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Identification and characterization of NAD-RNAs in Archaea

ABSTRACT: NAD captureSeq was employed to identify NAD-RNAs in Sulfolobus acidocaldarius and Haloferax volcanii

PROVIDER: PRJEB48624 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	ERR7341240.fastq.gz	Fastqsanger.gz
	ERR7341241.fastq.gz	Fastqsanger.gz
	ERR7341242.fastq.gz	Fastqsanger.gz
	ERR7341243.fastq.gz	Fastqsanger.gz

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Testing different rRNA removal methods in 4 species of model halophilic archaea

Project description:We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.

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Checking the origin utilisation of Haloferax mediterranei H13 through high-throughput DNA sequencing

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Project description:To clarify the function of Trm112 in archaea, we have characterized structurally and functionally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies.

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Transcriptome analysis of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

Project description:Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.

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Project description:Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, aptly named Small RNA in Haloferax Oxidative Stress (SHOxi). We demonstrated that SHOxi is a functional non-coding RNA that plays gene regulatory roles in the oxidative stress response of an extremophilic archaeon. We found that SHOxi likely regulates redox homeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. The decrease in the NAD+/NADH ratio resulting from the direct RNA-RNA interaction between SHOxi and its trans-target is instrumental in the survival of H. volcanii. The regulatory effects of SHOxi provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.

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MPLEx_Sulfolobus_acidocaldarius

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