Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference

The CRISPR-Cas prokaryotic ‘adaptive immune systems’ represent a sophisticated defence strategy providing bacteria and archaea with protection from invading genetic elements, such as bacteriophages or plasmids. Despite intensive research into their mechanism and application, how CRISPR-Cas systems are regulated is less clear, and nothing is known about the regulation of Type I-F systems. We used Pectobacterium atrosepticum, a Gram-negative phytopathogen, to study CRISPR-Cas regulation, since it contains a single Type I-F system. The CRP-cAMP complex activated the cas operon, increasing the expression of the adaptation genes cas1 and cas2–3 in addition to the genes encoding the Csy surveillance complex. Mutation of crp or cyaA (encoding adenylate cyclase) resulted in reductions in both primed spacer acquisition and interference. Furthermore, we identified a galactose mutarotase, GalM, which reduced cas operon expression in a CRP- and CyaA-dependent manner. We propose that the Type I-F system senses metabolic changes, such as sugar availability, and regulates cas genes to initiate an appropriate defence response. Indeed, elevated glucose levels reduced cas expression in a CRP- and CyaA-dependent manner. Taken together, these findings highlight that a metabolite-sensing regulatory pathway controls expression of the Type I-F CRISPR-Cas system to modulate levels of adaptation and interference.     

Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system

CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.     

Structural and mechanistic insights into the inhibition of type I-F CRISPR-Cas system by anti-CRISPR protein AcrIF23

Prokaryotes evolved clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins as a kind of adaptive immune defense against mobile genetic elements including harmful phages. To counteract this defense, many mobile genetic elements in turn encode anti-CRISPR proteins (Acrs) to inactivate the CRISPR-Cas system. While multiple mechanisms of Acrs have been uncovered, it remains unknown whether other mechanisms are utilized by uncharacterized Acrs. Here, we report a novel mechanism adopted by recently identified AcrIF23. We show that AcrIF23 interacts with the Cas2/3 helicase-nuclease in the type I-F CRISPR-Cas system, similar to AcrIF3. The structure of AcrIF23 demonstrated a novel fold and structure-based mutagenesis identified a surface region of AcrIF23 involved in both Cas2/3-binding and its inhibition capacity. Unlike AcrIF3, however, we found AcrIF23 only potently inhibits the DNA cleavage activity of Cas2/3 but does not hinder the recruitment of Cas2/3 to the CRISPR RNA-guided surveillance complex (the Csy complex). Also, in contrast to AcrIF3 which hinders substrate DNA recognition by Cas2/3, we show AcrIF23 promotes DNA binding to Cas2/3. Taken together, our study identifies a novel anti-CRISPR mechanism used by AcrIF23 and highlights the diverse mechanisms adopted by Acrs.     

Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis

CRISPR–Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as adaptation in the field. Some CRISPR–Cas systems rely on Cas1 and Cas2 to complete the adaptation process, which has been characterized in a few systems. In contrast, many other CRISPR–Cas systems require an additional factor of Cas4 for efficient adaptation, the mechanism of which remains less understood. Here we present biochemical reconstitution of the Synechocystis sp. PCC6803 type I-D adaptation system, X-ray crystal structures of Cas1–Cas2–prespacer complexes, and negative stained electron microscopy structure of the Cas4–Cas1 complex. Cas4 and Cas2 compete with each other to interact with Cas1. In the absence of prespacer, Cas4 but not Cas2 assembles with Cas1 into a very stable complex for processing the prespacer. Strikingly, the Cas1-prespacer complex develops a higher binding affinity toward Cas2 to form the Cas1–Cas2–prespacer ternary complex for integration. Together, we show a two-step sequential assembly mechanism for the type I-D adaptation module of Synechocystis, in which Cas4–Cas1 and Cas1–Cas2 function as two exclusive complexes for prespacer processing, capture, and integration.     

CRISPR-Cas系统调控细菌生理功能的机制研究进展

CRISPR-Cas系统是存在于部分细菌和绝大部分古细菌中的一种获得性免疫防御系统,使细菌在外源性基因入侵时具有免疫防御能力。此外,CRISPR-Cas系统对细菌自身生物膜的形成、耐药性、毒力等生理功能都有调控作用,这对于研究人员进行相关研究有着重要意义。本文以细菌CRISPR-Cas系统及其发挥免疫防御作用的相关研究为基础展开论述,重点阐述该系统对细菌生理功能的调控作用,并对其应用前景进行了展望,以期为进一步研究细菌耐药性和致病性提供新思路。     

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.     

利用内源CRISPR-Cas系统开展乳酸菌基因编辑的研究进展北大核心CSCD

CRISPR-Cas9技术是一种高效、精准的基因编辑工具,该技术的建立推动基因组编辑进入快速发展阶段。目前应用最广泛的Cas9蛋白是来源于酿脓链球菌(Streptococcuspyogenes)的SpyCas9,该蛋白作为“基因剪刀”在哺乳动物、植物等真核生物中应用较为广泛且成熟,但是该蛋白在一些乳酸菌中的应用仍然受到多种因素的限制。乳酸菌基因组上已发现多种类型的CRISPR系统,也蕴含着多种未表征的Cas蛋白,利用乳酸菌内源CRISPR-Cas系统,结合外源导入的向导RNA和同源修复模板,也可实现对乳酸菌基因组的编辑。这种基于内源CRISPR-Cas系统实现基因编辑的方式,具有打靶载体相对较小易转化、无外源Cas9蛋白对宿主细胞产生毒性等优势,相比于CRISPR-SpyCas9更适合于乳酸菌基因组进行编辑,可能是一些乳酸菌未来开展基因组编辑的主要手段,本文重点对此部分内容进行了综述。     

A new angle on clinging in geckos: incline,not substrate,triggers the deployment of the adhesive system

Lizards commonly climb in complex three-dimensional habitats, and gekkotans are particularly adept at doing this by using an intricate adhesive system involving setae on the ventral surface of their digits. However, it is not clear whether geckos always deploy their adhesive system, given that doing so may result in decreased (i.e. reduction in speed) locomotor performance. Here, we investigate circumstances under which the adhesive apparatus of clinging geckos becomes operative, and examine the potential trade-offs between speed and clinging. We quantify locomotor kinematics of a gecko with adhesive capabilities (Tarentola mauritanica) and one without (Eublepharis macularius). Whereas, somewhat unusually, E. macularius did not suffer a decrease in locomotor performance with an increase in incline, T. mauritanica exhibited a significant decrease in speed between the level and a 10° incline. We demonstrate that this results from the combined influence of slope and the deployment of the adhesive system. All individuals kept their digits hyperextended on the level, but three of the six individuals deployed their adhesive system on the 10° incline, and they exhibited the greatest decrease in velocity. The deployment of the adhesive system was dependent on incline, not surface texture (600 grit sandpaper and Plexiglas), despite slippage occurring on the level Plexiglas substrate. Our results highlight the type of sensory feedback (gravity) necessary for deployment of the adhesive system, and the trade-offs associated with adhesion.     

Protein zero, a nervous system adhesion molecule, triggers epithelial reversion in host carcinoma cells

Protein zero (P(o)) is the immunoglobulin gene superfamily glycoprotein that mediates the self-adhesion of the Schwann cell plasma membrane that yields compact myelin. HeLa is a poorly differentiated carcinoma cell line that has lost characteristic morphological features of the cervical epithelium from which it originated. Normally, HeLa cells are not self-adherent. However, when P(o) is artificially expressed in this line, cells rapidly aggregate, and P(o) concentrates specifically at cell-cell contact sites. Rows of desmosomes are generated at these interfaces, the plasma membrane localization of cingulin and ZO-1, proteins that have been shown to be associated with tight junctions, is substantially increased, and cytokeratins coalesce into a cohesive intracellular network. Immunofluorescence patterns for the adherens junction proteins N-cadherin, alpha-catenin, and vinculin, and the desmosomal polypeptides desmoplakin, desmocollin, and desmoglein, are also markedly enhanced at the cell surface. Our data demonstrate that obligatory cell-cell adhesion, which in this case is initially brought about by the homophilic association of P(o) molecules across the intercellular cleft, triggers pronounced augmentation of the normally sluggish or sub-basal cell adhesion program in HeLa cells, culminating in suppression of the transformed state and reversion of the monolayer to an epithelioid phenotype. Furthermore, this response is apparently accompanied by an increase in mRNA and protein levels for desmoplakin and N-cadherin which are normally associated with epithelial junctions. Our conclusions are supported by analyses of ten proteins we examined immunochemically (P(o), cingulin, ZO-1, desmoplakin, desmoglein, desmocollin, N-cadherin, alpha-catenin, vinculin, and cytokeratin-18), and by quantitative polymerase chain reactions to measure relative amounts of desmoplakin and N-cadherin mRNAs. P(o) has no known signaling properties; the dramatic phenotypic changes we observed are highly likely to have developed in direct response to P(o)-induced cell adhesion. More generally, the ability of this "foreign" membrane adhesion protein to stimulate desmosome and adherens junction formation by augmenting well-studied cadherin-based adhesion mechanisms raises the possibility that perhaps any bona fide cell adhesion molecule, when functionally expressed, can engage common intracellular pathways and trigger reversion of a carcinoma to an epithelial-like phenotype.     

Multiplex gene editing of the <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis> genome using the CRISPR-Cas9 system

Yarrowia lipolytica is categorized as a generally recognized as safe (GRAS) organism and is a heavily documented, unconventional yeast that has been widely incorporated into multiple industrial fields to produce valuable biochemicals. This study describes the construction of a CRISPR-Cas9 system for genome editing in Y. lipolytica using a single plasmid (pCAS1yl or pCAS2yl) to transport Cas9 and relevant guide RNA expression cassettes, with or without donor DNA, to target genes. Two Cas9 target genes, TRP1 and PEX10, were repaired by non-homologous end-joining (NHEJ) or homologous recombination, with maximal efficiencies in Y. lipolytica of 85.6 % for the wild-type strain and 94.1 % for the ku70/ku80 double-deficient strain, within 4 days. Simultaneous double and triple multigene editing was achieved with pCAS1yl by NHEJ, with efficiencies of 36.7 or 19.3 %, respectively, and the pCASyl system was successfully expanded to different Y. lipolytica breeding strains. This timesaving method will enable and improve synthetic biology, metabolic engineering and functional genomic studies of Y. lipolytica.     

CD8+ T cells primed in the periphery provide time-bound immune-surveillance to the central nervous system

After vaccination, memory CD8(+) T cells migrate to different organs to mediate immune surveillance. In most nonlymphoid organs, following an infection, CD8(+) T cells differentiate to become long-lived effector-memory cells, thereby providing long-term protection against a secondary infection. In this study, we demonstrated that Ag-specific CD8(+) T cells that migrate to the mouse brain following a systemic Listeria infection do not display markers reminiscent of long-term memory cells. In contrast to spleen and other nonlymphoid organs, none of the CD8(+) T cells in the brain reverted to a memory phenotype, and all of the cells were gradually eliminated. These nonmemory phenotype CD8(+) T cells were found primarily within the choroid plexus, as well as in the cerebrospinal fluid-filled spaces. Entry of these CD8(+) T cells into the brain was governed primarily by CD49d/VCAM-1, with the majority of entry occurring in the first week postinfection. When CD8(+) T cells were injected directly into the brain parenchyma, cells that remained in the brain retained a highly activated (CD69(hi)) phenotype and were gradually lost, whereas those that migrated out to the spleen were CD69(low) and persisted long-term. These results revealed a mechanism of time-bound immune surveillance to the brain by CD8(+) T cells that do not reside in the parenchyma.     

Simultaneous acquisition of ECG, BCG, and blood pressure from chick embryos in the egg

The applicability of the audiocartridge system to simultaneous measurements of the ballistic movements from multiple points of the egg was examined in late chick embryos. Despite direct contact between the cartridges and the egg, minute movements of the egg attributable to cardiac contractions of the embryo (ballistocardiogram, BCG) could be simultaneously detected from at least three points. The results showed that the amplitude of BCG waves was dependent on the site of detection, indicating that the BCG was a directional wave. The cartridge system for BCG measurement was incorporated in the electrocardiography and arterial catheterization to acquire simultaneously electrocardiogram (ECG), BCG, and blood pressure from the embryo confined in the egg. Isochronal comparison of these waves indicated that the ballistic movements of the embryo might be caused not only by the ventricular contraction but also by the atrial excitation, i.e., the BCG comprised waves appearing in the ventricular presystolic, contraction, and ejection periods. For wide changes in the heart rate, the approximate isometric ventricular contraction period remained almost constant.