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Mariner-like transposases are widespread and diverse in flowering plants.

ABSTRACT: Complete and partial sequences of mariner-like elements (MLEs) have been reported for hundreds of species of animals, but only two have been identified in plants. On the basis of these two plant MLEs and several related sequences identified by database searches, plant-specific degenerate primers were derived and used to amplify a conserved region of MLE transposase genes from a variety of plant genomes. Positive products were obtained for 6 dicots and 31 monocots of 54 plant species tested. Phylogenetic analysis of 68 distinct MLE transposase sequences from 25 grass species is consistent with vertical transmission and rapid diversification of multiple lineages of transposases. Surprisingly, the evolution of MLEs in grasses was accompanied by repeated and independent acquisition of introns in a localized region of the transposase gene.

SUBMITTER: Feschotte C

PROVIDER: S-EPMC117552 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

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Mariner-like transposases are widespread and diverse in flowering plants.

Feschotte Cédric C Wessler Susan R SR

Proceedings of the National Academy of Sciences of the United States of America 20011226 1

Complete and partial sequences of mariner-like elements (MLEs) have been reported for hundreds of species of animals, but only two have been identified in plants. On the basis of these two plant MLEs and several related sequences identified by database searches, plant-specific degenerate primers were derived and used to amplify a conserved region of MLE transposase genes from a variety of plant genomes. Positive products were obtained for 6 dicots and 31 monocots of 54 plant species tested. Phyl ...[more]

PMID: 11756687

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Project description:BACKGROUND: Sclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of several species. Transposons from the Tc1-Mariner superfamily are thought to be ubiquitous components of fungal genomes and are generally found in low copy numbers with large numbers of deleterious mutations in their transposase coding sequence. RESULTS: This study shows that the genome of S. sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3' regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation. CONCLUSIONS: Fourteen novel Tc1-Mariner families were characterized. Some families had evidence of introns, which might or might not be excised depending on the family or element in question, and this finding demonstrates a possible strategy for overcoming possible mutations that generate premature stop codons in a RNA sequence. Tc1-Mariner elements likely play an important role in the structure and evolution of the S. sclerotiorum genome.

Project description:Ppmar1 and Ppmar2 are two active mariner-like elements (MLEs) cloned from moso bamboo (Phyllostachys edulis (Carrière) J. Houz) genome possessing transposases that harbour nuclear export signal (NES) domain, but not any nuclear localization signal (NLS) domain. To understand the functions of NES in transposon activity, we have conducted two experiments, fluorescence and excision frequency assays in the yeast system. For this, by site-directed mutagenesis, three NES mutants were developed from each of the MLE. In the fluorescence assay, the mutants, NES-1, 2 and 3 along with the wild types (NES-0) were fused with fluorescent proteins, enhanced yellow fluorescent protein (EYFP) and enhanced cyan fluorescent protein (ECFP) were co-transformed into yeast system. To differentiate protein localisation under the NES influence, ECFP alone was fused to wild and mutant NES domains either on N- or C-terminal and not to EYFP. Fluorescence assay revealed that blue fluorescence of ECFP was more intense than the red fluorescence of the EYFP in the yeast cell matrix. Further, ECFP had a wider localisation in the cellular matrix, but EYFP was largely located in the nucleus. The NES-1 domain was related to the comparatively high spread of ECFP, while NES-2 and NES-3 indicated a low spread, implying that NES activity on nuclear export increased when the NES is made leucine-rich, while the signalling activity was reduced when the leucine content was lowered in the NES domain. In the transposon excision assay, the mutant and wild type NES of both the Ppmar elements were integrated into an Ade2 vector, and within the Ade2 gene. Co-transformation of the vector together with non-autonomous Ppmar transposons and NES-lacking transposases was used to assess the differential excision frequencies of the mutants NES domains. In both the MLEs, NES-1 had the highest excision suppression, which was less than half of the excision frequency of the wild type. NES-2 and NES-3 elements showed, up to three times increase in transposon excision than the wild types. The results suggested that NES is an important regulator of nuclear export of transposase in Ppmar elements and the mutation of the NES domains can either increase or decrease the export signalling. We speculate that in moso bamboo, NESs regulates the transposition activity of MLEs to maintain the genome integrity.

Project description:Many aquatic plant species are distributed over large areas and diverse environments with populations interconnected by abiotic and biotic mediators. Here, we examined differences and similarities in the population genetic structure of six sympatric and widespread aquatic plant species. We sampled the aquatic species from six Chinese lakes found on plateaus, plains, and different river systems and analyzed them using inter-simple sequence repeat (ISSR) markers. Samples originating from each lake tended to cluster together. Of the six species, only Nymphoides peltata and Myriophyllum spicatum could be divided into plateau and plain groups, once Taihu Lake individuals were excluded. Genetic similarities between populations connected by the Yangtze River were not consistently higher than unconnected populations. Populations from Taihu Lake and/or Weishanhu Lake were distant from other lake populations for all species except Potamogeton lucens. The Taihu and Weishanhu populations clustered for Ceratophyllum demersum and Typha latifolia. Hydrophilous C. demersum had the lowest gene flow (Nm = 0.913), whereas the entomophilous Hydrocharis dubia (Nm = 2.084) and N. peltata (Nm = 2.204) had the highest gene flow. The genetic relationships among distant populations of aquatic plants reflect the comprehensive effects of environmental selection pressure and biotic and abiotic connectivity. Differences in environmental factors between plateau and plain lakes and long distance hydrochory have limited importance on aquatic plant genetic structures. Among multiple evolutionary forces, gene flow mediated by birds may play the most important role in the formation of genetic patterns in the six species examined. For example, the close genetic relationship between Taihu Lake and Weishanhu Lake populations, each in different river systems and with different climates, may be related to the migration routes of birds. Differences in gene flow among the six aquatic plants may be attributable to different bird-transport and the fruit traits of each species.

Dataset Information

Mariner-like transposases are widespread and diverse in flowering plants.

Publications

Mariner-like transposases are widespread and diverse in flowering plants.

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