Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex

Bernal-Bernal, Diego; Abellón-Ruiz, Javier; Iniesta, Antonio A.; Pajares-Martínez, Elena; Bastida‐Martínez, Eva; Fontes, Marta; Padmanabhan, S.; Elías‐Arnanz, Montserrat

doi:10.1093/nar/gky475

Cited by 16 publications

(11 citation statements)

References 82 publications

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“…Chromatin Immunoprecipitation Sequencing (ChIP-seq). Chromatin immunoprecipitation was performed essentially as described before 96 . Briefly, cultures (50 ml) of each ChIP strain (ParB-3×FLAG, CdbA_3×FLAG, WT) were grown to mid-late exponential phase (OD 600 = 0.5-0.9) at 32°C with aeration.…”

Section: Discussionmentioning

confidence: 99%

CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus

et al. 2020

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Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria. Here we identify CdbA, a DNA-binding protein of the ribbon-helix-helix family that binds c-di-GMP in Myxococcus xanthus. CdbA is essential for viability, and its depletion causes defects in chromosome organization and segregation leading to a block in cell division. The protein binds to the M. xanthus genome at multiple sites, with moderate sequence specificity; however, its depletion causes only modest changes in transcription. The interactions of CdbA with c-di-GMP and DNA appear to be mutually exclusive and residue substitutions in CdbA regions important for c-di-GMP binding abolish binding to both c-di-GMP and DNA, rendering these protein variants non-functional in vivo. We propose that CdbA acts as a nucleoid-associated protein that contributes to chromosome organization and is modulated by c-di-GMP, thus revealing a link between c-di-GMP signaling and chromosome biology.

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Section: Discussionmentioning

confidence: 99%

CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus

et al. 2020

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“…All CRISPR-Cas systems require Cas proteins and crRNAs for function, and CRISPR- cas expression is a prerequisite to acquire new spacers, process pre-crRNA, and assemble ribonucleoprotein crRNA interference complexes for target degradation. Herein, we will focus on the CRISPR-Cas9 technology, the reader should keep in mind other available variants of the system such as CRISPR-Cas6 [ 5 ], CRISPR-Cas12a, -Cas12b [ 42 ], as well as the most recently discovered c2c2 (Cas13a) and c2c6 (Cas13b [ 19 , 69 ]. The CRISPR/Cas9 system is made of Cas9 nuclease and single-guide RNA (sgRNA).…”

Section: Main Textmentioning

confidence: 99%

The genome editing revolution: review

Khalil

2020

Journal of Genetic Engineering and Biotechnology

135

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Background Development of efficient strategies has always been one of the great perspectives for biotechnologists. During the last decade, genome editing of different organisms has been a fast advancing field and therefore has received a lot of attention from various researchers comprehensively reviewing latest achievements and offering opinions on future directions. This review presents a brief history, basic principles, advantages and disadvantages, as well as various aspects of each genome editing technology including the modes, applications, and challenges that face delivery of gene editing components. Main body Genetic modification techniques cover a wide range of studies, including the generation of transgenic animals, functional analysis of genes, model development for diseases, or drug development. The delivery of certain proteins such as monoclonal antibodies, enzymes, and growth hormones has been suffering from several obstacles because of their large size. These difficulties encouraged scientists to explore alternative approaches, leading to the progress in gene editing. The distinguished efforts and enormous experimentation have now been able to introduce methodologies that can change the genetic constitution of the living cell. The genome editing strategies have evolved during the last three decades, and nowadays, four types of “programmable” nucleases are available in this field: meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system. Each group has its own characteristics necessary for researchers to select the most suitable method for gene editing tool for a range of applications. Genome engineering/editing technology will revolutionize the creation of precisely manipulated genomes of cells or organisms in order to modify a specific characteristic. Of the potential applications are those in human health and agriculture. Introducing constructs into target cells or organisms is the key step in genome engineering. Conclusions Despite the success already achieved, the genome editing techniques are still suffering certain difficulties. Challenges must be overcome before the full potential of genome editing can be realized.

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“…Except for the light-induced CarQ-CarR pair, the signals that activate each of the other ECF-σ/anti-σ pairs that depend on CarD-CarG are unknown. One pair was, however, recently shown to direct the expression of one of the three CRISPR-Cas systems (type III-B) in M. xanthus , which suggested that this bacterial defense system is triggered by a phage [ 120 ]. Thus, CarD-CarG is a global regulator, like CdnL, but targets different genes.…”

Section: Blue Light Sensing Signaling and Gene Regulation In The B 12 -Independent Pathwaymentioning

confidence: 99%

Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation

et al. 2021

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Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.

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Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex

Cited by 16 publications

References 82 publications

CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus

CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus

The genome editing revolution: review

Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation

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