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Genetic and functional analysis of archaeal ATP-dependent RNA ligase in ribosomal RNA biogenesis

ABSTRACT: Genetic and functional analysis of archaeal ATP-dependent RNA ligase in ribosomal RNA biogenesis

PROVIDER: PRJNA776174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16633624_1.fastq.gz	Fastqsanger.gz
	SRR16633624_2.fastq.gz	Fastqsanger.gz
	SRR16633625_1.fastq.gz	Fastqsanger.gz
	SRR16633625_2.fastq.gz	Fastqsanger.gz
	SRR16633626_1.fastq.gz	Fastqsanger.gz

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Genetic and functional analysis of archaeal ATP-dependent RNA ligase in ribosomal RNA biogenesis

Project description:In this study, we generated allelic knockouts of ATP-dependent RNA ligase (Rnl) in hyperthermophilic archaeon T. kodakarensis and analyze the total and small RNA by RNA-Seq.

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Genetic and functional analyses of archaeal ATP-dependent RNA Ligase

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Genetic and functional analyses of archaeal ATP-dependent RNA Ligase

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The E3 SUMO ligase Mms21 controls ribosome biogenesis

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Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing.

Project description:RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon Thermococcus kodakarensis to identify its biological targets. A comparative analysis of circular RNA reveals that the Rnl-knockout strain represses circularization of C/D box sRNAs without affecting the circularization of tRNA and rRNA processing intermediates. Recombinant archaeal Rnl could circularize C/D box sRNAs with a mutation in the conserved C/D box sequence element but not when the terminal stem structures were disrupted, suggesting that proximity of the two ends could be critical for intramolecular ligation. Furthermore, T. kodakarensis accumulates aberrant RNA fragments derived from ribosomal RNA in the absence of Rnl. These results suggest that Rnl is responsible for C/D box sRNA circularization and may also play a role in ribosomal RNA processing.

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The E3 SUMO ligase Mms21 controls ribosome biogenesis

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Cleavage of 3'-terminal adenosine by archaeal ATP-dependent RNA ligase.

Project description:Methanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodiester bonds between the 5'-phosphate and 3'-hydroxyl termini of single-stranded RNAs. It can also react with RNA with a 3'-phosphate end to generate a 2',3'-cyclic phosphate. Here, we show that MthRnl can additionally remove adenosine from the 3'-terminus of the RNA to produce 3'-deadenylated RNA, RNA(3'-rA). This 3'-deadenylation activity is metal-dependent and requires a 2'-hydroxyl at both the terminal adenosine and the penultimate nucleoside. Residues that contact the ATP/AMP in the MthRnl crystal structures are essential for the 3'-deadenylation activity, suggesting that 3'-adenosine may occupy the ATP-binding pocket. The 3'-end of cleaved RNA(3'-rA) consists of 2',3'-cyclic phosphate which protects RNA(3'-rA) from ligation and further deadenylation. These findings suggest that ATP-dependent RNA ligase may act on a specific set of 3'-adenylated RNAs to regulate their processing and downstream biological events.

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Project description:An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (MthRnl) catalyzes intramolecular ligation of single-stranded RNA to form a closed circular RNA via covalent ligase-AMP and RNA-adenylylate intermediate. Here, we report the X-ray crystal structures of an MthRnl•ATP complex as well as the covalent MthRnl-AMP intermediate. We also performed structure-guided mutational analysis to survey the functions of 36 residues in three component steps of the ligation pathway including ligase-adenylylation (step 1), RNA adenylylation (step 2) and phosphodiester bond synthesis (step 3). Kinetic analysis underscored the importance of motif 1a loop structure in promoting phosphodiester bond synthesis. Alanine substitutions of Thr117 or Arg118 favor the reverse step 2 reaction to deadenylate the 5'-AMP from the RNA-adenylate, thereby inhibiting step 3 reaction. Tyr159, Phe281 and Glu285, which are conserved among archaeal ATP-dependent RNA ligases and are situated on the surface of the enzyme, are required for RNA binding. We propose an RNA binding interface of the MthRnl based on the mutational studies and two sulfate ions that co-crystallized at the active site cleft in the MthRnl-AMP complex.

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