Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets

Ichiyanagi, Kenji; Beauregard, Arthur; Lawrence, Stacey; Smith, Dorie; Cousineau, Benoit; Belfort, Marlene

doi:10.1046/j.1365-2958.2002.03226.x

Cited by 95 publications

(96 citation statements)

References 60 publications

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“…To the best of our knowledge, such a mechanism has not been identified or proposed previously for DNA transposons. However, homology between the MGE RNA and the integration region in the host genome is exploited during group II intron retrohoming (71,72), suggesting that RNA-guided target recognition evolved more than once in MGE evolution. Many questions remain regarding the functioning of the CRISPRCas in Tn7-like transposons, including the possibility of direct interaction between the CRISPR effector complexes and TnsD(TniQ), TnsABC, or other transposon-encoded accessory proteins.…”

Section: Discussionmentioning

confidence: 99%

Recruitment of CRISPR-Cas systems by Tn7-like transposons

Peters

Makarova

Shmakov

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

245

267

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A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Phylogenetic analysis demonstrates that evolution of the CRISPR-Cas-containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences and, in some cases, chromosomal sequences adjacent to the transposon. We hypothesize that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. These findings suggest the existence of RNAguided transposition and fit the guns-for-hire concept whereby mobile genetic elements capture host defense systems and repurpose them for different stages in the life cycle of the element.CRISPR-Cas systems | Tn7 transposon | transposition strategy | crRNA guide | target-site selection

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Section: Discussionmentioning

confidence: 99%

Recruitment of CRISPR-Cas systems by Tn7-like transposons

Peters

Makarova

Shmakov

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

245

267

View full text Add to dashboard Cite

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“…The most probable source is ssDNA at the DNA replication fork because this ssDNA is the substrate for other group II introns that lack endonuclease domains (20,21,32). In this pathway, the intron reverse splices into either ssDNA or dsDNA at the replication fork and then uses nascent DNA of the leading or lagging strands to prime reverse transcription of the intron.…”

Section: Discussionmentioning

confidence: 99%

“…Other bacterial introns also lack endonuclease domains (e.g., bacterial classes A, D, and E), but introns of these classes are nevertheless mobile (18,19). The mechanism has been shown to involve the DNA replication fork, with the intron reverse splicing into either ssDNA or dsDNA and the primer being provided by either the leading or lagging strand (20,21).To address how bacterial class C introns insert at terminator motifs, we have investigated the B.h.I1 intron of Bacillus halodurans because it initially appeared to have a degree of sitespecificity, which would facilitate characterization. There are five B.h.I1 intron copies in the B. halodurans genome (Ͼ99.8% identity), with four located at analogous sites after the terminators of ribosomal RNA (rrn) operons B, D, F, and G (Fig.…”

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confidence: 99%

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Insertion of group II intron retroelements after intrinsic transcriptional terminators

Robart

Seo²,

Zimmerly³

2007

Proc. Natl. Acad. Sci. U.S.A.

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Mobile DNAs use many mechanisms to minimize damage to their hosts. Here we show that a subclass of group II introns avoids host damage by inserting directly after transcriptional terminator motifs in bacterial genomes (stem-loops followed by Ts). This property contrasts with the site-specific behavior of most group II introns, which insert into homing site sequences. Reconstituted ribonucleoprotein particles of the Bacillus halodurans intron B.h.I1 are shown to reverse-splice into DNA targets in vitro but require the DNA to be single-stranded and fold into a stem-loop analogous to the RNA structure that forms during transcription termination. Recognition of this DNA stem-loop motif accounts for in vivo target specificity. Insertion after terminators is a previously unrecognized strategy for a selfish DNA because it prevents interruption of coding sequences and restricts expression of the mobile DNA after integration.reverse transcriptase ͉ ribozyme ͉ mobile DNA ͉ bacteria R eduction of host damage is a basic principle of survival for selfish DNAs. The most common mechanisms involve suppression of transcription and translation, and integration into comparatively innocuous sites (1-4). Among retroelements, for example, R2 elements insert site-specifically into defined sequences within rDNA arrays while leaving most rDNAs intact (5). LINE1 elements have a less stringent preference for the sequence TTTTA, which results in integrations into gene-poor regions (6). Other retroelements target genomic loci through protein-protein interactions, to insert at pol III promoters (7), into telomeric elements (8), or into heterochromatin regions (9).Group II intron retroelements avoid host damage in two ways. First, the introns splice out of interrupted sequence at the RNA level to reconstitute functional coding sequence. Second, the introns insert site-specifically into compatible targets through retrohoming, thereby limiting potential targets. The mechanism of retrohoming is well characterized and is carried out by a ribonucleoprotein (RNP) complex composed of excised intron lariat and intron-encoded protein (IEP). The process is initiated by reverse splicing of lariat RNA into the top strand of a DNA target. The bottom strand is cleaved by the endonuclease domain of the IEP, and the integrated intron is reverse transcribed by the IEP, using the cleaved DNA as a primer. Repair processes complete the insertion steps (10-12).Normally, retrohoming of group II introns is highly sitespecific because of an Ϸ20-to 35-bp target sequence. Thirteen positions of the DNA target are recognized by base pairings between the intron RNA and the DNA exons via the interactions IBS1-EBS1, IBS2-EBS2 (intron and exon binding sites 1 and 2; 6 bp each), and either ␦-␦Ј (IIA introns; 1 bp) or IBS3-EBS3 (IIB, IIC introns; 1 bp). Additional target-specificity comes from IEP recognition of upstream exon DNA sequences Ϫ23 to Ϫ1 and downstream exon sequences ϩ4 to ϩ9 (11,13,14).In contrast to such site-specificity, introns of the phylogenetic subclass ''b...

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“…Because these retroelements rely on either DNA replication forks (17) or damaged DNA, including nicks, as target sites (18), acquisition of an endonuclease domain would likely have enhanced the efficiency and range of such elements. Remarkably, the study by Gladyshev and Arkhipova (7) revealed that functional copies of nuclease-deficient PLEs in species from protist, fungal, and plant clades are effectively single-copy genes, unlike nucleasecontaining retrotransposons.…”

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confidence: 99%