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Muino JM, Ruwe H, Qu Y, Maschmann S, Chen W, Zoschke R, Ohler U, Kaufmann K, Schmitz-Linneweber C. MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39074058 DOI: 10.1111/tpj.16945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024]
Abstract
The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5'-splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA-K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK-matK over-expressor exhibited elevated levels of the spliced tRNA-K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up-shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA-K(UUU), enabling the differential expression of functional chloroplast gene groups.
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Affiliation(s)
- Jose M Muino
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Hannes Ruwe
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Yujiao Qu
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Sascha Maschmann
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
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Molina-Sánchez MD, García-Rodríguez FM, Andrés-León E, Toro N. Identification of Group II Intron RmInt1 Binding Sites in a Bacterial Genome. Front Mol Biosci 2022; 9:834020. [PMID: 35281263 PMCID: PMC8914252 DOI: 10.3389/fmolb.2022.834020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
RmInt1 is a group II intron encoding a reverse transcriptase protein (IEP) lacking the C-terminal endonuclease domain. RmInt1 is an efficient mobile retroelement that predominantly reverse splices into the transient single-stranded DNA at the template for lagging strand DNA synthesis during host replication, a process facilitated by the interaction of the RmInt1 IEP with DnaN at the replication fork. It has been suggested that group II intron ribonucleoprotein particles bind DNA nonspecifically, and then scan for their correct target site. In this study, we investigated RmInt1 binding sites throughout the Sinorhizobium meliloti genome, by chromatin-immunoprecipitation coupled with next-generation sequencing. We found that RmInt1 binding sites cluster around the bidirectional replication origin of each of the three replicons comprising the S. meliloti genome. Our results provide new evidence linking group II intron mobility to host DNA replication.
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Affiliation(s)
- María Dolores Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Estación Experimental del Zaidín, Department of Soil Microbiology and Symbiotic Systems, Spanish National Research Council (CSIC), Granada, Spain
| | - Fernando Manuel García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Estación Experimental del Zaidín, Department of Soil Microbiology and Symbiotic Systems, Spanish National Research Council (CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Estación Experimental del Zaidín, Department of Soil Microbiology and Symbiotic Systems, Spanish National Research Council (CSIC), Granada, Spain
- *Correspondence: Nicolás Toro,
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LaRoche-Johnston F, Monat C, Verreault E, Cousineau B. Molecular characterization of both transesterification reactions of the group II intron circularization pathway. Nucleic Acids Res 2021; 49:6996-7010. [PMID: 34157113 PMCID: PMC8266578 DOI: 10.1093/nar/gkab537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
Group II introns can self-splice from RNA transcripts through branching, hydrolysis and circularization, being released as lariats, linear introns and circles, respectively. In contrast to branching, the circularization pathway is mostly based on assumptions and has been largely overlooked. Here, we address the molecular details of both transesterification reactions of the group II intron circularization pathway in vivo. We show that free E1 is recruited by the intron through base pairing interactions and that released intron circles can generate free E1 by the spliced exon reopening reaction. The first transesterification reaction was found to be induced inaccurately by the 3′OH of the terminal residue of free E1 at the 3′ splice site, producing circularization intermediates with heterogeneous 3′ ends. Nevertheless, specific terminal 3′OH, selected by a molecular ruler, was shown to precisely attack the 5′ splice site and release intron circles with 3′–5′ rather than 2′–5′ bonds at their circularization junction. Our work supports a circularization model where the recruitment of free E1 and/or displacement of cis-E1 induce a conformational change of the intron active site from the pre-5′ to the pre-3′ splice site processing conformation, suggesting how circularization might initiate at the 3′ instead of the 5′ splice site.
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Affiliation(s)
- Félix LaRoche-Johnston
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Caroline Monat
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Erika Verreault
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Benoit Cousineau
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
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