命活动中不可或缺的调控枢纽。研究发现,WRKY转录因子参与植物生长发育过程及多种生物与非生物逆境响应。本文分析了WRKY转录因子的分类及结构,对其多种作用机制包括上游调控、下游调控、蛋白质相互作用等进行了归类,总结了近年来在各类植物上发现的WRKY转录因子调控植物生长发育和参与植物响应生物及非生物逆境的多重功能。并针对目前WRKY转录因子的研究所存在的问题,提出部分意见,为进一步挖掘WRKY家族的功能机制奠定了基础。     

中药网络药理学研究中的生物信息学方法

为了更有效地治疗癌症、心血管疾病、免疫系统疾病等复杂疾病,基于分子网络的多靶点药物发现理念逐渐成为一种新的趋势,而中药整体、辨证、协同的用药观再一次引起了药物发现领域的极大兴趣。中药在治疗复杂慢性疾病方面有确切的疗效和较小的毒副作用。中药网络药理学从分子网络调控的水平上阐明中药的作用机制,为多靶点药物发现提供有益的启示和借鉴,并有可能从临床有效的中药反向开发现代多组分、多靶点新药。针对基于生物分子网络的中药药理学研究路线中的4 个步骤,介绍近年来中药网络药理学研究中相关的生物信息学方法。     

磷烯纳米材料的生物毒性研究进展

磷烯,即单层黑磷（BP）,由于具有直接带隙、显著的结构和功能各向异性、高电荷载流子迁移率等,已经在生物医学、药物输送、生物传感、疾病的诊断和治疗等领域取得了很大的进展。和其他纳米材料相比,磷烯具有更优异的生物相容性和生物可降解性,在生物医药领域有很好的应用前景。虽然已有大量磷烯生物学效应的报道,但磷烯与生物大分子,如核酸、脂质、蛋白质之间相互作用的过程细节仍缺乏系统的研究。目前实验上无法观测磷烯与生物分子相互作用的动力学过程,分子模拟在获取精确动态结构方面具有独特的优势,被广泛应用于纳米材料和生物学领域。本文综述了近年来国内外利用计算机仿真和实验方法在磷烯纳米材料与蛋白质、脂质膜和DNA等生物大分子相互作用方面取得的最新研究进展,对磷烯生物毒性目前的研究进行了评述,并对未来需要解决的问题作了分析。本文将促进磷烯生物学效应的基础研究,也将推动磷烯纳米材料在生物医药领域的应用。     

基于蛋白质受体的药物分子计算机辅助设计策略

药物分子计算机辅助设计是一种在计算机或者理论上通过构建具有一定潜在药理活性的新化学实体的分子模拟方法。近十几年来,高通量组学技术的快速发展为生物和化学药物分子设计提供了良好的数据支撑和研究契机。另外,现代社会对生物制药合理性以及作用机理理解的要求越来越高,行业普遍要求药物需要有高效、无毒或者低毒以及靶向性强等特点。随着越来越多与药物靶点相关的蛋白质结构通过实验方法解析出来,基于蛋白质受体的药物分子设计方法可行性进一步提高,其方法也变得越来越重要。基于蛋白质受体的药物分子设计方法,一般是以蛋白质以及配体的三维结构出发进行分析,这让药物分子先导物的发现更加理性化。随着相关实验数据的积累以及深度学习等算法的发展,从而可以进行更加科学的药物分子设计,这在一定程度上加快了新药研发的进程,并更有利于探索相应的分子机理。本文对基于蛋白质受体的药物分子设计方法的常用策略进行系统的回顾、总结和展望。     

诱导多能干细胞技术在药物研发领域中的前景

由于基础研究环境和临床环境之间存在的转化差异,使得药物在临床阶段取得成功仍然具有挑战性。诱导多能干(iPS)细胞的诞生为药物研发领域带来了新的希望,使研究者能在体外人性化各种药理学和毒理学模型。人iPS衍生细胞的可获得性,特别是可以定向分化成特定的功能性细胞、组织和器官,一方面为疾病机制研究与细胞治疗提供了全新的途径。另一方面,转化研究中的生物标记物提供了评估临床前基础研究环境和临床环境下毒理学及药理学影响的可衡量的指标,而iPS细胞给生物标记物的研究带来了全新的思路。从转化研究的角度概述了基于iPS细胞药物发现的现行策略,阐明了iPS细胞的潜力以及生物标志物在药物发现和发展整个过程中的作用,突出在该领域有待改进的地方,以期为进一步相关性研究提供一定参考,为新药研发提供新的思路与方法。     

Comprehensive characterization of a theophylline riboswitch reveals two pivotal features of Shine-Dalgarno influencing activated translation property

Tuneable gene expression controlled by synthetic biological elements is of great importance to biotechnology and synthetic biology. The synthetic riboswitch is a pivotal type of elements that can easily control the heterologous gene expression in diverse bacteria. In this study, the theophylline-dependent synthetic riboswitch and the corresponding variants with varied spacings between Shine-Dalgarno (SD) sequence and start codon were employed to comprehensively characterize the induction and regulation properties through combining a strong promoter aprE in Bacillus subtilis. Amongst the sets of newly constructed expression elements, the expression element with 9-bp spacing exhibited the higher expression level, a superior induction fold performance, and a considerably lower leaky expression than those with longer or shorter spacings. The riboswitch expression element with 9-bp spacing showed an approximately linear dose dependence from 0 to 8 mM of theophylline. Modification of the SD sequence through the insertion of a single A base prior to the native sequence enables the increase of the expression level post induction while decreasing the induction fold as a result of the elevated leaky level. The riboswitch elements with the engineered SD and the optimal 9-bp spacing exhibit an altered dose dependency in which the approximately linear range shifts to 0–4 mM, although it has a similar profile to the induction process. These results not only provide comprehensive data for the induced expression by a theophylline riboswitch combined with a strong native promoter from B. subtilis but also provide the two pivotal features of SD essential to the modular design of other synthetic riboswitches.

     

Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.     

Conformational capture of the SAM-II riboswitch

Riboswitches are gene regulation elements in mRNA that function by specifically responding to metabolites. Although the metabolite-bound states of riboswitches have proven amenable to structure determination efforts, knowledge of the structural features of riboswitches in their ligand-free forms and their ligand-response mechanisms giving rise to regulatory control is lacking. Here we explore the ligand-induced folding process of the S-adenosylmethionine type II (SAM-II) riboswitch using chemical and biophysical methods, including NMR and fluorescence spectroscopy, and single-molecule fluorescence imaging. The data reveal that the unliganded SAM-II riboswitch is dynamic in nature, in that its stem-loop element becomes engaged in a pseudoknot fold through base-pairing with nucleosides in the 3' overhang containing the Shine-Dalgarno sequence. Although the pseudoknot structure is highly transient in the absence of its ligand, S-adenosylmethionine (SAM), it becomes conformationally restrained upon ligand recognition, through a conformational capture mechanism. These insights provide a molecular understanding of riboswitch dynamics that shed new light on the mechanism of riboswitch-mediated translational regulation.     

Recent advances in natural products exploitation in Streptomyces via synthetic biology

Natural products of microbial origin have proven to be the wellspring of clinically useful compounds for human therapeutics. Streptomyces species are predominant sources of bioactive compounds, most of which serve as potential drug candidates. While the exploitation of natural products has been severely reduced over the past two decades, the growing crisis of evolution and dissemination of drug resistant pathogens have again attracted great interest in this field. The emerging synthetic biology has been heralded as a new bioengineering platform to discover novel bioactive compounds and expand bioactive natural products diversity and production. Herein, we review recent advances in the natural products exploitation of Streptomyces with the applications of synthetic biology from three major aspects, including recently developed synthetic biology tools, natural products biosynthetic pathway engineering strategies as well as chassis host modifications.     

Enzymatic Probing Analysis of an Engineered Riboswitch Reveals Multiple off Conformations

We investigated the gene regulatory mechanism of a previously engineered riboswitch +thiMN₁₅#19 that turns on gene expression in response to thiamine pyrophosphate (TPP). In vitro enzymatic probing was performed to identify the secondary structures of the OFF conformations predicted by Mfold. Interestingly, enzymatic probing data of the riboswitch and its variants indicated that the riboswitch in its OFF state adopts two distinct structures. Moreover, further in vivo experiments suggested that both OFF structures contribute to the riboswitch function. A deeper understanding of how riboswitches function at the molecular level should enhance our ability to design synthetic riboswitches with new or improved characteristics.     

拟孢囊菌属放线菌的研究进展

拟孢囊菌属(Kibdelosporangium)是一个经典的丝状放线菌类群。自Shearer等于1986年建立该属以来,不断有新的菌株从不同生境中被纯培养分离得到,目前已有效发表8个种、2个亚种。拟孢囊菌属作为稀有放线菌属,是获得新型抗生素类次生代谢产物的重要资源。本文结合我们分离到的一株该属菌株的功能研究、基因组分析和相关文献资料,系统综述了拟孢囊菌属放线菌的建立、分类学特征、属内种的分布、活性次级代谢产物的发现以及其他功能应用和开发前景,以期为该属其他新分离菌株的分类鉴定、新颖次级代谢产物的发现、功能基因资源的挖掘与开发提供借鉴。     

The rose and the name: the unresolved debate on biotechnological terms

The largest survey on the perception of synthetic biology-related disciplines (Porcar et al., 2019,EMBO Rep 20) recently revealed that the Spanish society does not have a very positive perception of the term synthetic biology. On the other hand, the terms biotechnology and even genetic engineering received relatively higher scores. The issue of nomenclature and perception is a classical one in science perception studies. Synthetic biologists have been debating their neologism (Synthetic Biology, from now on SB) for years. Even in a 2006 blog, Rob Carlson discussed the various labels for the new field, such as intentional biology, constructive biology, natural engineering, synthetic genomics and biological engineering. This diversity of names, along with the above mentioned negative public perception of the term synthetic biology, raises the question on whether the term itself is suitable or whether it could, in an extreme scenario, be replaced by another combining scientific consensus with public acceptance.     

Molecular diversity--the toolbox for synthetic gene switches and networks

The rapid development of synthetic biology is a paradigm of how the molecular diversity of naturally occurring gene control components can be used to design synthetic control devices and gene networks that provide precisely programmed transgene expression dynamics in space and time. Here we offer an overview on recent advances in the modular design of trigger-inducible mammalian expression devices that are either responsive by exogenous stimuli such as chemicals and physical cues or controlled by endogenous metabolites driving prosthetic circuits to treat metabolic disorders in a self-sufficient manner. Compatible genetic switches can also be assembled to synthetic gene networks that show highly complex expression dynamics such as temporally resolved band-detect functions or oscillating transgene expression profiles. The ongoing metagenomic discovery and characterization of the unexplored sequence space is constantly increasing the molecular diversity in fundamental control components that fuels the further development of synthetic biology.