scholarly journals Specificities of and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups

2020 ◽  
Author(s):  
Viktoria Reimann ◽  
Marcus Ziemann ◽  
Hui Li ◽  
Tao Zhu ◽  
Juliane Behler ◽  
...  
Keyword(s):  
Translation System ◽  
Type I ◽  
Direct Repeats ◽  
Gene Cassettes ◽  
Mutant Strains ◽  
A Cell ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Cas Proteins

AbstractThe majority of bacteria and archaea possess an RNA-guided adaptive and inheritable immune system against viruses and other foreign genetic elements that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. In some bacteria, multiple instances of cas gene-free (orphan) repeat-spacer arrays exist, while additional instances of arrays that are linked to cas gene cassettes are present elsewhere in the genome.In the cyanobacterium Anabaena sp. PCC 7120, ten CRISPR-Cas repeat-spacer arrays are present, but only two cas gene cassettes plus a Tn7-associated eleventh array are observed. In this study, we deleted the two cas6 genes alr1482 (Type III-D) or alr1566 (Type I-D) and tested the specificities of the two corresponding enzymes in the resulting mutant strains, as recombinant proteins and in a cell-free transcription-translation system. The results assign the direct repeats (DRs) to three different groups. While Alr1566 is specific for one group, Alr1482 has a higher preference for the DRs of the second group but can also cleave those of the first group. We found that this cross-recognition limits crRNA accumulation for the Type I-D system in vivo.We also show that the DR of the cas gene-free CRISPR array of cyanophage N-1 is processed by these enzymes, suggesting that it is fully competent in association with host-encoded Cas proteins. The data support a strong tendency for array fragmentation in multicellular cyanobacteria and disfavor other possibilities, such as the nonfunctionality of these orphan repeat-spacer arrays. Our data demonstrate the functional coordination of Cas6 endonucleases with both neighboring and remote repeat-spacer arrays in the CRISPR-Cas system of cyanobacteria.

scholarly journals The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

2010 ◽  
Vol 192 (20) ◽  
pp. 5289-5303 ◽  
Author(s):  
C. Peter Wolk ◽  
Sigal Lechno-Yossef ◽  
Karin M. Jäger
Keyword(s):  
Transposable Elements ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Direct Repeats ◽  
Homologous Sequences ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Flanking Regions ◽  
Adaptive Role ◽  
Reading Frames

ABSTRACT Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/ ) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.

scholarly journals Pro-apoptotic caspase deficiency reveals a cell-extrinsic mechanism of NK cell regulation

2021 ◽  
Author(s):  
Tayla M. Olsen ◽  
Wei Hong Tan ◽  
Arne C. Knudsen ◽  
Anthony Rongvaux
Keyword(s):  
Cell Death ◽  
Nk Cells ◽  
Nk Cell ◽  
Apoptotic Cell ◽  
Type I ◽  
Dependent Manner ◽  
Apoptosis Pathway ◽  
A Cell

AbstractRegulated cell death is essential for the maintenance of cellular and tissue homeostasis. In the hematopoietic system, genetic defects in apoptotic cell death generally produce the accumulation of immune cells, inflammation and autoimmunity. In contrast, we found that genetic deletion of caspases of the mitochondrial apoptosis pathway reduces natural killer (NK) cell numbers and makes NK cells functionally defective in vivo and in vitro. Caspase deficiency results in constitutive activation of a type I interferon (IFN) response, due to leakage of mitochondrial DNA and activation of the cGAS/STING pathway. The NK cell defect in caspase-deficient mice is independent of the type I IFN response, but the phenotype is partially rescued by cGAS or STING deficiency. Finally, caspase deficiency alters NK cells in a cell-extrinsic manner. Type I IFNs and NK cells are two essential effectors of antiviral immunity, and our results demonstrate that they are both regulated in a caspase-dependent manner. Beyond caspase-deficient animals, our observations may have implications in infections that trigger mitochondrial stress and caspase-dependent cell death.

scholarly journals Biosensors-Based In Vivo Quantification of 2-Oxoglutarate in Cyanobacteria and Proteobacteria

Life ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 51 ◽  
Author(s):  
Hai-Lin Chen ◽  
Amel Latifi ◽  
Cheng-Cai Zhang ◽  
Christophe Bernard
Keyword(s):  
Conformational Changes ◽  
Nitrogen Assimilation ◽  
Krebs Cycle ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Cellular Level ◽  
Cyanobacterium Anabaena ◽  
Anabaena Sp ◽  
Pcc 7120

2-oxoglutarate (α-ketoglutarate; 2-OG) is an intermediate of the Krebs cycle, and constitutes the carbon skeleton for nitrogen assimilation and the synthesis of a variety of compounds. In addition to being an important metabolite, 2-OG is a signaling molecule with a broad regulatory repertoire in a variety of organisms, including plants, animals, and bacteria. Although challenging, measuring the levels and variations of metabolic signals in vivo is critical to better understand how cells control specific processes. To measure cellular 2-OG concentrations and dynamics, we designed a set of biosensors based on the fluorescence resonance energy transfer (FRET) technology that can be used in vivo in different organisms. For this purpose, we took advantage of the conformational changes of two cyanobacterial proteins induced by 2-OG binding. We show that these biosensors responded immediately and specifically to different 2-OG levels, and hence allowed to measure 2-OG variations in function of environmental modifications in the proteobacterium Escherichia coli and in the cyanobacterium Anabaena sp. PCC 7120. Our results pave the way to study 2-OG dynamics at the cellular level in uni- and multi-cellular organisms.

scholarly journals Site-Directed Mutagenesis of the Anabaena sp. Strain PCC 7120 Nitrogenase Active Site To Increase Photobiological Hydrogen Production

2010 ◽  
Vol 76 (20) ◽  
pp. 6741-6750 ◽  
Author(s):  
Hajime Masukawa ◽  
Kazuhito Inoue ◽  
Hidehiro Sakurai ◽  
C. Peter Wolk ◽  
Robert P. Hausinger
Keyword(s):  
Active Site ◽  
Electron Flow ◽  
Hydrogen Gas ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Proton Reduction ◽  
Anabaena Sp ◽  
Pcc 7120 ◽  
Iron Molybdenum Cofactor

ABSTRACT Cyanobacteria use sunlight and water to produce hydrogen gas (H2), which is potentially useful as a clean and renewable biofuel. Photobiological H2 arises primarily as an inevitable by-product of N2 fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In Anabaena sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H2 production by this strain, six nitrogenase amino acid residues predicted to reside within 5 � of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N2. Most of the 49 variants examined were deficient in N2-fixing growth and exhibited decreases in their in vivo rates of acetylene reduction. Of greater interest, several variants examined under an N2 atmosphere significantly increased their in vivo rates of H2 production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H2 compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H2 in an aerobic, nitrogen-containing environment.

scholarly journals Thioredoxin Dependent Changes in the Redox States of FurA from Anabaena sp. PCC 7120

Antioxidants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 913
Author(s):  
Jorge Guío ◽  
María Teresa Bes ◽  
Mónica Balsera ◽  
Laura Calvo-Begueria ◽  
Emma Sevilla ◽  
...  
Keyword(s):  
Reductase Activity ◽  
Thioredoxin Reductase ◽  
Zinc Ion ◽  
Exchange Reactions ◽  
Redox Partner ◽  
Redox Partners ◽  
Anabaena Sp ◽  
Pcc 7120

FurA is a multifunctional regulator in cyanobacteria that contains five cysteines, four of them arranged into two CXXC motifs. Lack of a structural zinc ion enables FurA to develop disulfide reductase activity. In vivo, FurA displays several redox isoforms, and the oxidation state of its cysteines determines its activity as regulator and its ability to bind different metabolites. Because of the relationship between FurA and the control of genes involved in oxidative stress defense and photosynthetic metabolism, we sought to investigate the role of type m thioredoxin TrxA as a potential redox partner mediating dithiol-disulfide exchange reactions necessary to facilitate the interaction of FurA with its different ligands. Both in vitro cross-linking assays and in vivo two-hybrid studies confirmed the interaction between FurA and TrxA. Light to dark transitions resulted in reversible oxidation of a fraction of the regulator present in Anabaena sp. PCC7120. Reconstitution of an electron transport chain using E. coli NADPH-thioredoxin-reductase followed by alkylation of FurA reduced cysteines evidenced the ability of TrxA to reduce FurA. Furthermore, the use of site-directed mutants allowed us to propose a plausible mechanism for FurA reduction. These results point to TrxA as one of the redox partners that modulates FurA performance.

scholarly journals A cell-free assay implicates a role of sphingomyelin and cholesterol in STING phosphorylation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kanoko Takahashi ◽  
Takahiro Niki ◽  
Emari Ogawa ◽  
Kiku Fumika ◽  
Yu Nishioka ◽  
...  
Keyword(s):  
Membrane Fraction ◽  
Microsomal Membrane ◽  
Interferon Response ◽  
Type I ◽  
Phosphorylation Reaction ◽  
A Cell ◽  
Golgi Network ◽  
Microbial Dna

AbstractStimulator of interferon genes (STING) is essential for the type I interferon response induced by microbial DNA from virus or self-DNA from mitochondria/nuclei. In response to emergence of such DNAs in the cytosol, STING translocates from the endoplasmic reticulum to the Golgi, and activates TANK-binding kinase 1 (TBK1) at the trans-Golgi network (TGN). Activated TBK1 then phosphorylates STING at Ser365, generating an interferon regulatory factor 3-docking site on STING. How this reaction proceeds specifically at the TGN remains poorly understood. Here we report a cell-free reaction in which endogenous STING is phosphorylated by TBK1. The reaction utilizes microsomal membrane fraction prepared from TBK1-knockout cells and recombinant TBK1. We observed agonist-, TBK1-, “ER-to-Golgi” traffic-, and palmitoylation-dependent phosphorylation of STING at Ser365, mirroring the nature of STING phosphorylation in vivo. Treating the microsomal membrane fraction with sphingomyelinase or methyl-β-cyclodextrin, an agent to extract cholesterol from membranes, suppressed the phosphorylation of STING by TBK1. Given the enrichment of sphingomyelin and cholesterol in the TGN, these results may provide the molecular basis underlying the specific phosphorylation reaction of STING at the TGN.

scholarly journals ThetrpEGene Negatively Regulates Differentiation of Heterocysts at the Level of Induction in Anabaena sp. Strain PCC 7120

2014 ◽  
Vol 197 (2) ◽  
pp. 362-370 ◽  
Author(s):  
Patrick Videau ◽  
Loralyn M. Cozy ◽  
Jasmine E. Young ◽  
Blake Ushijima ◽  
Reid T. Oshiro ◽  
...  
Keyword(s):  
Repeat Sequence ◽  
Mutant Phenotype ◽  
Wild Type ◽  
Content Type ◽  
Type Pattern ◽  
In The Wild ◽  
Anabaena Sp ◽  
Pcc 7120

Levels of 2-oxoglutarate (2-OG) reflect nitrogen status in many bacteria. In heterocystous cyanobacteria, a spike in the 2-OG level occurs shortly after the removal of combined nitrogen from cultures and is an integral part of the induction of heterocyst differentiation. In this work, deletion of one of the two annotatedtrpEgenes inAnabaenasp. strain PCC 7120 resulted in a spike in the 2-OG level and subsequent differentiation of a wild-type pattern of heterocysts when filaments of the mutant were transferred from growth on ammonia to growth on nitrate. In contrast, 2-OG levels were unaffected in the wild type, which did not differentiate under the same conditions. An inverted-repeat sequence located upstream oftrpEbound a central regulator of differentiation, HetR,in vitroand was necessary for HetR-dependent transcription of a reporter fusion and complementation of the mutant phenotypein vivo. Functional complementation of the mutant phenotype with the addition of tryptophan suggested that levels of tryptophan, rather than the demonstrated anthranilate synthase activity of TrpE, mediated the developmental response of the wild type to nitrate. A model is presented for the observed increase in 2-OG in thetrpEmutant.

scholarly journals Prototyping and Implementation of a Novel Feedforward Loop in a Cell-Free Transcription-Translation System and Cells

2017 ◽  
Author(s):  
Shaobin Guo ◽  
Richard M. Murray
Keyword(s):  
Circuit Design ◽  
Free Field ◽  
Network Motif ◽  
Translation System ◽  
Free System ◽  
Future Studies ◽  
A Cell ◽  
Made In ◽  
In Cells

AbstractBuilding novel synthetic biological devices is a time-consuming task because of the lengthy cell-based testing and optimization processes. Recent progress made in the cell-free field suggests that the utilization of mathematical models and cell-free transcription-translation testing platforms to systematically design and test novel synthetic biocircuits may help streamline some of the processes. Here we present a study of building a novel functional biological network motif from scratch with the aid of the mathematical modeling and the cell-free prototyping. In this work, we demonstrated that we were able to make a 3-promoter feedforward circuit from a concept to a working biocircuit in cells within a month. We started with performing simulations with a cell-free transcription-translation simulation toolbox. After verifying the feasibility of the circuit design, we used a fast assembling method to build the constructs and used the linear DNAs directly in the cell-free system for prototyping. After additional tests and assemblies, we implemented the circuit in plasmid forms in cells and showed that the in vivo results were consistent with the simulations and the outcomes in the cell-free platform. This study showed the usefulness of modeling and prototyping in building synthetic biocircuits and that we can use these tools to help streamline the process of circuit optimizations in future studies.

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