Flexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope.

TnpBs encoded by the IS200/IS605 family transposon are among the most abundant prokaryotic proteins from which type V CRISPR-Cas nucleases may have evolved. Since bacterial TnpBs can be programmed for RNA-guided dsDNA cleavage in the presence of a transposon-adjacent motif (TAM), these nucleases hold immense promise for genome editing. However, the activity and targeting specificity of TnpB in homology-directed gene editing remain unknown. Here we report that a thermophilic archaeal TnpB enables efficient gene editing in the natural host. Interestingly, the TnpB has different TAM requirements for eliciting cell death and for facilitating gene editing. By systematically characterizing TAM variants, we reveal that the TnpB recognizes a broad range of TAM sequences for gene editing including those that do not elicit apparent cell death. Importantly, TnpB shows a very high targeting specificity on targets flanked by a weak TAM. Taking advantage of this feature, we successfully leverage TnpB for efficient single-nucleotide editing with templated repair. The use of different weak TAM sequences not only facilitates more flexible gene editing with increased cell survival, but also greatly expands targeting scopes, and this strategy is probably applicable to diverse CRISPR-Cas systems.

Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection.

Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.

Effect of Composition Adjustment on the Thermoelectric Properties of Mg3Bi2-Based Thermoelectric Materials.

Thermoelectric materials are widely used in refrigeration chips, thermal power generation, catalysis and other fields. Mg3Bi2-based thermoelectric material is one of the most promising thermoelectric materials. Herein, the Mg3Bi2-based samples were prepared by high temperature synthesis, and the influence of Mg/Sb content on the electrical transport properties and semi-conductivity/semi-metallicity of the materials has been studied. The results indicate that the efficiency of introducing electrons from excess Mg prepared by high temperature synthesis is lower than that introduced by ball milling, due to the high vapor pressure of Mg. The doping of Sb/Te at the Bi site would make it easier for the material to change from p-type conduction to n-type conduction. With the increase in Mg content, the semi-conductivity of the material becomes weaker, the semi-metallicity becomes stronger, and the corresponding conductivity increases. With the increase in Sb content, the samples exhibit the opposite changes. The highest power factor of ~1.98 mWm-1K-2 is obtained from the Mg3.55Bi1.27Sb0.7Te0.03 sample.

Study on the Targeted Improvement Mechanism of the Carrier Concentration and Mobility of BiCuSeO Ceramics.

BiCuSeO has great application prospects in thermoelectric power generation and thermoelectric catalysis, but it is limited by its lower thermoelectric performance. Herein, BiCuSeO bulk materials were prepared using a solid-phase reaction method and a ball-milling method combined with spark plasma sintering, and then the thermoelectric properties were improved by synergistically increasing carrier concentration and mobility. Al was adopted to dope into the BiCuSeO matrix, aiming to adjust the carrier mobility through energy band adjustment. The results show that Al doping would widen the bandgap and enhance the carrier mobility of BiCuSeO. After Al doping, the thermoelectric properties of the material are improved in the middle- and high-temperature range. Based on Al doping, Pb is adopted as the doping element to dope BiCuSeO to modify the carrier concentration. The results show that Al/Pb dual doping in the BiCuSeO matrix can increase the carrier concentration under the premise of increasing carrier mobility. Therefore, the electrical conductivity of BiCuSeO can be improved while maintaining a large Seebeck coefficient. The power factor of Al/Pb doping reached ~7.67 µWcm-1K-2 at 873 K. At the same time, the thermal conductivity of all doped samples within the test temperature range maintained a low level (<1.2 Wm-1K-1). Finally, the ZT value of the Al/Pb-doped BiCuSeO reached ~1.14 at 873 K, which is ~2.72 times that of the pure phase, and the thermoelectric properties of the matrix were effectively improved.

High-performance photocatalytic peroxymonosulfate activation by carbon quantum dots via precise surface chemistry regulation: Insight into the structure-function relations.

Carbon quantum dots (CQDs) are considered promising metal-free green catalysts for the activation of persulfates, but direct experimental evidence to identify the true active sites on the surface of CQDs is still lacking. We prepared CQDs with different oxygen contents by controlling the carbonisation temperature, using a simple pyrolysis method. Photocatalytic activity experiments show that CQDs200 exhibits the best PMS activation performance. By investigating the relationship between the oxygen functional groups on CQDs surface and photocatalytic activity, it was postulated that the C=O groups might be the predominant active site, which was confirmed by selective chemical titrations of the C=O, C-OH and COOH groups. Furthermore, limited to the weak photocatalytic properties of the pristine CQDs, ammonia and phenylhydrazine were used to precisely nitrogen-modify the o-CQD surface. We found that phenylhydrazine-modified o-CQDs-PH promoted the absorption of visible light and the separation of photocarriers, thus enhancing the activation of PMS. Theoretical calculations provide more insights from different levels of the pollutant, fine-tuned CQDs, and their interactions.

The abortive infection functions of CRISPR-Cas and Argonaute.

CRISPR-Cas and prokaryotic Argonaute (pAgo) are nucleic acid (NA)-guided defense systems that protect prokaryotes against the invasion of mobile genetic elements. Previous studies established that they are directed by NA fragments (guides) to recognize invading complementary NA (targets), and that they cleave the targets to silence the invaders. Nevertheless, growing evidence indicates that many CRISPR-Cas and pAgo systems exploit the abortive infection (Abi) strategy to confer immunity. The CRISPR-Cas and pAgo Abi systems typically sense invaders using the NA recognition ability and activate various toxic effectors to kill the infected cells to prevent the invaders from spreading. This review summarizes the diverse mechanisms of these CRISPR-Cas and pAgo systems, and highlights their critical roles in the arms race between microbes and invaders.

Genetic engineering for enhanced production of a novel alkaline protease BSP-1 in Bacillus amyloliquefaciens.

Alkaline protease has been widely applied in food, medicine, environmental protection and other industrial fields. However, the current activity and yield of alkaline protease cannot meet the demand. Therefore, it is important to identify new alkaline proteases with high activity. In this study, we cloned a potential alkaline protease gene bsp-1 from a Bacillus subtilis strain isolated in our laboratory. BSP-1 shows the highest sequence similarity to subtilisin NAT (S51909) from B. subtilis natto. Then, we expressed BSP-1 in Bacillus amyloliquefaciens BAX-9 and analyzed the protein expression level under a collection of promoters. The results show that the P43 promoter resulted in the highest transcription level, protein level and enzyme activity. Finally, we obtained a maximum activity of 524.12 U/mL using the P43 promoter after fermentation medium optimization. In conclusion, this study identified an alkaline protease gene bsp-1 from B. subtilis and provided a new method for high-efficiency alkaline protease expression in B. amyloliquefaciens.

Inactivation of Target RNA Cleavage of a III-B CRISPR-Cas System Induces Robust Autoimmunity in Saccharolobus islandicus.

Type III CRISPR-Cas systems show the target (tg)RNA-activated indiscriminate DNA cleavage and synthesis of oligoadenylates (cOA) and a secondary signal that activates downstream nuclease effectors to exert indiscriminate RNA/DNA cleavage, and both activities are regulated in a spatiotemporal fashion. In III-B Cmr systems, cognate tgRNAs activate the two Cmr2-based activities, which are then inactivated via tgRNA cleavage by Cmr4, but how Cmr4 nuclease regulates the Cmr immunization remains to be experimentally characterized. Here, we conducted mutagenesis of Cmr4 conserved amino acids in Saccharolobus islandicus, and this revealed that Cmr4α RNase-dead (dCmr4α) mutation yields cell dormancy/death. We also found that plasmid-borne expression of dCmr4α in the wild-type strain strongly reduced plasmid transformation efficiency, and deletion of CRISPR arrays in the host genome reversed the dCmr4α inhibition. Expression of dCmr4α also strongly inhibited plasmid transformation with Cmr2αHD and Cmr2αPalm mutants, but the inhibition was diminished in Cmr2αHD,Palm. Since dCmr4α-containing effectors lack spatiotemporal regulation, this allows an everlasting interaction between crRNA and cellular RNAs to occur. As a result, some cellular RNAs, which are not effective in mediating immunity due to the presence of spatiotemporal regulation, trigger autoimmunity of the Cmr-α system in the S. islandicus cells expressing dCmr4α. Together, these results pinpoint the crucial importance of tgRNA cleavage in autoimmunity avoidance and in the regulation of immunization of type III systems.

Development and application of a rapid all-in-one plasmid CRISPR-Cas9 system for iterative genome editing in Bacillus subtilis.

BACKGROUND: Bacillus subtilis, an important industrial microorganism, is commonly used in the production of industrial enzymes. Genome modification is often necessary to improve the production performance of cell. The dual-plasmid CRISPR-Cas9 system suitable for iterative genome editing has been applied in Bacillus subtilis. However, it is limited by the selection of knockout genes, long editing cycle and instability. RESULTS: To address these problems, we constructed an all-in-one plasmid CRISPR-Cas9 system, which was suitable for iterative genome editing of B. subtilis. The PEG4000-assisted monomer plasmid ligation (PAMPL) method greatly improved the transformation efficiency of B. subtilis SCK6. Self-targeting sgRNArep transcription was tightly controlled by rigorous promoter PacoR, which could induce the elimination of plasmids after genome editing and prepare for next round of genome editing. Our system achieved 100% efficiency for single gene deletions and point mutations, 96% efficiency for gene insertions, and at least 90% efficiency for plasmid curing. As a proof of concept, two extracellular protease genes epr and bpr were continuously knocked out using this system, and it only took 2.5 days to complete one round of genome editing. The engineering strain was used to express Douchi fibrinolytic enzyme DFE27, and its extracellular enzyme activity reached 159.5 FU/mL. CONCLUSIONS: We developed and applied a rapid all-in-one plasmid CRISPR-Cas9 system for iterative genome editing in B. subtilis, which required only one plasmid transformation and curing, and accelerated the cycle of genome editing. To the best of our knowledge, this is the rapidest iterative genome editing system for B. subtilis. We hope that the system can be used to reconstruct the B. subtilis cell factory for the production of various biological molecules.

The trans DNA cleavage activity of Cas12a provides no detectable immunity against plasmid or phage.

Cas12a is a type V-A CRISPR-Cas RNA-guided endonuclease. It cleaves dsDNA at specific site, and then is activated for nonspecific ssDNA cleavage in trans in vitro. The immune function of the trans activity is still unknown. To address this question, we constructed a Cas12a targeting system in Escherichia coli, where Cas12a cleaved a high-copy target plasmid to unleash the trans ssDNA cleavage activity. Then, we analyzed the effect of the Cas12a targeting on a non-target plasmid and a ssDNA phage. The results show that Cas12a efficiently eliminates target plasmid but exerts no impact on the maintenance of the non-target plasmid or plague formation efficiency of the phage. In addition, a two-spacer CRISPR array, which facilitates target plasmid depletion, still has no detectable effect on the non-target plasmid or phage either. Together, the data suggest that the trans ssDNA cleavage of Cas12a does not contribute to immunity in vivo.

[Exploration and practice of synthetic biology teaching mode based on research frontiers and hotspots].

Synthetic biology, a course with a sound theoretical system and a wide application range, plays a role in the cultivation of innovative talents in the field of bioengineering. To this end, we have set up a synthetic biology course in our university. First, according to the concept of imparting basic knowledge, highlighting innovative practice, and keeping up with cutting-edge progress, we assembled a high-level teaching team for synthetic biology. The team constantly adjusted and optimized the course contents and achieved a novel and reasonable course system. Second, we introduced frontier cases of synthetic biology reported in high-level journals, as well as breaking news in this field in classroom teaching, which enriched the teaching contents and aroused students' interest. Third, taking these cases as the breakthrough point, we guided students to in-depth discussions through the learning-centered teaching mode to improve students' abilities of critical thinking and theoretical innovation. In summary, the course has achieved good teaching outcomes and improved the cultivation of innovative talents. Therefore, we share our work with peer teachers, aiming to give new insights into the teaching reform of synthetic biology and other related courses.

A short prokaryotic Argonaute activates membrane effector to confer antiviral defense.

Argonaute (Ago) proteins are widespread nucleic-acid-guided enzymes that recognize targets through complementary base pairing. Although, in eukaryotes, Agos are involved in RNA silencing, the functions of prokaryotic Agos (pAgos) remain largely unknown. In particular, a clade of truncated and catalytically inactive pAgos (short pAgos) lacks characterization. Here, we reveal that a short pAgo protein in the archaeon Sulfolobus islandicus, together with its two genetically associated proteins, Aga1 and Aga2, provide robust antiviral protection via abortive infection. Aga2 is a toxic transmembrane effector that binds anionic phospholipids via a basic pocket, resulting in membrane depolarization and cell killing. Ago and Aga1 form a stable complex that exhibits nucleic-acid-directed nucleic-acid-recognition ability and directly interacts with Aga2, pointing to an immune sensing mechanism. Together, our results highlight the cooperation between pAgos and their widespread associated proteins, suggesting an uncharted diversity of pAgo-derived immune systems.

Phosphorus flow analysis of different crops in Dongying District, Shandong Province, China, 1995-2016.

Investigating the phosphorus (P) sources, pathways, and final sinks are important to reduce P pollution and improve P management. In this study, substance flow analysis (SFA) was performed for P flow analysis from 1995 to 2016 in different crops of Dongying District, a core region of the alluvial delta at the estuary of the Yellow River. The results showed that P input steadily increased from 1.48 × 104 t in 1995 to 2.16 × 104 t in 2007, and then decreased from 1.90 × 104 t in 2010 to 1.78 × 104 t in 2016. Chemical fertilizers made the highest contribution to P input. The cotton with the highest P load was on the top of P load risk ranks. More importantly, this study applied the Partial Least Squares Path Modeling (PLS-PM) model for P flow analysis and established the numerical relationship between the variables (including fertilizers, straws return-to-field, harvested grains, discarded straw, and P erosion and runoff), P use efficiency (PUE) and P load. The analysis revealed that fertilizer and crop production are the key factors affecting the PUE. Therefore, optimizing the use of P-fertilizer whilst maintaining yields can be an effective strategy to improve the local region PUE.

Enhanced adsorption and visible-light photocatalysis on TiO2 with in situ formed carbon quantum dots.

Carbon quantum dots (CQDs) can be used to modify TiO2 to extend the light absorption threshold and enhance its photocatalytic efficiency. In this study, different amounts of CQDs modified TiO2 (CQDs-x/TiO2) were synthesized by a facile, mild, and environmental friendly hydrothermal method at a low temperature. The physicochemical properties were investigated by a variety of advanced characterization techniques. It was found that the anchoring of CQDs endowed the CQDs-x/TiO2 with a large specific surface area, which is beneficial to adsorb more organic pollutants and promote the rate of photocatalytic oxidation. The XRD results also showed that the in situ formation of CQDs on the surface of TiO2 made the crystallinity of TiO2 tend to be complete. Among these photocatalysts, CQDs-20/TiO2 showed the highest pollutant removal efficiency under visible light irradiations. The classical quenching tests revealed that the O2•-, •OH, and hole (h+) were the oxidizing species. Among them, h+ was the primary factor contributing to the degradation. The electrochemical tests showed that the anchoring of CQDs on TiO2 increased the photocurrent by about four times, as compared with the pure TiO2. In particular, the cyclic voltammetry results showed that the photo-generated electrons of CQDs were freer to transfer to TiO2 under visible light irradiations, promoting the separation of photo-generated electrons and holes. This study explains adequately why the CQDs/TiO2 system has a good photocatalytic degradation of organic compounds.

Expression, purification, and characterization of a membrane-associated cyclic oligo-adenylate degrader from Sulfolobus islandicus.

Type III CRISPR-cas systems initiate cyclic oligo-adenylate (cOA) signaling to initiate immune response. Previously, we identified that a membrane-associated DHH-DHHA1 family protein from Sulfolobus islandicus efficiently degrades cOA. Here, we provide detailed protocols for expression and purification of the protein from its native host and a cOA degradation assay with the purified enzyme. The methodology should be of interest for researchers studying Sulfolobus, membrane-associated proteins, or type III CRISPR-cas systems. For complete details on the use and execution of this protocol, please refer to Zhao et al. (2020).

CRISPR-Associated Factor Csa3b Regulates CRISPR Adaptation and Cmr-Mediated RNA Interference in Sulfolobus islandicus.

Acquisition of spacers confers the CRISPR-Cas system with the memory to defend against invading mobile genetic elements. We previously reported that the CRISPR-associated factor Csa3a triggers CRISPR adaptation in Sulfolobus islandicus. However, a feedback regulation of CRISPR adaptation remains unclear. Here we show that another CRISPR-associated factor, Csa3b, binds a cyclic oligoadenylate (cOA) analog (5'-CAAAA-3') and mutation at its CARF domain, which reduces the binding affinity. Csa3b also binds the promoter of adaptation cas genes, and the cOA analog enhances their binding probably by allosteric regulation. Deletion of the csa3b gene triggers spacer acquisition from both plasmid and viral DNAs, indicating that Csa3b acted as a repressor for CRISPR adaptation. Moreover, we also find that Csa3b activates the expression of subtype cmr-α and cmr-ß genes according to transcriptome data and demonstrate that Csa3b binds the promoters of cmr genes. The deletion of the csa3b gene reduces Cmr-mediated RNA interference activity, indicating that Csa3b acts as a transcriptional activator for Cmr-mediated RNA interference. In summary, our findings reveal a novel pathway for the regulation of CRISPR adaptation and CRISPR-Cmr RNA interference in S. islandicus. Our results also suggest a feedback repression of CRIPSR adaptation by the Csa3b factor and the cOA signal produced by the Cmr complex at the CRISPR interference stage.

A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger.

Type III CRISPR-Cas systems initiate an intracellular signaling pathway to confer immunity. The signaling pathway includes synthesis of cyclic oligo-adenylate (cOA) and activation of the RNase activity of type III accessory ribonuclease Csm6/Csx1 by cOA. After the immune response, cOA should be cleared on time to avoid constant cellular RNA degradation. In this study, we find a metal-dependent cOA degradation activity in Sulfolobus islandicus. The activity is associated with the cell membrane and able to accelerate cOA clearance at a high cOA level. Further, we show that a metal-dependent and membrane-associated DHH-DHHA1 family nuclease (MAD) rapidly cleaves cOA and deactivates Csx1 ribonuclease. The cOA degradation efficiency of MAD is much higher than the cellular ring nuclease. However, the subcellular organization may prevent it from degrading nascent cOA. Together, the data suggest that MAD acts as the second cOA degrader after the ring nuclease to remove diffused redundant cOA.

A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota.

Sulfolobus islandicus codes for four DNA polymerases: three are of the B-family (Dpo1, Dpo2, and Dpo3), and one is of the Y-family (Dpo4). Western analysis revealed that among the four polymerases, only Dpo2 exhibited DNA damage-inducible expression. To investigate how these DNA polymerases could contribute to DNA damage tolerance in S. islandicus, we conducted genetic analysis of their encoding genes in this archaeon. Plasmid-borne gene expression revealed that Dpo2 increases cell survival upon DNA damage at the expense of mutagenesis. Gene deletion studies showed although dpo1 is essential, the remaining three genes are dispensable. Furthermore, although Dpo4 functions in housekeeping translesion DNA synthesis (TLS), Dpo2, a B-family DNA polymerase once predicted to be inactive, functions as a damage-inducible TLS enzyme solely responsible for targeted mutagenesis, facilitating GC to AT/TA conversions in the process. Together, our data indicate that Dpo2 is the main DNA polymerase responsible for DNA damage tolerance and is the primary source of targeted mutagenesis. Given that crenarchaea encoding a Dpo2 also have a low-GC composition genome, the Dpo2-dependent DNA repair pathway may be conserved in this archaeal lineage.

Photocatalytic activation of peroxymonosulfate by surface-tailored carbon quantum dots.

In this study, carbon quantum dots (CQDs) were synthesized by a low-cost and scalable approach and the oxygen functional groups were fine-tuned by chemical post-treatment. It was found that the CQDs could be applied as visible-light-responsive photocatalysts for activation of peroxymonosulfate (PMS) and remediation of aqueous organic dyes. Phenylhydrazine modified CQDs (CQDs-PH) presented high efficiency for degradation of methylene blue due to selective removal of carboxylic groups and inhibited recombination of photogenerated electron-hole pairs. The effects of catalyst dosage, species and concentrations of dyes, and initial pH values on the photodegradation efficiency were systematically investigated and the alkaline condition facilitates the separation of photoinduced charge carriers and promotes the dye decoloration. The reactive oxygen species produced in the photocatalysis were identified by radical quenching tests and the mechanism was elucidated. Superoxide radicals were generated from PMS activation via electron transfer from CQDs and played the primary role in organic oxidation. In addition, photogenerated holes on the valence band of CQDs also participated in the dye decomposition.

Cmr3 regulates the suppression on cyclic oligoadenylate synthesis by tag complementarity in a Type III-B CRISPR-Cas system.

Type III CRISPR-Cas systems code for a multi-subunit ribonucleoprotein (RNP) complex that mediates DNA cleavage and synthesizes cyclic oligoadenylate (cOA) second messenger to confer anti-viral immunity. Both immune activities are to be activated upon binding to target RNA transcripts by their complementarity to crRNA, and autoimmunity avoidance is determined by extended complementarity between the 5'-repeat tag of crRNA and 3'-flanking sequences of target transcripts (anti-tag). However, as to how the strategy could achieve stringent autoimmunity avoidance remained elusive. In this study, we systematically investigated how the complementarity of the crRNA 5'-tag and anti-tag (i.e., tag complementarity) could affect the interference activities (DNA cleavage activity and cOA synthesis activity) of Cmr-α, a type III-B system in Sulfolobus islandicus Rey15A. The results revealed an increasing suppression on both activities by increasing degrees of tag complementarity and a critical function of the 7th nucleotide of crRNA in avoiding autoimmunity. More importantly, mutagenesis of Cmr3α exerts either positive or negative effects on the cOA synthesis activity depending on the degrees of tag complementarity, suggesting that the subunit, coupling with the interaction between crRNA tag and anti-tag, function in facilitating immunity and avoiding autoimmunity in Type III-B systems.