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Schwarz TS, Berkemer SJ, Bernhart SH, Weiß M, Ferreira-Cerca S, Stadler PF, Marchfelder A. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. Front Microbiol 2020; 11:594838. [PMID: 33329479 PMCID: PMC7714728 DOI: 10.3389/fmicb.2020.594838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.
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Affiliation(s)
| | - Sarah J Berkemer
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions, Leipzig University, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Matthias Weiß
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Peter F Stadler
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Santa Fe Institute, Santa Fe, NM, United States
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Stachler AE, Schwarz TS, Schreiber S, Marchfelder A. CRISPRi as an efficient tool for gene repression in archaea. Methods 2020; 172:76-85. [DOI: 10.1016/j.ymeth.2019.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 11/30/2022] Open
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Maier LK, Stachler AE, Saunders SJ, Backofen R, Marchfelder A. An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. J Biol Chem 2014; 290:4192-201. [PMID: 25512373 PMCID: PMC4326828 DOI: 10.1074/jbc.m114.617506] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3′ handle are still active in triggering an interference reaction. The complete 3′ handle could be removed without loss of activity. However, manipulations of the 5′ handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference.
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Affiliation(s)
| | | | - Sita J Saunders
- the Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, and
| | - Rolf Backofen
- the Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, and the BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, Albert-Ludwigs-University Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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