DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs

Nucleic Acids Research, Jan 2005

Mariner-like elements (MLEs) are DNA transposons found throughout the plant and animal kingdoms. A previous computational survey of the rice (Oryza sativa) genome sequence revealed 34 full length MLEs (Osmars) belonging to 25 distinct families. This survey, which also identified sequence similarities between the Osmar elements and the Stowaway superfamily of MITEs, led to the formulation of a hypothesis whereby Stowaways are mobilized by OSMAR transposases. Here we investigate the DNA-binding activities and specificities of two OSMAR transposases, OSMAR5 and OSMAR10. Like other mariner-like transposases, the OSMARs bind specifically to the terminal inverted repeat (TIR) sequences of their encoding transposons. OSMAR5 binds DNA through a bipartite N-terminal domain containing two functionally separable helix-turn-helix motifs, resembling the paired domain of Tc1-like transposases and PAX transcription factors in metazoans. Furthermore, binding of the OSMARs is not limited to their own TIRs; OSMAR5 transposase can also interact in vitro with TIRs from closely related Osmar elements and with consensus TIRs of several Stowaway families mined from the rice genome sequence. These results provide the first biochemical evidence for a functional relationship between Osmar elements and Stowaway MITEs and lead us to suggest that there is extensive cross-talk among related but distinct transposon families co-existing in a single eukaryote genome.

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DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs

Nucleic Acids Research DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs Ce´ dric Feschotte 0 1 Mark T. Osterlund 1 Ryan Peeler 1 Susan R. Wessler 1 0 Department of Biology, University of Texas at Arlington , Arlington, TX 76019 , USA 1 Department of Plant Biology, University of Georgia , Athens, GA 30602 , USA *To whom correspondence should be addressed. Tel: +1 706 542 1870; Fax: +1 706 542 1805; Email: Correspondence may also be addressed to Ce´dric Feschotte. Tel: +1 817 272 2426; Fax: +1 817 272 2855; Email: - Mariner-like elements (MLEs) are DNA transposons found throughout the plant and animal kingdoms. A previous computational survey of the rice (Oryza sativa) genome sequence revealed 34 full length MLEs (Osmars) belonging to 25 distinct families. This survey, which also identified sequence similarities between the Osmar elements and the Stowaway superfamily of MITEs, led to the formulation of a hypothesis whereby Stowaways are mobilized by OSMAR transposases. Here we investigate the DNAbinding activities and specificities of two OSMAR transposases, OSMAR5 and OSMAR10. Like other mariner-like transposases, the OSMARs bind specifically to the terminal inverted repeat (TIR) sequences of their encoding transposons. OSMAR5 binds DNA through a bipartite N-terminal domain containing two functionally separable helix-turn-helix motifs, resembling the paired domain of Tc1-like transposases and PAX transcription factors in metazoans. Furthermore, binding of the OSMARs is not limited to their own TIRs; OSMAR5 transposase can also interact in vitro with TIRs from closely related Osmar elements and with consensus TIRs of several Stowaway families mined from the rice genome sequence. These results provide the first biochemical evidence for a functional relationship between Osmar elements and Stowaway MITEs and lead us to suggest that there is extensive cross-talk among related but distinct transposon families co-existing in a single eukaryote genome. Transposable elements make up the largest fraction of many eukaryotic genomes. They are divided into two classes based on their mechanism of transposition (1–3). Class 1 elements (retrotransposons) transpose by means of an RNA intermediate in a reaction involving several enzymes, including reverse transcriptase and integrase. In contrast, class 2 elements (DNA transposons) move directly via DNA and the transposition reaction is catalyzed by an element-encoded enzyme called transposase. During transposition of class 2 elements, transposase molecules bind to the transposon in a sequence-specific manner and catalyze both the DNA cleavage and strand transfer steps of the so-called ‘cut-and-paste’ reaction (3). Nonautonomous DNA transposons do not encode transposase, but can still undergo transposition using transposase encoded by an autonomous element [for a review, see (2)]. Because nonautonomous elements are often internal deletion derivatives of autonomous elements, they retain the terminal binding sites necessary to interact with transposase. A seemingly distinct class of nonautonomous elements, called miniature-inverted repeat elements (MITEs), was first identified in plant genomes (4–7) and was subsequently identified in a wide range of animal genomes, including those of nematodes, mosquitoes, sea squirt, zebrafish, frogs and humans [for a review, see (6)]. Elements structurally reminiscent of MITEs were also described in eubacteria and archaea (8–10). Like most other nonautonomous transposons, MITEs have no coding capacity and thus must rely on transposase encoded in trans by autonomous elements. MITE families are distinguished from other nonautonomous DNA transposons by their high copy numbers and structural homogeneity. These features are consistent with the initial amplification of one or a few MITEs. Because MITEs do not encode transposase, their initial classification was based on similarities in noncoding sequences The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors including the terminal inverted repeat (TIR) and target site duplication (TSD). Using these criteria, most plant MITEs were assigned to one of two groups, Tourist or Stowaway [for a review, see (6,7)]. Subsequently, sequence similarity was detected between the TIRs and TSDs of MITEs and of transposase-encoding elements in the same genome. For example, Tourist MITEs share sequence similarity with the TIRs of the transpoase-encoding PIF/Harbinger superfamily (11–13), while the TIR and TSD of Stowaway MITEs are similar to the TIR and TSD of Tc1/mariner elements (5,14,15). In a recent genome-wide analysis of rice, the sequences of virtually all Stowaway MITEs and mariner-like elements (MLEs) (called Osmars) were identified and compared (16). More than 22 000 Stowaway MITEs were classified into 36 families, while 34 different Osmars were found to group into three major clades (...truncated)


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Cédric Feschotte, Mark T. Osterlund, Ryan Peeler, Susan R. Wessler. DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs, Nucleic Acids Research, 2005, pp. 2153-2165, 33/7, DOI: 10.1093/nar/gki509