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Bacterial Retrons Function in Anti-Phage Defense

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Bacterial Retrons Function in Anti-Phage Defense Article Bacterial Retrons Function In Anti-Phage Defense Graphical Abstract Authors Adi Millman, Aude Bernheim, Retrons appear in an operon Retrons generate an RNA-DNA hybrid via reverse transcription with additional “effector” genes Avigail Stokar-Avihail, ..., Azita Leavitt, ncRNA Reverse Transcriptase (RT) msDNA Ribosyltransferase Yaara Oppenheimer-Shaanan, (RNA-DNA hybrid) DNA-binding RT Rotem Sorek RNA Retron function 2 transmembrane 5’ G RT domains 2’-5’ 3’ was unknown 3’ RT Correspondence cDNA RT Cold-shock [email protected] 5’ G 2’ 3’ G G cDNA RT RT ATPase Nuclease In Brief reverse transcription RNase H Retrons are part of a large family of anti- Retrons protect bacteria from phage Inhibition of RecBCD by phages triggers retron Ec48 defense phage defense systems that are widespread in bacteria and confer Bacterial density during phage infection Growth resistance against a broad range of B Effector arrest RT D RT activation with retron C B phages, mediated by abortive infection. Effector no retron Ec48 “guards” the bacterial Effector activation leads RecBCD complex to abortive infection bacterial density Retron Ec48 RT 2TM time RecBCD inhibitor B B D D RT Bacteria without retron Bacteria with retron C C B B Phage proteins inhibit RecBCD Retron Ec48 senses RecBCD inhibition Highlights d Retrons are preferentially located in defense islands d Retrons, together with their effector genes, protect bacteria from phages d Protection from phage is mediated by abortive infection d Retron Ec48 guards RecBCD. Inhibition of RecBCD by phages triggers retron defense Millman et al., 2020, Cell 183, 1–11 December 10, 2020 ª 2020 Elsevier Inc. https://doi.org/10.1016/j.cell.2020.09.065 ll Please cite this article in press as: Millman et al., Bacterial Retrons Function In Anti-Phage Defense, Cell (2020), https://doi.org/10.1016/ j.cell.2020.09.065 ll Article Bacterial Retrons Function In Anti-Phage Defense Adi Millman,1,3 Aude Bernheim,1,3 Avigail Stokar-Avihail,1,3 Taya Fedorenko,1 Maya Voichek,1,2 Azita Leavitt,1 Yaara Oppenheimer-Shaanan,1 and Rotem Sorek1,4,* 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel 2Present address: Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria 3These authors contributed equally 4Lead Contact *Correspondence: [email protected] https://doi.org/10.1016/j.cell.2020.09.065 SUMMARY Retrons are bacterial genetic elements comprised of a reverse transcriptase (RT) and a non-coding RNA (ncRNA). The RT uses the ncRNA as template, generating a chimeric RNA/DNA molecule in which the RNA and DNA components are covalently linked. Although retrons were discovered three decades ago, their func- tion remained unknown. We report that retrons function as anti-phage defense systems. The defensive unit is composed of three components: the RT, the ncRNA, and an effector protein. We examined multiple retron systems and show that they confer defense against a broad range of phages via abortive infection. Focusing on retron Ec48, we show evidence that it ‘‘guards’’ RecBCD, a complex with central anti-phage functions in bacteria. Inhibition of RecBCD by phage proteins activates the retron, leading to abortive infection and cell death. Thus, the Ec48 retron forms a second line of defense that is triggered if the first lines of defense have collapsed. INTRODUCTION mentally in detail (Simon et al., 2019). The documented ret- rons were all named following a naming convention that in- Retrons are genetic elements composed of a non-coding RNA cludes the first letters of their genus and species names, as (ncRNA) and a specialized reverse transcriptase (RT). These ele- well as the length of reverse-transcribed DNA (e.g., Ec48 is ments typically generate a chimeric RNA-DNA molecule, in which a retron found in Escherichia coli whose reverse transcribed the RNA and DNA components are covalently attached by a 20-50 DNA segment is 48 nt long). All studied retrons contain an phosphodiester bond (Figure S1). Retrons were originally discov- RT and a ncRNA, with the conserved guanosine from which ered in 1984 in Myxococcus xanthus,whenYee et al. (1984)iden- reverse transcription is initiated (Lampson et al., 2001). tified a short, multi-copy single-stranded DNA (msDNA) that is However, the sequences and lengths of the reverse tran- abundantly present in the bacterial cell. Further studies showed scribed template significantly vary and frequently show no that this single-stranded DNA (ssDNA) is covalently linked to an sequence similarity between retrons (Das et al., 2011). The RNA molecule (Dhundale et al., 1987) and later deciphered in ability of retrons to produce ssDNA in situ has been adapted detail the biochemical steps leading to the formation of the for multiple applications of synthetic biology and genome RNA-DNA hybrid (Lampson et al., 1989). It was found that the ret- engineering (Farzadfard and Lu, 2014; Sharon et al., 2018; ron ncRNA is the precursor of the hybrid molecule and folds into a Simon et al., 2018, 2019). typical structure that is recognized by the RT (Hsu et al., 1989). Although retrons have been studied for over 35 years, their The RT then reverse transcribes part of the ncRNA, starting biological function remained unknown. It has been suggested from the 20-end of a conserved guanosine residue found immedi- that retrons are a form of selfish genetic elements (Rice and ately after a double-stranded RNA structure within the ncRNA Lampson, 1995) or have a function in coping with starvation (Lampson et al., 1989). A portion of the ncRNA serves as a tem- (Herzer, 1996), pathogenesis (Elfenbein et al., 2015), and cell- plate for reverse transcription, which terminates at a defined posi- specialization (Simon et al., 2019). However, evidence for these tion within the ncRNA (Lampson et al., 1989). During reverse tran- functions was circumstantial, and the mechanism by which ret- scription, cellular RNase H degrades the segment of the ncRNA rons would exert these putative functions was not identified. In that serves as template, but not other parts of the ncRNA, yielding the current study, we show that retrons form a functional compo- the mature RNA-DNA hybrid (Lampson et al., 1989; Figure S1). nent in a large family of anti-phage defense systems that are Dozens of retrons have been documented in a variety of widespread in bacteria and confer resistance against a broad microbial genomes, and 16 of them were studied experi- range of phages. Cell 183, 1–11, December 10, 2020 ª 2020 Elsevier Inc. 1 Please cite this article in press as: Millman et al., Bacterial Retrons Function In Anti-Phage Defense, Cell (2020), https://doi.org/10.1016/ j.cell.2020.09.065 ll Article RESULTS that the new defense system we discovered contains a previ- ously unidentified retron. A Retron-Containing Genetic System Protects against To examine whether the retron features are involved in the Phage Infection anti-phage activity of the new defense system, we experimented We initiated the current study by searching for RT genes that may with mutated versions of the system. Point mutations in the participate in defense against phages. This search was inspired conserved YADD motif of the catalytic core of the RT (D200A by prior reports on the involvement of RTs in bacterial defense and D201A) (Lampson et al., 2005) rendered the system inactive (Fortier et al., 2005; Silas et al., 2016; Wang et al., 2011) and (Figure 1G). Similarly, a point mutation in the ncRNA, mutating phage counter-defense mechanisms (Doulatov et al., 2004). the guanosine predicted as the branching residue priming the Because bacterial defense systems tend to cluster in ‘‘defense reverse transcription (Hsu et al., 1992) (G > C at position 17 of islands’’ in microbial genomes (Cohen et al., 2019; Doron et al., the ncRNA), or the second conserved guanosine that was shown 2018; Makarova et al., 2011), we focused on RT genes of un- in other retrons to be essential for initiation of reverse transcrip- known function that are frequently encoded near known anti- tion (Hsu et al., 1992) (G > A at position 147), completely abol- phage systems such as restriction enzymes (STAR Methods). ished defense against phages (Figure 1G). These results suggest One of these RT genes is presented in Figures 1A and 1B. Ho- that proper reverse transcription of the retron ncRNA is essential mologs of this gene appear in a diverse set of bacteria (102 ho- for its defensive function. We also found that a point mutation in mologs found in species belonging to the Proteobacteria and Fir- the ATP-binding motif of the associated predicted OLD-family micutes phyla) and show marked tendency to co-localize with endonuclease gene (K36A) completely eliminated the defense known defense systems, with 60 (59%) located near known phenotype, showing that the predicted endonuclease gene is anti-phage operons (Figures 1A and 1B). The RT gene is always an indispensable component of the retron-containing defense found next to a second gene with a predicted OLD-family endo- system. We therefore conclude that the new defense system nuclease domain (Schiltz et al., 2020), and we therefore hypoth- consists of three components essential for its anti-phage activ- esized that the RT together with the endonuclease form a two- ity: the RT and ncRNA (that together form an active retron) and gene phage resistance system. To test this hypothesis, we an additional gene that contains a predicted endonuclease cloned this two-gene system from E. coli 200499, together domain. Following a recently proposed revised nomenclature with its flanking intergenic regions, into the laboratory strain for retrons (Simon et al., 2019), we termed this defense system E.
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