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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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González-Delgado A, Mestre MR, Martínez-Abarca F, Toro N. Prokaryotic reverse transcriptases: from retroelements to specialized defense systems. FEMS Microbiol Rev 2021; 45:fuab025. [PMID: 33983378 PMCID: PMC8632793 DOI: 10.1093/femsre/fuab025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/07/2021] [Indexed: 12/30/2022] Open
Abstract
Reverse transcriptases (RTs) catalyze the polymerization of DNA from an RNA template. These enzymes were first discovered in RNA tumor viruses in 1970, but it was not until 1989 that they were found in prokaryotes as a key component of retrons. Apart from RTs encoded by the 'selfish' mobile retroelements known as group II introns, prokaryotic RTs are extraordinarily diverse, but their function has remained elusive. However, recent studies have revealed that different lineages of prokaryotic RTs, including retrons, those associated with CRISPR-Cas systems, Abi-like RTs and other yet uncharacterized RTs, are key components of different lines of defense against phages and other mobile genetic elements. Prokaryotic RTs participate in various antiviral strategies, including abortive infection (Abi), in which the infected cell is induced to commit suicide to protect the host population, adaptive immunity, in which a memory of previous infection is used to build an efficient defense, and other as yet unidentified mechanisms. These prokaryotic enzymes are attracting considerable attention, both for use in cutting-edge technologies, such as genome editing, and as an emerging research topic. In this review, we discuss what is known about prokaryotic RTs, and the exciting evidence for their domestication from retroelements to create specialized defense systems.
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Affiliation(s)
- Alejandro González-Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Mario Rodríguez Mestre
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, Madrid, Spain
| | - Francisco Martínez-Abarca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
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García-Rodríguez FM, Neira JL, Marcia M, Molina-Sánchez MD, Toro N. A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp. Nucleic Acids Res 2019; 47:7605-7617. [PMID: 31127285 PMCID: PMC6698660 DOI: 10.1093/nar/gkz468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Group II introns are self-splicing mobile genetic retroelements. The spliced intron RNA and the intron-encoded protein (IEP) form ribonucleoprotein particles (RNPs) that recognize and invade specific DNA target sites. The IEP is a reverse transcriptase/maturase that may bear a C-terminal endonuclease domain enabling the RNP to cleave the target DNA strand to prime reverse transcription. However, some mobile introns, such as RmInt1, lack the En domain but nevertheless retrohome efficiently to transient single-stranded DNA target sites at a DNA replication fork. Their mobility is associated with host DNA replication, and they use the nascent lagging strand as a primer for reverse transcription. We searched for proteins that interact with RmInt1 RNPs and direct these RNPs to the DNA replication fork. Co-immunoprecipitation assays suggested that DnaN (the β-sliding clamp), a component of DNA polymerase III, interacts with the protein component of the RmInt1 RNP. Pulldown assays, far-western blots and biolayer interferometry supported this interaction. Peptide binding assays also identified a putative DnaN-interacting motif in the RmInt1 IEP structurally conserved in group II intron IEPs. Our results suggest that intron RNP interacts with the β-sliding clamp of the DNA replication machinery, favouring reverse splicing into the transient ssDNA at DNA replication forks.
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Affiliation(s)
- Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.,Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, Grenoble 38042, France
| | - María D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain
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Molina-Sánchez MD, Toro N. DNA cleavage and reverse splicing of ribonucleoprotein particles reconstituted in vitro with linear RmInt1 RNA. RNA Biol 2019; 16:930-939. [PMID: 30943851 DOI: 10.1080/15476286.2019.1601379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The RmInt1 group II intron is an efficient self-splicing mobile retroelement that catalyzes its own excision as lariat, linear and circular molecules. In vivo, the RmInt1 lariat and the reverse transcriptase (IEP) it encodes form a ribonucleoprotein particle (RNP) that recognizes the DNA target for site-specific full intron insertion via a two-step reverse splicing reaction. RNPs containing linear group II intron RNA are generally thought to be unable to complete the reverse splicing reaction. Here, we show that reconstituted in vitro RNPs containing linear RmInt1 ΔORF RNA can mediate the cleavage of single-stranded DNA substrates in a very precise manner with the attachment of the intron RNA to the 3´exon as the first step of a reverse splicing reaction. Notably, we also observe molecules in which the 5´exon is linked to the RmInt1 RNA, suggesting the completion of the reverse splicing reaction, albeit rather low and inefficiently. That process depends on DNA target recognition and can be successful completed by RmInt1 RNPs with linear RNA displaying 5´ modifications.
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Affiliation(s)
- María Dolores Molina-Sánchez
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
| | - Nicolás Toro
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
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Novikova O, Belfort M. Mobile Group II Introns as Ancestral Eukaryotic Elements. Trends Genet 2017; 33:773-783. [PMID: 28818345 DOI: 10.1016/j.tig.2017.07.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/06/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes. Although there is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable differences in survival strategies between them. Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including telomeres, and spliceosomes is unmistakable.
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Affiliation(s)
- Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA.
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Belfort M. Mobile self-splicing introns and inteins as environmental sensors. Curr Opin Microbiol 2017; 38:51-58. [PMID: 28482231 DOI: 10.1016/j.mib.2017.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/12/2017] [Indexed: 12/31/2022]
Abstract
Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be selfish parasites, group I and group II introns and inteins can be triggered by environmental cues to splice and/or to mobilize. These cues include stressors such as oxidizing agents, reactive oxygen and nitrogen species, starvation, temperature, osmolarity and DNA damage. Their sensitivity to these stimuli leads to a carefully choreographed dance between the mobile element and its host that is in tune with the cellular environment. This responsiveness to a changing milieu provides strong evidence that these diverse, self-splicing mobile elements have adapted to react to prevailing conditions, to the potential advantage of both the element and its host.
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Affiliation(s)
- Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Life Sciences Research Building 2061, 1400 Washington Avenue, Albany, NY 12222, USA.
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Guha TK, Wai A, Hausner G. Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering. Comput Struct Biotechnol J 2017; 15:146-160. [PMID: 28179977 PMCID: PMC5279741 DOI: 10.1016/j.csbj.2016.12.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 12/26/2022] Open
Abstract
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.
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Affiliation(s)
| | | | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
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