scholarly journals Sequence motifs recognized by the casposon integrase of Aciduliprofundum boonei

2019 ◽  
Vol 47 (12) ◽  
pp. 6386-6395 ◽  
Author(s):  
Pierre Béguin ◽  
Yankel Chekli ◽  
Guennadi Sezonov ◽  
Patrick Forterre ◽  
Mart Krupovic
Keyword(s):  
Integration Site ◽  
Target Site ◽  
Inverted Repeats ◽  
Leader Region ◽  
Sequence Motifs ◽  
Dna Transposons ◽  
Terminal Inverted Repeats ◽  
Thermophilic Archaeon ◽  
Evolutionary Connection

Abstract Casposons are a group of bacterial and archaeal DNA transposons encoding a specific integrase, termed casposase, which is homologous to the Cas1 enzyme responsible for the integration of new spacers into CRISPR loci. Here, we characterized the sequence motifs recognized by the casposase from a thermophilic archaeon Aciduliprofundum boonei. We identified a stretch of residues, located in the leader region upstream of the actual integration site, whose deletion or mutagenesis impaired the concerted integration reaction. However, deletions of two-thirds of the target site were fully functional. Various single-stranded 6-FAM-labelled oligonucleotides derived from casposon terminal inverted repeats were as efficiently incorporated as duplexes into the target site. This result suggests that, as in the case of spacer insertion by the CRISPR Cas1–Cas2 integrase, casposon integration involves splaying of the casposon termini, with single-stranded ends being the actual substrates. The sequence critical for incorporation was limited to the five terminal residues derived from the 3′ end of the casposon. Furthermore, we characterize the casposase from Nitrosopumilus koreensis, a marine member of the phylum Thaumarchaeota, and show that it shares similar properties with the A. boonei enzyme, despite belonging to a different family. These findings further reinforce the mechanistic similarities and evolutionary connection between the casposons and the adaptation module of the CRISPR–Cas systems.

scholarly journals Mutator-Like Elements with Multiple Long Terminal Inverted Repeats in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Ann A. Ferguson ◽  
Ning Jiang
Keyword(s):  
Transposable Elements ◽  
Binding Sites ◽  
Sequence Conservation ◽  
Inverted Repeats ◽  
Gene Fragment ◽  
Gene Sequences ◽  
Dna Transposons ◽  
Terminal Inverted Repeats ◽  
Multiple Copies ◽  
Successful Amplification

Mutator-like transposable elements (MULEs) are widespread in plants and the majority have long terminal inverted repeats (TIRs), which distinguish them from other DNA transposons. It is known that the long TIRs ofMutatorelements harbor transposase binding sites and promoters for transcription, indicating that the TIR sequence is critical for transposition and for expression of sequences between the TIRs. Here, we report the presence of MULEs with multiple TIRs mostly located in tandem. These elements are detected in the genomes of maize, tomato, rice, andArabidopsis. Some of these elements are present in multiple copies, suggesting their mobility. For those elements that have amplified, sequence conservation was observed for both of the tandem TIRs. For one MULE family carrying a gene fragment, the elements with tandem TIRs are more prevalent than their counterparts with a single TIR. The successful amplification of this particular MULE demonstrates that MULEs with tandem TIRs are functional in both transposition and duplication of gene sequences.

scholarly journals Maize Mu Transposons Are Targeted to the 5′ Untranslated Region of the gl8 Gene and Sequences Flanking Mu Target-Site Duplications Exhibit Nonrandom Nucleotide Composition Throughout the Genome

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 697-716 ◽  
Author(s):  
Charles R Dietrich ◽  
Feng Cui ◽  
Mark L Packila ◽  
Jin Li ◽  
Daniel A Ashlock ◽  
...  
Keyword(s):  
Strong Evidence ◽  
Site Selection ◽  
Untranslated Region ◽  
Insertion Site ◽  
Nucleotide Composition ◽  
Target Site ◽  
Large Percentage ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Insertion Sites

Abstract The widespread use of the maize Mutator (Mu) system to generate mutants exploits the preference of Mu transposons to insert into genic regions. However, little is known about the specificity of Mu insertions within genes. Analysis of 79 independently isolated Mu-induced alleles at the gl8 locus established that at least 75 contain Mu insertions. Analysis of the terminal inverted repeats (TIRs) of the inserted transposons defined three new Mu transposons: Mu10, Mu11, and Mu12. A large percentage (>80%) of the insertions are located in the 5′ untranslated region (UTR) of the gl8 gene. Ten positions within the 5′ UTR experienced multiple independent Mu insertions. Analyses of the nucleotide composition of the 9-bp TSD and the sequences directly flanking the TSD reveals that the nucleotide composition of Mu insertion sites differs dramatically from that of random DNA. In particular, the frequencies at which C's and G's are observed at positions −2 and +2 (relative to the TSD) are substantially higher than expected. Insertion sites of 315 RescueMu insertions displayed the same nonrandom nucleotide composition observed for the gl8-Mu alleles. Hence, this study provides strong evidence for the involvement of sequences flanking the TSD in Mu insertion-site selection.

scholarly journals The IS1111 Family Members IS4321 and IS5075 Have Subterminal Inverted Repeats and Target the Terminal Inverted Repeats of Tn21 Family Transposons

2003 ◽  
Vol 185 (21) ◽  
pp. 6371-6384 ◽  
Author(s):  
Sally R. Partridge ◽  
Ruth M. Hall
Keyword(s):  
Inverted Repeat ◽  
Insertion Sequence ◽  
Family Members ◽  
Target Site ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Is Elements ◽  
Target Sites ◽  
Specific Position ◽  
The Right

ABSTRACT IS5075 and IS4321 are closely related (93.1% identical) members of the IS1111 family that target a specific position in the 38-bp terminal inverted repeats of Tn21 family transposons and that are inserted in only one orientation. They are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (TAATGAG) or 6 bp (AATGAG) to the left of the left inverted repeats and 3 bp (AGA) or 4 bp (AGAT) to the right of the right inverted repeat. Circular forms of IS5075 and IS4321 in which the inverted repeats are separated by abutting terminal sequences (AGATAATGAG) were detected. A similar circular product was found for the related ISPa11. Transposition of IS4321 into the 38-bp target site was detected, but a flanking duplication was not generated. The precisely reconstituted target site was also identified. Over 50 members of the IS1111 family were identified. They encode related transposases, have related inverted repeats, and include related bases that lie outside these inverted repeats. In some, the flanking bases number 5 or 6 on the left and 4 or 3 on the right. Specific target sites were found for several of these insertion sequence (IS) elements. IS1111 family members therefore differ from the majority of IS elements, which are characterized by terminal inverted repeats and a target site duplication, and from members of the related IS110 family, which do not have obvious inverted repeats near their termini.

Evidence for an ancient bilaterian origin of the RAG-like transposon

2019 ◽  
Author(s):  
Eliza C. Martin ◽  
Celia Vicari ◽  
Louis Tsakou-Ngouafo ◽  
Pierre Pontarotti ◽  
Andrei J. Petrescu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Adaptive Immunity ◽  
Active Site ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Target Site ◽  
Inverted Repeats ◽  
Adjacent Gene ◽  
Terminal Inverted Repeats ◽  
History Of

Abstract Background V(D)J recombination is essential for adaptive immunity in jawed vertebrates and is initiated by the RAG1-RAG2 endonuclease. The RAG1 and RAG2 genes are thought to have evolved from a RAGL (RAG-like) transposon containing convergently-oriented RAG1-like (RAG1L) and RAG2-like (RAG2L) genes. Elements resembling this presumptive evolutionary precursor have thus far only been detected convincingly in deuterostomes, leading to the model that the RAGL transposon first appeared in an early deuterostome. Results We have identified numerous RAGL transposons in the genomes of protostomes, including oysters and mussels (phylum Mollusca) and a ribbon worm (phylum Nemertea), and in the genomes of several cnidarians. Phylogenetic analyses indicate that the RAGL transposon family evolved in a vertical manner within the Bilateria clade. Many of the RAGL transposons identified in protostomes are intact elements containing convergently oriented RAG1L and RAG2L genes flanked by terminal inverted repeats (TIRs) and target site duplications with striking similarities with the corresponding elements in deuterostomes. In addition, protostome genomes contain numerous intact RAG1L-RAG2L adjacent gene pairs that lack detectable flanking TIRs. Domains and critical active site and structural amino acids needed for endonuclease and transposase activity are present and conserved in many of the predicted RAG1L and RAG2L proteins encoded in protostome genomes. Conclusions Active RAGL transposons were present in multiple protostome lineages and were transmitted vertically during protostome evolution. It appears that the RAGL transposon family was broadly active during bilaterian evolution, undergoing multiple duplication and loss/fossilization events, with the RAGL genes that persist in present day protostomes perhaps constituting both active RAGL transposons and domesticated RAGL genes. Our findings indicate that the RAGL transposon arose earlier in evolution than previously thought, either in an early bilaterian or prior to the divergence of bilaterians and non-bilaterians, and alter our understanding of the evolutionary history of this important transposon family.

scholarly journals IS481 and IS1002 ofBordetella pertussis Create a 6-Base-Pair Duplication upon Insertion at a Consensus Target Site

1998 ◽  
Vol 180 (18) ◽  
pp. 4963-4966 ◽  
Author(s):  
Scott Stibitz
Keyword(s):  
Dna Sequence ◽  
Bordetella Pertussis ◽  
Base Pair ◽  
Insertion Sequence ◽  
Target Site ◽  
Inverted Repeats ◽  
Recognition Sequence ◽  
Base Pairs ◽  
Terminal Inverted Repeats ◽  
Ofbordetella Pertussis

ABSTRACT The insertion sequence IS481 and its isoform IS1002 have been observed to transpose into thebvgAS locus of Bordetella pertussis, for which the DNA sequence has previously been determined. Upon insertion of IS481 at three different sites and IS1002 at one site, a 6-bp sequence originally present was found at the junction of bvg and insertion sequence DNA. This indicates that, contrary to prior reports, IS481 and IS1002 do create a duplication upon insertion. In this light, examination of these and other examples of IS481 and IS1002reported in the literature leads to the observation that the 6-bp recognition sequence usually fits the consensus NCTAGN. The near-palindromic nature of this sequence, when directly repeated at the ends of IS481 or IS1002, apparently led to the interpretation that 5 of these base pairs were part of the terminal inverted repeats flanking these elements.

scholarly journals Functional requirement of terminal inverted repeats for efficient ProtoRAG activity reveals the early evolution of V(D)J recombination

2019 ◽  
Vol 7 (2) ◽  
pp. 403-417 ◽  
Author(s):  
Xin Tao ◽  
Shaochun Yuan ◽  
Fan Chen ◽  
Xiaoman Gao ◽  
Xinli Wang ◽  
...  
Keyword(s):  
Consensus Sequence ◽  
Protein Stabilization ◽  
Inverted Repeats ◽  
Functional Requirement ◽  
Signal Sequences ◽  
Terminal Inverted Repeats ◽  
Homologous Sequences ◽  
Recombination Signal Sequences ◽  
Chordate Evolution ◽  
The Common

Abstract The discovery of ProtoRAG in amphioxus indicated that vertebrate RAG recombinases originated from an ancient transposon. However, the sequences of ProtoRAG terminal inverted repeats (TIRs) were obviously dissimilar to the consensus sequence of mouse 12/23RSS and recombination mediated by ProtoRAG or RAG made them incompatible with each other. Thus, it is difficult to determine whether or how 12/23RSS persisted in the vertebrate RAG system that evolved from the TIRs of ancient RAG transposons. Here, we found that the activity of ProtoRAG is highly dependent on its asymmetric 5′TIR and 3′TIR, which are composed of conserved TR1 and TR5 elements and a partially conserved TRsp element of 27/31 bp to separate them. Similar to the requirements for the recombination signal sequences (RSSs) of RAG recombinase, the first CAC in TR1, the three dinucleotides in TR5 and the specific length of the partially conserved TRsp are important for the efficient recombination activity of ProtoRAG. In addition, the homologous sequences flanking the signal sequences facilitate ProtoRAG- but not RAG-mediated recombination. In addition to the diverged TIRs, two differentiated functional domains in BbRAG1L were defined to coordinate with the divergence between TIRs and RSSs. One of these is the CTT* domain, which facilitates the specific TIR recognition of the BbRAGL complex, and the other is NBD*, which is responsible for DNA binding and the protein stabilization of the BbRAGL complex. Thus, our findings reveal that the functional requirement for ProtoRAG TIRs is similar to that for RSS in RAG-mediated recombination, which not only supports the common origin of ProtoRAG TIRs and RSSs from the asymmetric TIRs of ancient RAG transposons, but also reveals the development of RAG and RAG-like machineries during chordate evolution.

scholarly journals Two Chimeric Chromosomes of Streptomyces coelicolor A3(2) Generated by Single Crossover of the Wild-Type Chromosome and Linear Plasmid SCP1

2004 ◽  
Vol 186 (19) ◽  
pp. 6553-6559 ◽  
Author(s):  
Masayuki Yamasaki ◽  
Haruyasu Kinashi
Keyword(s):  
Genome Evolution ◽  
Streptomyces Coelicolor ◽  
Linear Plasmid ◽  
Nucleotide Sequencing ◽  
Inverted Repeats ◽  
Wild Type ◽  
Linear Chromosome ◽  
Terminal Inverted Repeats ◽  
Type Chromosome ◽  
Chromosomal Duplication

ABSTRACT Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1′-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1′-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1′-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1′-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.

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