Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans

Wang, Wuzhou; Ma, Yun; He, Junyan; Qi, Huizhou; Xiao, Fangzhu; He, Shuya

doi:10.1016/j.gene.2019.144008

Cited by 20 publications

(9 citation statements)

References 144 publications

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“…5 ), showed antagonistic abundance in ecological disaggregation between La Punta and La Brava, likely due to abiotic factors. In genomic and metagenomic studies, the phylum Acidobacteria was predicted to possess relevant capabilities, such as using nitrite as an N source ( 54 ) and expressing multiple active transporters ( 55 , 56 ). In the above studies, usable sources of nitrogen, such as nitrite, are present in the La Punta–La Brava lake system ( Table 1 ) and are hypothetically usable by these taxa.…”

Section: Discussionmentioning

confidence: 99%

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems

et al. 2023

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In this study, we analyzed the persistence of the water column through satellite images and physicochemical characterization to investigate the composition and diversity in High Andean Lake Systems in a hyperarid environment. In addition to the persistence of the water column, this approach can be used to analyze changes in the morphology of saline accumulations and persistence of snow or ice; for example, for establishing variable plant cover over time and evaluating the microbiota associated with soils with seasonal changes in plants.

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Section: Discussionmentioning

confidence: 99%

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems

et al. 2023

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“…Not all the transcriptional regulators have been characterized in this microbe and the role of sRNAs in radiation response requires further investigation. Crosstalk among intricate regulatory networks that may play an important role in radiation resistance has not been well-studied owing to a lack of appropriate tools to regulate the expression of multiple genes in this microbe ( 45 ). The realization of full potential of this organism in industrial biotechnology has also been hampered by the absence of convenient genetic tools.…”

Section: Discussionmentioning

confidence: 99%

Effective gene silencing using type I–E CRISPR system in the multiploid, radiation-resistant bacterium Deinococcus radiodurans

Misra,

Pandey,

Appukuttan

et al. 2023

Microbiol Spectr

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The extremely radiation-resistant bacterium, Deinococcus radiodurans , is a microbe of importance, both, for studying stress tolerance mechanisms and as a chassis for industrial biotechnology. However, the molecular tools available for use in this organism continue to be limiting, with its multiploid genome presenting an additional challenge. In view of this, the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas tools provide a large repertoire of applications for gene manipulation. We show the utility of the type I-E Cascade system for knocking down gene expression in this organism. A single-vector system was designed for the expression of the Cascade components as well as the crRNA. The type I-E Cascade system was better tolerated than the type II-A dCas9 system in D. radiodurans . An assayable acid phosphatase gene, phoN integrated into the genome of this organism could be knocked down to 10% of its activity using the Cascade system. Cascade-based knockdown of ssb , a gene important for radiation resistance resulted in poor recovery post-irradiation. Targeting the Radiation and Desiccation Response Motif (RDRM), upstream of the ssb , prevented de-repression of its expression upon radiation exposure. In addition to this, multi-locus targeting was demonstrated on the deinococcal genome, by knocking down both phoN and ssb expression simultaneously. The programmable CRISPR interference tool developed in this study will facilitate the study of essential genes, hypothetical genes, and cis -elements involved in radiation response as well as enable metabolic engineering in this organism. Further, the tool can be extended for implementing high-throughput approaches in such studies. IMPORTANCE Deinococcus radiodurans is a microbe that exhibits a very high degree of radiation resistance. In addition, it is also identified as an organism of industrial importance. We report the development of a gene-knockdown system in this organism by engineering a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-Cascade system. We used this system to silence an assayable acid phosphatase gene, phoN to 10% of its activity. The study further shows the application of the Cascade system to target an essential gene ssb , that caused poor recovery from radiation. We demonstrate the utility of CRISPR-Cascade to study the role of a regulatory cis -element in radiation response as well as for multi-gene silencing. This easy-to-implement CRISPR interference system would provide an effective tool for better understanding of complex phenomena such as radiation response in D. radiodurans and may also enhance the potential of this microbe for industrial application.

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“…Not all the transcriptional regulators have been characterized in this microbe and the role of sRNAs in radiation response requires further investigation. Crosstalk among intricate regulatory networks that may play an important role in radiation resistance have not been well-studied owing lack of appropriate tools to regulate expression of multiple genes in this microbe (Wang et al, 2019). The realization of full potential of this organism in industrial biotechnology has also been hampered by absence of convenient genetic tools.…”

Section: Discussionmentioning

confidence: 99%

CRISPRi inDeinococcus radiodurans

Misra¹,

Pandey²,

Appukuttan

et al. 2022

Preprint

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The extremely radiation resistant bacterium,Deinococcus radiodurans, is a microbe of importance, both, for studying stress tolerance mechanisms and as a chassis for industrial biotechnology. However, the molecular tools available for use in this organism continue to be limiting. In view of this, the CRISPR-Cas tools provide a large repertoire of applications for gene manipulation. We show the utility of the type I-E Cascade system for knocking down gene expression in this organism. A single-vector system was designed for expression of the Cascade components as well as the crRNA. The type I-E Cascade system was better tolerated than the type II-A Cas9 system inD. radiodurans. An assayable acid phosphatase gene,phoNintegrated into the genome of this organism could be knocked down to 10% of its activity using the Cascade system. Cascade-based knockdown ofssb, a gene important for radiation resistance resulted in poor recovery post irradiation. Targeting the Radiation and Desiccation Resistance Motif (RDRM), upstream of thessb, prevented de-repression of its expression upon radiation exposure. In addition to this, multi-locus targeting was demonstrated on the deinococcal genome, by knocking down bothphoNandssbexpression simultaneously. The programmable CRISPRi tool developed in this study will facilitate study of essential genes, hypothetical genes, cis-elements involved in radiation response as well as enable metabolic engineering in this organism. Further the tool is amenable for implementing high-throughput approaches for such studies.

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Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans

Cited by 20 publications

References 144 publications

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems

Effective gene silencing using type I–E CRISPR system in the multiploid, radiation-resistant bacterium Deinococcus radiodurans

CRISPRi inDeinococcus radiodurans

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