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Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Crawford KD, Shipman SL. An experimental census of retrons for DNA production and genome editing. Nat Biotechnol 2024:10.1038/s41587-024-02384-z. [PMID: 39289529 DOI: 10.1038/s41587-024-02384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/12/2024] [Indexed: 09/19/2024]
Abstract
Retrons are bacterial immune systems that use reverse-transcribed DNA (RT-DNA) to detect phage infection. They are also deployed for genome editing, where they are modified so that the RT-DNA encodes an editing donor. Retrons are common in bacterial genomes, and thousands of unique retrons have been predicted bioinformatically. However, few have been characterized experimentally. We add to the corpus of experimentally studied retrons, finding 62 empirically determined, natural RT-DNAs that are not predictable from the retron sequence alone. We synthesize >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production and test the relative efficacy of editing using retron-derived donors to edit bacterial, phage and human genomes. We observe large diversity in RT-DNA production and editing rates across retrons, finding that top-performing editors are drawn from a subset of the retron phylogeny and outperform those used in previous studies, reaching precise editing rates of up to 40% in human cells.
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Affiliation(s)
- Asim G Khan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | | | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco and University of California, Berkeley, Berkeley, CA, USA
| | - Rebecca F Fang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA, USA
| | - Kate D Crawford
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco, San Francisco and University of California, Berkeley, Berkeley, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
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Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL. An experimental census of retrons for DNA production and genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577267. [PMID: 38328236 PMCID: PMC10849725 DOI: 10.1101/2024.01.25.577267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.
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Affiliation(s)
- Asim G. Khan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | | | - Santiago C. Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Rebecca F. Fang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Neuroscience, University of California, San Francisco, CA, USA
| | - Seth L. Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
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Palka C, Fishman CB, Bhattarai-Kline S, Myers SA, Shipman S. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3490-3504. [PMID: 35293583 PMCID: PMC8989520 DOI: 10.1093/nar/gkac177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
Abstract
Retrons are bacterial retroelements that produce single-stranded, reverse-transcribed DNA (RT-DNA) that is a critical part of a newly discovered phage defense system. Short retron RT-DNAs are produced from larger, structured RNAs via a unique 2′-5′ initiation and a mechanism for precise termination that is not yet understood. Interestingly, retron reverse transcriptases (RTs) typically lack an RNase H domain and, therefore, depend on endogenous RNase H1 to remove RNA templates from RT-DNA. We find evidence for an expanded role of RNase H1 in the mechanism of RT-DNA termination, beyond the mere removal of RNA from RT-DNA:RNA hybrids. We show that endogenous RNase H1 determines the termination point of the retron RT-DNA, with differing effects across retron subtypes, and that these effects can be recapitulated using a reduced, in vitro system. We exclude mechanisms of termination that rely on steric effects of RNase H1 or RNA secondary structure and, instead, propose a model in which the tertiary structure of the single-stranded RT-DNA and remaining RNA template results in termination. Finally, we show that this mechanism affects cellular function, as retron-based phage defense is weaker in the absence of RNase H1.
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Affiliation(s)
| | | | | | | | - Seth L Shipman
- To whom correspondence should be addressed. Tel: +1 415 734 4058;
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Simon AJ, Ellington AD, Finkelstein IJ. Retrons and their applications in genome engineering. Nucleic Acids Res 2020; 47:11007-11019. [PMID: 31598685 PMCID: PMC6868368 DOI: 10.1093/nar/gkz865] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 11/14/2022] Open
Abstract
Precision genome editing technologies have transformed modern biology. These technologies have arisen from the redirection of natural biological machinery, such as bacteriophage lambda proteins for recombineering and CRISPR nucleases for eliciting site-specific double-strand breaks. Less well-known is a widely distributed class of bacterial retroelements, retrons, that employ specialized reverse transcriptases to produce noncoding intracellular DNAs. Retrons' natural function and mechanism of genetic transmission have remained enigmatic. However, recent studies have harnessed their ability to produce DNA in situ for genome editing and evolution. This review describes retron biology and function in both natural and synthetic contexts. We also highlight areas that require further study to advance retron-based precision genome editing platforms.
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Affiliation(s)
- Anna J Simon
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J Finkelstein
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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Characterization of cell death in Escherichia coli mediated by XseA, a large subunit of exonuclease VII. J Microbiol 2015; 53:820-8. [PMID: 26626352 DOI: 10.1007/s12275-015-5304-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 11/06/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Exonuclease VII (ExoVII) of Escherichia coli is a single strandspecific DNA nuclease composed of two different subunits: the large subunit, XseA, and the small subunit, XseB. In this study, we found that multicopy single-stranded DNAs (msDNAs), Ec83 and Ec78, are the in vivo substrates of ExoVII; the enzyme cuts the phosphodiester bond between the fourth and fifth nucleotides from the 5'end. We used this msDNA cleavage to assess ExoVII activity in vivo. Both subunits were required for enzyme activity. Expression of XseA without XseB caused cell death, even though no ExoVII activity was detected. The lethality caused by XseA was rescued by surplus XseB. In XseA-induced death, cells were elongated and multinucleated, and their chromosomes were fragmented and condensed; these are the morphological hallmarks of apoptotic cell death in bacteria. A putative caspase recognition sequence (FVAD) was found in XseA, and its hypothetical caspase product with 257 amino acids was as active as the intact protein in inducing cell death. We propose that under ordinary conditions, XseA protects chromosome as a component of the ExoVII enzyme, but in some conditions, the protein causes cell death; the destruction of cell is probably carried out by the amino terminal fragment derived from the cleavage of XseA by caspase-like enzyme.
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Das R, Shimamoto T, Hosen SMZ, Arifuzzaman M. Comparative Study of different msDNA (multicopy single-stranded DNA) structures and phylogenetic comparison of reverse transcriptases (RTs): evidence for vertical inheritance. Bioinformation 2011; 7:176-9. [PMID: 22102774 PMCID: PMC3218519 DOI: 10.6026/97320630007176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 10/02/2011] [Indexed: 11/23/2022] Open
Abstract
The multi-copy single-stranded DNA (msDNA) is yielded by the action of reverse transcriptase of retro-element in a wide range of pathogenic bacteria. Upon this phenomenon, it has been shown that msDNA is only produced by Eubacteria because many Eubacteria species contained reverse transcriptase in their special retro-element. We have screened around 111 Archaea at KEGG (Kyoto Encyclopedia of Genes and Genomes) database available at genome net server and observed three Methanosarcina species (M.acetivorans, M.barkeri and M.mazei), which also contained reverse transcriptase in their genome sequences. This observation of reverse transcriptase in Archaea raises questions regarding the origin of this enzyme. The evolutionary relationship between these two domains of life (Eubacteria and Archaea) hinges upon the phenomenon of retrons. Interestingly, the evolutionary trees based on the reverse transcriptases (RTs) and 16S ribosomal RNAs point out that all the Eubacteria RTs were descended from Archaea RTs during their evolutionary times. In addition, we also have shown some significant structural features among the newly identified msDNA-Yf79 in Yersinia frederiksenii with other of its related msDNAs (msDNA-St85, msDNA-Vc95, msDNA-Vp96, msDNA-Ec78 and msDNA-Ec83) from pathogenic bacteria. Together the degree of sequence conservation among these msDNAs, the evolutionary trees and the distribution of these ret (reverse transcriptase) genes suggest a possible evolutionary scenario. The single common ancestor of the organisms of Eubacteria and Archaea subgroups probably achieved this ret gene during their evolution through the vertical descent rather than the horizontal transformations followed by integration into this organism genome by a mechanism related to phage recognition and/or transposition.
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Affiliation(s)
- Rasel Das
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy’s Lake, Pahartali Chittagong – 4202, Bangladesh
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | | | - Mohammad Arifuzzaman
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy’s Lake, Pahartali Chittagong – 4202, Bangladesh
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Lampson BC, Inouye M, Inouye S. Retrons, msDNA, and the bacterial genome. Cytogenet Genome Res 2005; 110:491-9. [PMID: 16093702 DOI: 10.1159/000084982] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2003] [Accepted: 10/16/2003] [Indexed: 12/23/2022] Open
Abstract
Retrons are distinct DNA sequences that code for a reverse transcriptase (RT) similar to the RTs produced by retroviruses and other types of retroelements. Retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different bacteria. The retron RT is used to synthesize a strange satellite DNA known as msDNA. msDNA is actually a complex of DNA, RNA, and probably protein. It is composed of a small, single-stranded DNA, linked to a small, single-stranded RNA molecule. The 5' end of the DNA molecule is joined to an internal guanosine residue of the RNA molecule by a unique 2'-5' phosphodiester bond. msDNA is produced in many hundreds of copies per cell, but its function remains unknown. Although retrons are absent from the genome of most members of a population of related bacteria, retrons may not be entirely benign DNAs. Evidence is beginning to suggest that retron elements may produce small but potentially significant effects on the host cell. This includes the generation of repeated copies of the msDNA sequence in the genome, and increasing the frequency of spontaneous mutations. Because these events involve the retron RT, this may represent a source of reverse transcription in the bacterial cell. Thus, the process of reverse transcription, a force that has profoundly affected the content and structure of most eukaryotic genomes, may likewise be responsible for changes in some prokaryotic genomes.
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Affiliation(s)
- B C Lampson
- Department of Health Sciences, East Tennessee State University, Johnson City, TN, USA
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Lampson B, Inouye M, Inouye S. The msDNAs of bacteria. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2001; 67:65-91. [PMID: 11525386 DOI: 10.1016/s0079-6603(01)67025-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
msDNAs are small, structurally unique satellite DNAs found in a number of Gram-negative bacteria. Composed of hundreds of copies of single-stranded DNA--hence the name multicopy single-stranded DNA--msDNA is actually a complex of DNA, RNA, and probably protein. These peculiar molecules are synthesized by a reverse transcription mechanism catalyzed by a reverse transcriptase (RT) that is evolutionarily related to the polymerase found in the HIV virus. The genes, including the RT gene, responsible for the synthesis of msDNA are encoded in a retron, a genetic element that is carried on the bacterial chromosome. The retron is, in fact, the first such retroelement to be discovered in prokaryotic cells. This report is a comprehensive review of the many interesting questions raised by this unique DNA and the fascinating answers it has revealed. We have learned a great deal about the structure of msDNA: how it is synthesized, the structure and functions of the RT protein required to make it, its effects on the host cell, the retron element that encodes it, its possible origins and evolution, and even its potential usefulness as a practical genetic tool. Despite the impressive gains in our understanding of the msDNAs, however, the simple, fundamental question of its natural function remains an enduring mystery. Thus, we have much more to learn about the msDNAs of bacteria.
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MESH Headings
- Bacteria/enzymology
- Bacteria/genetics
- Base Sequence
- DNA, Bacterial/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Single-Stranded/biosynthesis
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- Evolution, Molecular
- Molecular Sequence Data
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA-Directed DNA Polymerase/metabolism
- Transcription, Genetic
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Affiliation(s)
- B Lampson
- Department of Health Sciences, East Tennessee State University, Johnson City 37614, USA
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