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1.
Microb Cell Fact ; 21(1): 173, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-35999638

RESUMO

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.


Assuntos
Bacillus subtilis , Edição de Genes , Bacillus subtilis/genética , Sistemas CRISPR-Cas , Edição de Genes/métodos , Técnicas de Inativação de Genes , Plasmídeos/genética
2.
Int J Mol Sci ; 23(15)2022 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-35955649

RESUMO

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.


Assuntos
Proteínas Associadas a CRISPR , Sulfolobus , Autoimunidade/genética , Proteínas Associadas a CRISPR/genética , Sistemas CRISPR-Cas/genética , RNA/genética , Clivagem do RNA , Sulfolobus/genética
3.
Nucleic Acids Res ; 46(14): 7085-7096, 2018 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-29618058

RESUMO

Previously it was shown that UV irradiation induces a strong upregulation of tfb3 coding for a paralog of the archaeal transcriptional factor B (TFB) in Sulfolobus solfataricus, a crenarchaea. To investigate the function of this gene in DNA damage response (DDR), tfb3 was inactivated by gene deletion in Sulfolobus islandicus and the resulting Δtfb3 was more sensitive to DNA damage agents than the original strain. Transcriptome analysis revealed that a large set of genes show TFB3-dependent activation, including genes of the ups operon and ced system. Furthermore, the TFB3 protein was found to be associated with DDR gene promoters and functional dissection of TFB3 showed that the conserved Zn-ribbon and coiled-coil motif are essential for the activation. Together, the results indicated that TFB3 activates the expression of DDR genes by interaction with other transcriptional factors at the promoter regions of DDR genes to facilitate the formation of transcription initiation complex. Strikingly, TFB3 and Ced systems are present in a wide range of crenarchaea, suggesting that the Ced system function as a primary DNA damage repair mechanism in Crenarchaeota. Our findings further suggest that TFB3 and the concurrent TFB1 form a TFB3-dependent DNA damage-responsive circuit with their target genes, which is evolutionarily conserved in the major lineage of Archaea.


Assuntos
Proteínas Arqueais/metabolismo , Reparo do DNA , Sulfolobus/genética , Fatores de Transcrição/metabolismo , 4-Nitroquinolina-1-Óxido/farmacologia , Proteínas Arqueais/biossíntese , Proteínas Arqueais/química , Proteínas Arqueais/genética , Crenarchaeota/genética , Dano ao DNA , Evolução Molecular , Deleção de Genes , Regiões Promotoras Genéticas , Domínios Proteicos , Sulfolobus/citologia , Sulfolobus/efeitos dos fármacos , Sulfolobus/metabolismo , Fatores de Transcrição/biossíntese , Fatores de Transcrição/química , Fatores de Transcrição/genética , Ativação Transcricional
4.
Nucleic Acids Res ; 46(13): 6697-6711, 2018 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-29878182

RESUMO

While bacteria and eukaryotes show distinct mechanisms of DNA damage response (DDR) regulation, investigation of ultraviolet (UV)-responsive expression in a few archaea did not yield any conclusive evidence for an archaeal DDR regulatory network. Nevertheless, expression of Orc1-2, an ortholog of the archaeal origin recognition complex 1/cell division control protein 6 (Orc1/Cdc6) superfamily proteins was strongly activated in Sulfolobus solfataricus and Sulfolobus acidocaldarius upon UV irradiation. Here, a series of experiments were conducted to investigate the possible functions of Orc1-2 in DNA damage repair in Sulfolobus islandicus. Study of DDR in Δorc1-2 revealed that Orc1-2 deficiency abolishes DNA damage-induced differential expression of a large number of genes and the mutant showed hypersensitivity to DNA damage treatment. Reporter gene and DNase I footprinting assays demonstrated that Orc1-2 interacts with a conserved hexanucleotide motif present in several DDR gene promoters and regulates their expression. Manipulation of orc1-2 expression by promoter substitution in this archaeon revealed that a high level of orc1-2 expression is essential but not sufficient to trigger DDR. Together, these results have placed Orc1-2 in the heart of the archaeal DDR regulation, and the resulting Orc1-2-centered regulatory circuit represents the first DDR network identified in Archaea, the third domain of life.


Assuntos
Proteínas Arqueais/fisiologia , Proteínas de Ciclo Celular/fisiologia , Reparo do DNA , Complexo de Reconhecimento de Origem/fisiologia , Sulfolobus/genética , 4-Nitroquinolina-1-Óxido/toxicidade , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Ciclo Celular , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Dano ao DNA , DNA Arqueal/química , Deleção de Genes , Expressão Gênica/efeitos dos fármacos , Motivos de Nucleotídeos , Complexo de Reconhecimento de Origem/genética , Complexo de Reconhecimento de Origem/metabolismo , Regiões Promotoras Genéticas , Sulfolobus/efeitos dos fármacos , Sulfolobus/metabolismo
5.
Nucleic Acids Res ; 46(19): 10319-10330, 2018 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-30239876

RESUMO

Recently, Type III-A CRISPR-Cas systems were found to catalyze the synthesis of cyclic oligoadenylates (cOAs), a second messenger that specifically activates Csm6, a Cas accessory RNase and confers antiviral defense in bacteria. To test if III-B CRISPR-Cas systems could mediate a similar CRISPR signaling pathway, the Sulfolobus islandicus Cmr-α ribonucleoprotein complex (Cmr-α-RNP) was purified from the native host and tested for cOA synthesis. We found that the system showed a robust production of cyclic tetra-adenylate (c-A4), and that c-A4 functions as a second messenger to activate the III-B-associated RNase Csx1 by binding to its CRISPR-associated Rossmann Fold domain. Investigation of the kinetics of cOA synthesis revealed that Cmr-α-RNP displayed positively cooperative binding to the adenosine triphosphate (ATP) substrate. Furthermore, mutagenesis of conserved domains in Cmr2α confirmed that, while Palm 2 hosts the active site of cOA synthesis, Palm 1 domain serves as the primary site in the enzyme-substrate interaction. Together, our data suggest that the two Palm domains cooperatively interact with ATP molecules to achieve a robust cOA synthesis by the III-B CRISPR-Cas system.


Assuntos
Nucleotídeos de Adenina/metabolismo , Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , Proteínas de Membrana/metabolismo , Oligorribonucleotídeos/metabolismo , Sistemas do Segundo Mensageiro , Nucleotídeos de Adenina/biossíntese , Trifosfato de Adenosina/metabolismo , Catálise , Proteínas de Membrana/química , Oligorribonucleotídeos/biossíntese , Ligação Proteica , Ribonucleases/química , Ribonucleases/metabolismo , Ribonucleoproteínas/metabolismo , Transdução de Sinais , Especificidade por Substrato , Sulfolobus
6.
RNA Biol ; 16(4): 549-556, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-29629622

RESUMO

Sulfolobus islandicus Rey15A encodes one Type I-A and two Type III-B systems, all of which are active in mediating nucleic acids interference. However, the effectiveness of each CRISPR system against virus infection was not tested in this archaeon. Here we constructed S. islandicus strains that constitutively express the antiviral immunity from either I-A, or III-B, or I-A plus III-B systems against SMV1 and tested the response of each host to SMV1 infection. We found that, although both CRISPR immunities showed a strong inhibition to viral DNA replication at an early stage of incubation, the host I-A CRISPR immunity gradually lost the control on virus proliferation, allowing accumulation of cellular viral DNA and release of a large number of viral particles. In contrast, the III-B CRISPR immunity showed a tight control on both viral DNA replication and virus particle formation. Furthermore, the SMV1 tolerance to the I-A CRISPR immunity did not result from the occurrence of escape mutations, suggesting the virus probably encodes an anti-CRISPR protein (Acr) to compromise the host I-A CRISPR immunity. Together, this suggests that the interplay between viral Acrs and CRISPR-Cas systems in thermophilic archaea could have shaped the stable virus-host relationship that is observed for many archaeal viruses.


Assuntos
Vírus de Archaea/fisiologia , Sistemas CRISPR-Cas/genética , Imunidade , Sulfolobus/imunologia , Sulfolobus/virologia , Replicação do DNA/genética , Genoma Viral , Sulfolobus/genética , Vírion/metabolismo
7.
RNA Biol ; 16(10): 1513-1520, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31298604

RESUMO

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.


Assuntos
Nucleotídeos de Adenina/biossíntese , Sistemas CRISPR-Cas , Oligorribonucleotídeos/biossíntese , Sequência de Aminoácidos , Clivagem do DNA , Sulfolobus/genética , Sulfolobus/metabolismo
8.
RNA Biol ; 16(4): 530-542, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-29911924

RESUMO

A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk .


Assuntos
Archaea/genética , Bactérias/genética , Proteínas Associadas a CRISPR/genética , Sistemas CRISPR-Cas/genética , Família Multigênica , Proteínas Associadas a CRISPR/química , Mapeamento Cromossômico , Deleção de Genes , Filogenia , Domínios Proteicos , Synechocystis/genética
9.
Nucleic Acids Res ; 45(18): 10740-10750, 2017 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-28977519

RESUMO

CRISPR-Cas systems protect prokaryotes against invading viruses and plasmids. The system is associated with a large number of Cas accessory proteins among which many contain a CARF (CRISPR-associated Rossmann fold) domain implicated in ligand binding and a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) nuclease domain. Here, such a dual domain protein, i.e. the Sulfolobus islandicus Csx1 (SisCsx1) was characterized. The enzyme exhibited metal-independent single-strand specific ribonuclease activity. In fact, SisCsx1 showed a basal RNase activity in the absence of ligand; upon the binding of an RNA ligand carrying four continuous adenosines at the 3'-end (3'-tetra-rA), the activated SisCsx1 degraded RNA substrate with a much higher turnover rate. Amino acid substitution mutants of SisCsx1 were obtained, and characterization of these mutant proteins showed that the CARF domain of the enzyme is responsible for binding to 3'-tetra-rA and the ligand binding strongly activates RNA cleavage by the HEPN domain. Since RNA polyadenylation is an important step in RNA decay in prokaryotes, and poly(A) RNAs can activate CARF domain proteins, the poly(A) RNA may function as an important signal in the cellular responses to viral infection and environmental stimuli, leading to degradation of both viral and host transcripts and eventually to cell dormancy or cell death.


Assuntos
Proteínas Arqueais/metabolismo , Endorribonucleases/metabolismo , RNA Mensageiro/química , Sulfolobus/enzimologia , Regulação Alostérica , Proteínas Arqueais/química , Endorribonucleases/química , Ligantes , Metais/metabolismo , Poli A/química , Ligação Proteica , Domínios Proteicos , Clivagem do RNA , Sulfolobus/metabolismo
10.
Nucleic Acids Res ; 45(19): 11305-11314, 2017 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-28977458

RESUMO

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems provide adaptive immunity against invasive nucleic acids guided by CRISPR RNAs (crRNAs) in archaea and bacteria. Type III CRISPR-Cas effector complexes show RNA cleavage and RNA-activated DNA cleavage activity, representing the only known system of dual nucleic acid interference. Here, we investigated the function of Cmr1 by genetic assays of DNA and RNA interference activity in the mutants and biochemical characterization of their mutated Cmr complexes. Three cmr1α mutants were constructed including ΔßΔ1α, Δß1α-M1 and Δß1α-M2 among which the last two mutants carried a double and a quadruple mutation in the first α-helix region of Cmr1α. Whereas the double mutation of Cmr1α (W58A and F59A) greatly influenced target RNA capture, the quadruple mutation almost abolished crRNA binding to Cmr1α. We found that Cmr2α-6α formed a stable core complex that is active in both RNA and DNA cleavage and that Cmr1α strongly enhances the basal activity of the core complex upon incorporation into the ribonucleoprotein complex. Therefore, Cmr1 functions as an integral activation module in III-B systems, and the unique occurrence of Cmr1 in III-B systems may reflect the adaptive evolution of type III CRISPR-Cas systems in thermophiles.


Assuntos
Proteínas Arqueais/metabolismo , Sistemas CRISPR-Cas , DNA/metabolismo , RNA/metabolismo , Proteínas Arqueais/genética , Sequência de Bases , DNA/genética , Clivagem do DNA , Mutação , Ligação Proteica , RNA/genética , Clivagem do RNA , Interferência de RNA , Sulfolobus/genética , Sulfolobus/metabolismo
11.
Nucleic Acids Res ; 45(4): 1983-1993, 2017 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-27986854

RESUMO

The CRISPR (clustered regularly interspaced short palindromic repeats) system protects archaea and bacteria by eliminating nucleic acid invaders in a crRNA-guided manner. The Sulfolobus islandicus type III-B Cmr-α system targets invading nucleic acid at both RNA and DNA levels and DNA targeting relies on the directional transcription of the protospacer in vivo. To gain further insight into the involved mechanism, we purified a native effector complex of III-B Cmr-α from S. islandicus and characterized it in vitro. Cmr-α cleaved RNAs complementary to crRNA present in the complex and its ssDNA destruction activity was activated by target RNA. The ssDNA cleavage required mismatches between the 5΄-tag of crRNA and the 3΄-flanking region of target RNA. An invader plasmid assay showed that mutation either in the histidine-aspartate acid (HD) domain (a quadruple mutation) or in the GGDD motif of the Cmr-2α protein resulted in attenuation of the DNA interference in vivo. However, double mutation of the HD motif only abolished the DNase activity in vitro. Furthermore, the activated Cmr-α binary complex functioned as a highly active DNase to destroy a large excess DNA substrate, which could provide a powerful means to rapidly degrade replicating viral DNA.


Assuntos
Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Clivagem do DNA , DNA Arqueal/química , DNA Arqueal/genética , DNA Arqueal/metabolismo , Complexos Multiproteicos/metabolismo , Plasmídeos/genética , Ligação Proteica , RNA Arqueal/química , RNA Arqueal/genética , RNA Arqueal/metabolismo , Ribonucleoproteínas/metabolismo , Sulfolobus/genética , Sulfolobus/metabolismo
12.
Int J Mol Sci ; 18(7)2017 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-28640207

RESUMO

Reverse gyrase introduces positive supercoils to circular DNA and is implicated in genome stability maintenance in thermophiles. The extremely thermophilic crenarchaeon Sulfolobus encodes two reverse gyrase proteins, TopR1 (topoisomerase reverse gyrase 1) and TopR2, whose functions in thermophilic life remain to be demonstrated. Here, we investigated the roles of TopR1 in genome stability maintenance in S. islandicus in response to the treatment of methyl methanesulfonate (MMS), a DNA alkylation agent. Lethal MMS treatment induced two successive events: massive chromosomal DNA backbone breakage and subsequent DNA degradation. The former occurred immediately after drug treatment, leading to chromosomal DNA degradation that concurred with TopR1 degradation, followed by chromatin protein degradation and DNA-less cell formation. To gain a further insight into TopR1 function, the expression of the enzyme was reduced in S. islandicus cells using a CRISPR-mediated mRNA interference approach (CRISPRi) in which topR1 mRNAs were targeted for degradation by endogenous III-B CRISPR-Cas systems. We found that the TopR1 level was reduced in the S. islandicus CRISPRi cells and that the cells underwent accelerated genomic DNA degradation during MMS treatment, accompanied by a higher rate of cell death. Taken together, these results indicate that TopR1 probably facilitates genome integrity maintenance by protecting DNA breaks from thermo-degradation in vivo.


Assuntos
Proteínas Arqueais/metabolismo , Quebras de DNA , DNA Topoisomerases Tipo I/metabolismo , DNA Arqueal/genética , Sulfolobus/genética , Proteínas Arqueais/genética , Sistemas CRISPR-Cas , DNA Topoisomerases Tipo I/genética , DNA Arqueal/metabolismo , Instabilidade Genômica , RNA Mensageiro/genética , Sulfolobus/enzimologia , Sulfolobus/metabolismo
14.
Guang Pu Xue Yu Guang Pu Fen Xi ; 35(10): 2686-90, 2015 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-26904800

RESUMO

Under the condition of mesopic vision, the spectral luminous efficiency function is shown as a series of curves. Its peak wavelength and intensity are affected by light spectrum, background brightness and other aspects. The impact of light source to lighting visibility could not be carried out via a single optical parametric characterization. The reaction time of visual cognition is regard as evaluating indexes in this experiment. Under the condition of different speed and luminous environment, testing visual cognition based on vision function method. The light sources include high pressure sodium, electrodeless fluorescent lamp and white LED with three kinds of color temperature (the range of color temperature is from 1 958 to 5 537 K). The background brightness value is used for basic section of highway tunnel illumination and general outdoor illumination, its range is between 1 and 5 cd x m(-)2. All values are in the scope of mesopic vision. Test results show that: under the same condition of speed and luminance, the reaction time of visual cognition that corresponding to high color temperature of light source is shorter than it corresponding to low color temperature; the reaction time corresponding to visual target in high speed is shorter than it in low speed. At the end moment, however, the visual angle of target in observer's visual field that corresponding to low speed was larger than it corresponding to high speed. Based on MOVE model, calculating the equivalent luminance of human mesopic vision, which is on condition of different emission spectrum and background brightness that formed by test lighting sources. Compared with photopic vision result, the standard deviation (CV) of time-reaction curve corresponding to equivalent brightness of mesopic vision is smaller. Under the condition of mesopic vision, the discrepancy between equivalent brightness of different lighting source and photopic vision, that is one of the main reasons for causing the discrepancy of visual recognition. The emission spectrum peak of GaN chip is approximate to the wave length peak of efficiency function in photopic vision. The lighting visual effect of write LED in high color temperature is better than it in low color temperature and electrodeless fluorescent lamp. The lighting visual effect of high pressure sodium is weak. Because of its peak value is around the Na+ characteristic spectra.

15.
Nat Commun ; 15(1): 3464, 2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38658536

RESUMO

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.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Edição de Genes/métodos , Elementos de DNA Transponíveis/genética , Proteínas Arqueais/metabolismo , Proteínas Arqueais/genética , Transposases/metabolismo , Transposases/genética
16.
Trends Microbiol ; 31(4): 405-418, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36463018

RESUMO

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.


Assuntos
Sistemas CRISPR-Cas , Células Procarióticas , Sistemas CRISPR-Cas/genética
17.
J Colloid Interface Sci ; 646: 633-648, 2023 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-37216711

RESUMO

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.

18.
Nat Commun ; 14(1): 6970, 2023 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-37914725

RESUMO

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.


Assuntos
Proteínas Argonautas , Ácidos Nucleicos , Proteínas Argonautas/genética , Proteínas Argonautas/metabolismo , Células Procarióticas/metabolismo , DNA/metabolismo , Plasmídeos , Ácidos Nucleicos/metabolismo
19.
Micromachines (Basel) ; 14(9)2023 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-37763920

RESUMO

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.

20.
Micromachines (Basel) ; 14(10)2023 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-37893281

RESUMO

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.

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