Sequence Elements Distal to the Ligand Binding Pocket Modulate the Efficiency of a Synthetic Riboswitch

Synthetic riboswitches can serve as sophisticated genetic control devices in synthetic biology, regulating gene expression through direct RNA–ligand interactions. We analyzed a synthetic neomycin riboswitch, which folds into a stem loop structure with an internal loop important for ligand binding and regulation. It is closed by a terminal hexaloop containing a U‐turn and a looped‐out adenine. We investigated the relationship between sequence, structure, and biological activity in the terminal loop by saturating mutagenesis, ITC, and NMR. Mutants corresponding to the canonical U‐turn fold retained biological activity. An improvement of stacking interactions in the U‐turn led to an RNA element with slightly enhanced regulatory activity. For the first position of the U‐turn motif and the looped out base, sequence–activity relationships that could not initially be explained on the basis of the structure of the aptamer–ligand complex were observed. However, NMR studies of these mutants revealed subtle relationships between structure and dynamics of the aptamer in its free or bound state and biological activity.     

Phosphate-group recognition by the aptamer domain of the thiamine pyrophosphate sensing riboswitch

Riboswitches are highly structured RNA elements that control gene expression by binding directly to small metabolite molecules. Remarkably, many of these metabolites contain negatively charged phosphate groups that contribute significantly to the binding affinity. An example is the thiamine pyrophosphate-sensing riboswitch in the 5'-untranslated region of the E. coli thiM mRNA. This riboswitch binds, in order of decreasing affinity, to thiamine pyrophosphate (TPP), thiamine monophosphate (TMP), and thiamine, which contain two, one, and no phosphate groups, respectively. We examined the binding of TPP and TMP to this riboswitch by using (31)P NMR spectroscopy. Chemical-shift changes were observed for the alpha- and beta-phosphate group of TPP and the phosphate group of TMP upon RNA binding; this indicates that they are in close contact with the RNA. Titration experiments with paramagnetic Mn(2+) ions revealed strong line-broadening effects for both (31)P signals of the bound TPP; this indicates a Mg(2+) binding site in close proximity and suggests that the phosphate group(s) of the ligand is/are recognized in a magnesium ion-mediated manner by the RNA.     

牛种布鲁菌VirB12蛋白的原核表达及纯化

目的原核表达并纯化牛种布鲁菌(Brucella)VirB12蛋白。方法利用PCR法从牛种布鲁菌基因组中扩增VirB12基因,插入pET-30a(+)载体,构建重组表达质粒pETV12,转化大肠埃希菌BL21(DE3),IPTG诱导表达。表达的重组蛋白经组氨酸结合树脂柱纯化后,进行SDS-PAGE及Western blot分析。结果重组表达质粒pETV12经双酶切及测序证明构建正确;表达的重组蛋白相对分子质量约22 000,纯化的重组蛋白纯度达94%,可被布鲁菌免疫兔血清特异性识别。结论原核表达并纯化了牛种布鲁菌VirB12蛋白,为进一步研究VirB12蛋白的结构、功能及相关疫苗的研制奠定了基础。     

Lactobacillus diolivorans二醇脱水酶的分离纯化与酶学性质

引 言 1,3-丙二醇(1,3-propanediol, 1,3-PD)是一种重要的化工和医药中间体原料,是良好的溶剂、抗冻剂或保护剂,是聚酯--聚对苯二甲酸丙二醇酯(PTT)和聚氨酯的单体,可在地毯、纺织、工程塑料等领域中广泛应用,也可用于食品、化妆品和制药等行业食品.当前化工合成是生产1,3-丙二醇的主要方法,但需要在高温和昂贵催化剂作用下进行,并有多种副产物产生,产品分离困难,生产成本高,产生的废气对环境污染大.生物法较化学合成法具有条件温和、操作简便、副产物少、无环境污染等特点,因此如何用微生物发酵法低成本低污染地制备1,3-丙二醇已经成为各国研发者感兴趣的课题.     

Intracellular Light‐Activation of Riboswitch Activity

By combining a riboswitch with a cell‐permeable photocaged small‐molecule ligand, an optochemical gene control element was constructed that enabled spatial and temporal control of gene expression in bacterial cells. The simplicity of this strategy, coupled with the ability to create synthetic riboswitches with tailored ligand specificities and output in a variety of microorganisms, plants, and fungi might afford a general strategy to photocontrol gene expression in vivo. The ability to activate riboswitches by using light enables the interrogation and manipulation of a wide range of biological processes with high precision, and will have broad utility in the regulation of artificial genetic circuits.     

The Puzzle of RNAs that Target Gene Promoters

Setting the right target : Most researchers who use small RNAs in mammalian cells assume that mRNA will be the target. Recent studies suggest that small RNAs can also target chromosomal DNA.

     

Mechanism‐Guided Library Design and Dual Genetic Selection of Synthetic OFF Riboswitches

After the recent discovery of bacterial riboswitches, synthetic riboswitches have been engineered by using natural and artificial RNA aptamers. In contrast to natural riboswitches, the majority of synthetic riboswitches in bacteria reported to date are ON switches that activate gene expression in response to the aptamer ligand. In this study, we adopted a mechanism‐guided approach to design libraries predisposed to contain OFF riboswitches that respond to thiamine pyrophosphate (TPP). The first library design exploited a pseudo‐Shine‐Dalgarno (SD) sequence located near the 3′‐end of the TPP aptamer, which would be less accessible to the ribosome when the aptamer is bound to TPP. In the second library, an SD sequence was strategically placed in the aptamer's P1 stem, which is stabilized upon ligand binding. OFF riboswitches were obtained by dual genetic selection of these libraries. The results underscore the importance of effective library design to achieve desired riboswitch functions.     

Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds

RNA interference is triggered by small hairpin precursors that are processed by the endonuclease dicer to yield active species such as siRNAs and miRNAs. To regulate the RNAi-mediated suppression of gene expression, we imagined a strategy that relies on the sequence-specific inhibition of shRNA precursor processing by immediate RNA-small molecule interactions. Here, we present a first step in this direction by augmenting shRNAs with guanosine-rich sequences that are prone to fold into four-stranded structures. The addition of small molecules that selectively bind to such quadruplex sequences should allow for the specific inhibition of dicing of shRNAs that contain suitable G-rich elements. In an attempt to find compounds that protect against dicer processing, we have examined the effects of quadruplex-binding compounds on the dicer processing of shRNAs containing G-quadruplexes. Although a variety of small molecules that are known to bind to quadruplexes inhibited in vitro dicing of shRNAs, only two substance classes, namely certain porphyrazines and bisquinolinium compounds, showed selective inhibition of G-rich shRNAs compared to control sequences lacking guanine-rich elements. The G-rich shRNAs displayed a potent knockdown of gene expression in mammalian cell culture, but the effect was not influenced by addition of the respective quadruplex-binding compounds.