Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3)

RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.     

复合诱变原生质体选育耐热碱性蛋白酶高产菌

以地衣芽孢杆菌(Bacillus licheniformis)53号为原始菌株,在原生质体形成和再生的最佳条件下制备原生质体,对原生质体进行复合诱变,对大量再生突变株进行筛选,最终获得了高产、稳定、耐热的碱性蛋白酶产生菌53-G38-6,产酶活力由1104U/ml提高到22080U/ml。适宜的发酵条件:培养基(％)胰蛋白胨1,酵母膏0.5,玉米粉5,Na_2HP0_4·12H_20 0.4,KH_2P0_4 0.03,Na_2CO_3 0.1,自然pH。42℃旋转培养44～48h,得到的蛋白酶热稳定性强,60℃处理1h剩余酶活55％。酶反应最适条件:62℃,pH10.0,在pH9～10.5范围内稳定。     

光合自养缺陷型小球藻的筛选及生物能源应用

小球藻Chlorella protothecoides(C.protothecoides)是潜在的、可用于工业生产生物柴油的高产油微藻.本研究通过体外诱变的手段,获得了一株完全不能进行光合自养生长的突变体Al64.利用尼罗红染色和叶绿素自发荧光分析和电子显微镜分析细胞的亚显微结构,结果显示该突变体中叶绿体严重退化,其中类囊体膜结构缺失,导致该突变体缺乏叶绿素,无法进行光合自养生长.在富糖富氮的培养条件下,该光合自养缺陷型突变体的细胞密度和油脂含量比野生型细胞分别高5.54%和6.76%,分析还发现,该突变体产油能力为0.158 g L?1 h?1,比野生型提高12.8%.本文通过缺失光合作用突变体的构建,在异养高氮条件下实现了生物量及细胞内油脂含量的同步提高,为进一步提高微藻生产生物柴油的产量提供了新的研究平台.     

Nucleoside Modification and Concerted Mutagenesis of the Human A3 Adenosine Receptor to Probe Interactions Between the 2-Position of Adenosine Analogs and Gln167 in the Second Extracellular Loop

Residues of the second extracellular loop are believed to be important for ligand recognition in adenosine receptors. Molecular modeling studies have suggested that one such residue, Gln ¹⁶⁷ of the human A ³ receptor, is in proximity to the C2 moiety of some adenosine analogs when bound. Here this putative interaction was systematically explored using a neoceptor strategy, i.e., by site-directed mutagenesis and examination of the affinities of nucleosides modified to have complementary functionality. Gln ¹⁶⁷ was mutated to Ala, Glu, and Arg, while the 2-position of several adenosine analogs was substituted with amine or carboxylic acid groups. All compounds tested lost affinity to the mutant receptors in comparison to the wild type. However, comparing affinities among the mutant receptors, several compounds bearing charge at the 2-position demonstrated preferential affinity for the mutant receptor bearing a residue of complementary charge. 13, with a positively-charged C2 moiety, displayed an 8.5-fold increase in affinity at the Q167E mutant receptor versus the Q167R mutant receptor. Preferential affinity for specific mutant receptors was also observed for 8 and 12. The data suggests that a direct contact is made between the C2 substituent of some charged ligands and the mutant receptor bearing the opposite charge at position 167.     

原生质体诱变选育高产异抗坏血酸菌株

以灰黄青霉菌(Penicillium griseofulvum HL)为出发菌株,试验得到灰黄青霉原生质体制备的优化条件为:菌体培养48h,用0.7mol/L的NaC1溶液作为渗透压稳定剂,用0.5％的蜗牛酶+0.5％的纤维素酶,在pH为6,30℃条件下酶解3h,所得原生质体数最多,达到3.14×107/ml.原生质体再生的最佳条件为采用双层平板培养法,在用0.7mol/L的蔗糖溶液配制的改进察氏培养基上其再生率最高,达到24.93％.灰黄青霉原生质体经过紫外线诱变,DES诱变,紫外线-DES诱变复合诱变,紫外线-氯化锂复合诱变选育异抗坏血酸高产菌株,通过对再生平板上长出的诱变菌株进行初筛和摇瓶复筛,最终获得一株异抗坏血酸产量较高的菌株ZD4,其产量为5.28mg/ml,提高到出发菌株产量(1.08 mg/ml)的488.9％,且连续传代6代遗传稳定.     

Human Pol ɛ-dependent replication errors and the influence of mismatch repair on their correction

Mutations in human DNA polymerase (Pol) ?, one of three eukaryotic Pols required for DNA replication, have recently been found associated with an ultramutator phenotype in tumors from somatic colorectal and endometrial cancers and in a familial colorectal cancer. Possibly, Pol ? mutations reduce the accuracy of DNA synthesis, thereby increasing the mutational burden and contributing to tumor development. To test this possibility in vivo, we characterized an active site mutant allele of human Pol ? that exhibits a strong mutator phenotype in vitro when the proofreading exonuclease activity of the enzyme is inactive. This mutant has a strong bias toward mispairs opposite template pyrimidine bases, particularly T•dTTP mispairs. Expression of mutant Pol ? in human cells lacking functional mismatch repair caused an increase in mutation rate primarily due to T•dTTP mispairs. Functional mismatch repair eliminated the increased mutagenesis. The results indicate that the mutant Pol ? causes replication errors in vivo, and is at least partially dominant over the endogenous, wild type Pol ?. Since tumors from familial and somatic colorectal patients arise with Pol ? mutations in a single allele, are microsatellite stable and have a large increase in base pair substitutions, our data are consistent with a Pol ? mutation requiring additional factors to promote tumor development.     

Improvement of antagonism and carbendazim tolerance in native Trichoderma isolates through ethyl methane sulfonate (EMS) mutagenesis

Genetic enhancement of TCT₄ and TCT₁₀ was aimed in the present paper. Trichoderma reesei (TCT₁₀/M₁₈) mutant isolate evolved by ethyl methane sulfonate mutations was found to exhibit altered properties compared to its parent isolates. This mutant grew well in the potato dextrose agar (PDA) medium containing carbendazim (50 ppm). RAPD-PCR results suggested the uniqueness of mutants, which was useful in differentiating mutant and wild Trichoderma isolates. These mutants established well in the rhizosphere of rough lemon seedlings. The seedlings treated with carbendazim followed by an application of carbendazim-resistant mutant (TCT₁₀/M₁₈) resulted in a better seedling emergence and a less dry root rot disease caused by Fusarium solani in nursery conditions.     

Recombinase-mediated cassette exchange (RMCE) — A rapidly-expanding toolbox for targeted genomic modifications

Starting in 1991, the advance of Tyr-recombinases Flp and Cre enabled superior strategies for the predictable insertion of transgenes into compatible target sites of mammalian cells. Early approaches suffered from the reversibility of integration routes and the fact that co-introduction of prokaryotic vector parts triggered uncontrolled heterochromatization. Shortcomings of this kind were overcome when Flp-Recombinase Mediated Cassette Exchange entered the field in 1994. RMCE enables enhanced tag-and-exchange strategies by precisely replacing a genomic target cassette by a compatible donor construct. After “gene swapping” the donor cassette is safely locked in, but can nevertheless be re-mobilized in case other compatible donor cassettes are provided (“serial RMCE”). These features considerably expand the options for systematic, stepwise genome modifications. The first decade was dominated by the systematic generation of cell lines for biotechnological purposes. Based on the reproducible expression capacity of the resulting strains, a comprehensive toolbox emerged to serve a multitude of purposes, which constitute the first part of this review. The concept per se did not, however, provide access to high-producer strains able to outcompete industrial multiple-copy cell lines. This fact gave rise to systematic improvements, among these certain accumulative site-specific integration pathways. The exceptional value of RMCE emerged after its entry into the stem cell field, where it started to contribute to the generation of induced pluripotent stem (iPS-) cells and their subsequent differentiation yielding a variety of cell types for diagnostic and therapeutic purposes. This topic firmly relies on the strategies developed in the first decade and can be seen as the major ambition of the present article. In this context an unanticipated, potent property of serial Flp-RMCE setups concerns the potential to re-open loci that have served to establish the iPS status before the site underwent the obligatory silencing process. Other relevant options relate to the introduction of composite Flp-recognition target sites (“heterospecific FRT-doublets”), into the LTRs of lentiviral vectors. These “twin sites” enhance the safety of iPS re-programming and -differentiation as they enable the subsequent quantitative excision of a transgene, leaving behind a single “FRT-twin”. Such a strategy combines the established expression potential of the common retro- and lentiviral systems with options to terminate the process at will. The remaining genomic tag serves to identify and characterize the insertion site with the goal to identify genomic “safe harbors” (GOIs) for re-use. This is enabled by the capacity of “FRT-twins” to accommodate any incoming RMCE-donor cassette with a compatible design.     

Molecular Basis of Cannabinoid CB1 Receptor Coupling to the G Protein Heterotrimer Gαiβγ: IDENTIFICATION OF KEY CB1 CONTACTS WITH THE C-TERMINAL HELIX α5 OF Gαi*

The cannabinoid (CB1) receptor is a member of the rhodopsin-like G protein-coupled receptor superfamily. The human CB1 receptor, which is among the most expressed receptors in the brain, has been implicated in several disease states, including drug addiction, anxiety, depression, obesity, and chronic pain. Different classes of CB1 agonists evoke signaling pathways through the activation of specific subtypes of G proteins. The molecular basis of CB1 receptor coupling to its cognate G protein is unknown. As a first step toward understanding CB1 receptor-mediated G protein signaling, we have constructed a ternary complex structural model of the CB1 receptor and G_i heterotrimer (CB1-G_i), guided by the x-ray structure of β₂-adrenergic receptor (β₂AR) in complex with G_s (β₂AR-G_s), through 824-ns duration molecular dynamics simulations in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer environment. We identified a group of residues at the juxtamembrane regions of the intracellular loops 2 and 3 (IC2 and IC3) of the CB1 receptor, including Ile-218^3.54, Tyr-224^IC2, Asp-338^6.30, Arg-340^6.32, Leu-341^6.33, and Thr-344^6.36, as potential key contacts with the extreme C-terminal helix α₅ of Gα_i. Ala mutations of these residues at the receptor-G_i interface resulted in little G protein coupling activity, consistent with the present model of the CB1-G_i complex, which suggests tight interactions between CB1 and the extreme C-terminal helix α₅ of Gα_i. The model also suggests that unique conformational changes in the extreme C-terminal helix α₅ of Gα play a crucial role in the receptor-mediated G protein activation.