Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Miniature inverted-repeat transposable elements (MITEs) are small and high copy number transposons, related to and mobilized by some class II autonomous elements. New MITE families can be identified by computer-based mining of sequenced genomes. We describe four MITE families related to MtPH transposons mined de novo in the genome of Medicago truncatula, together with one previously described family MITRAV. Different levels of their intra-family sequence diversity and insertion polymorphism indicate that they were active at different evolutionary periods. MetMIT1 and MITRAV families were uniform in sequence and produced highly polymorphic insertion sites in 26 ecotypes representing a M. truncatula core collection. A subset of insertions was present only in the reference genome of A17 ‘Jemalong’, suggesting that the two families might have been active in the course of domestication. In contrast, all investigated insertions of the MetMIT2 family were fixed, showing that it was not active after M. truncatula speciation. MetMIT1 elements were divided into three clusters, i.e. (I) relatively heterogenous copies fixed in the genome of M. truncatula, (II) uniform but also mostly fixed, and (III) uniform and polymorphic among the investigated accessions. It might reflect the evolutionary history of the MetMIT1 family, showing multiple bursts of activity. A number of MetMIT1 and MITRAV insertions were present within 1 kb upstream or downstream the ORF. A high proportion of insertions proximal to coding regions was unique to A17 ‘Jemalong’.     

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.     

Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana : characterisation of the Emigrant family of elements

Although the genome of Arabidopsis thaliana has a small amount of repetitive DNA, it contains representatives of most classes of mobile elements. However, to date, no miniature inverted-repeat transposable element (MITE) has been described in this plant. Here, we describe a new family of repeated sequences that we have named Emigrant , which are dispersed in the genome of Arabidopsi s and fulfil all the requirements of MITEs. These sequences are short, AT-rich, have terminal inverted repeats (TIRs), and do not seem to have any coding capacity. Evidence for the mobility of Emigrant elements has been obtained from the absence of one of these elements in a specific Arabidopsis ecotype. Emigrant is also present in the genome of different Brassicae and its TIRs are 74% identical to those of Wujin elements, a recently described family of MITEs from the yellow fever mosquito Aedes aegypti.      

Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)

Recent studies of rice miniature inverted repeat transposable elements (MITEs), largely fueled by the availability of genomic sequence, have provided answers to many of the outstanding questions regarding the existence of active MITEs, their source of transposases (TPases) and their chromosomal distribution. Although many questions remain about MITE origins and mode of amplification, data accumulated over the past two years have led to the formulation of testable models.     

Interactions between transposable elements and Argonautes have (probably) been shaping the Drosophila genome throughout evolution

Transposable elements (TEs) are powerful mutagenic agents responsible for generating variation in the host genome. As TEs can be overtly deleterious, a variety of different mechanisms have evolved to keep their activities in check. In plants, fungi, and animals, RNA silencing has been implicated as a major defense against repetitive element transposition. This nucleic acid-based defense mechanism also appears to be directed at inherited silencing of TEs without altering the underlying DNA sequence. Complex interactions between TEs and RNA silencing machineries have been co-opted to regulate cellular genes.     

A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies

To reveal the genome-wide aspects of Xenopus T2 family miniature inverted-repeat transposable elements (MITEs), we performed a systematic search and classification of MITEs by a newly developed procedure. A terminal sequence motif (T2-motif: TTAAAGGRR) was retrieved from the Xenopus tropicalis genome database. We then selected 51- to 1,000-bp MITE candidates framed by an inverted pair of 2 T2-motifs. The 34,398 candidates were classified into possible clusters by a novel terminal sequence (TS)-clustering method on the basis of differences in their short terminal sequences. Finally, 19,242 MITEs were classified into 16 major MITE subfamilies (TS subfamilies), 10 of which showed apparent homologies to known T2 MITE subfamilies, and the rest were novel TS subfamilies. Intra- and inter-subfamily similarities or differences were investigated by analyses of diversity in GC content, total length, and sequence alignments. Furthermore, genome-wide conservation of the inverted pair structure of subfamily-specific TS stretches and their target site sequence (TTAA) were analyzed. The results suggested that some TS subfamilies might include active or at least recently active MITEs for transposition and/or amplification, but some others might have lost such activities a long time ago. The present methodology was efficient in identifying and classifying MITEs, thereby providing information on the evolutionary dynamics of MITEs.     

Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (<Emphasis Type="Italic">Phyllostachys heterocycla</Emphasis>)

Main conclusion

Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8–11 million years ago (mya) ago and 22–28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.

     

Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis (RDA)

Representational Difference Analysis was applied to characterize genomic differentiations between rice ( Oryza sativa) and foxtail millet ( Setaria italica) and subsequently to identify rice transposable elements. Rice was used as the tester and millet as the driver. A total of eleven, non-redundant, positive clones were isolated from the library. Their analysis revealed that they all represent dispersed repetitive DNA sequences. In addition, homology searches using the BLAST procedure showed that they correspond to seven distinct rice transposable elements. Three had been previously identified as gypsy-like retroelements ( Retrosat1, RIRE3 and RIRE8). The remaining four are novel: we named them hipa (a CACTA-like transposon), houba (a copia-like retroelement), hopi and dagul (two gypsy-like retroelements). The RDA clones were used as probes in Southern hybridization experiments with genomic DNAs of several species from the family Poaceae. The results suggest that the genomic differentiations associated with the activity of these transposable elements are of relatively recent origin. In addition, comparison of the hybridization patterns obtained for several Oryza species suggests that several independent amplifications of these transposable elements might have occurred within the genus.     

水稻N-糖酰胺酶基因 (OsPNGase A) 的克隆及在毕赤酵母中的分泌表达

N-聚糖酶是一类广泛应用于糖蛋白的N-糖基化修饰研究中的去糖基化酶。本研究通过RT-PCR从水稻中克隆了一个高GC含量(69.48%)的N-聚糖酶基因(Os PNGase A,XM_015775832),通过无缝克隆技术构建酵母分泌型表达载体p PICZ(α)A-Os PNGase A,在毕赤酵母SMD1168H中进行诱导表达,发酵液经DEAE Sepharose阴离子交换层析和His Trap HP金属离子螯合层析纯化,产量可达到12.3 mg/L,比活力为258 U/mg。SDS-PAGE结果显示,纯化的Os PNGase A为单一条带且与预期分子量一致。Os PNGase A能作用于水稻中重组表达的人转铁蛋白(TRF)、玉米中重组表达的鸡蛋抗生物素蛋白(Avidin)以及辣根过氧化物酶(HRP),并且对Avidin的酶切效果优于商业化的PNGase F。Os PNGase A反应的最适p H和温度分别为p H 6.0和40℃,在中性和碱性以及含有100 mmol/L还原剂β-ME和DTT的条件下仍具有活性。水稻Os PNGase A的成功表达为植物糖蛋白的研究提供一个新的工具酶,酵母分泌表达体系的建立为PNGase A的大量制备奠定了基础。     

Cloning and expression of a lipase gene from rice (Oryza sativa cv. Dongjin)

Lipases are useful enzymes that are primarily responsible for the hydrolysis of acylglycerides during lipid processing. We have cloned a lipase gene from a rice seed coat cDNA library (Oryza sativa cv. Dongjin). The cDNA was 1,445 bp in length and encoded 361 amino acid residues (GenBank accession No. AY580163). The deduced amino acid sequence had 82 and 56% identity to Oryza sativa (cv. Chuchung) and Arabidopsis thaliana lipase genes, respectively, and there was a GxSxG consensus motif near the catalytic triad at the active serine site. The deduced sequence had little homology to mammalian and microbial lipases. When the Oryza sativa lipase gene was expressed in Escherichia coli with the pET expression system, activity was found mainly in the pellet fraction. The purified product had lipolytic activity towards tributyrin and was about 40 kDa in size.     

Genomewide survey and characterization of metacaspase gene family in rice (Oryza sativa)

Metacaspases (MCs), which are cysteine-dependent proteases found in plants, fungi, and protozoa, may be involved in programmed cell death processes, being distant relatives of metazoan caspases. In this study, we analysed the structures, phylogenetic relationship, genome localizations, expression patterns and domestic selections of eight MC genes identified in rice (OsMC). Alignment analysis of the corresponding protein sequences suggested OsMC proteins can be classified into two subtypes. The expression profiles of eight OsMC genes were analysed in 27 tissues covering the whole life cycle of rice. There are four OsMC genes uniquely expressed in mature tissues, indicating that these genes might play certain roles in senescence. Under abiotic and biotic stresses, four OsMC genes were expressed with treatments of one or more of Magnaporthe oryzae (M. oryzae) infected, pest damaged, cold stress and drought stress, indicating they might be involved in plant defense. In addition, gene trees and genetic diversity (π) were performed to measure whether candidate genes were selected during rice domestication. The results suggested that all the type I genes could not be domestication genes. However, two of five type II OsMC genes showed strong evidence for selective sweep, suggesting that these genes might be involved in cultivated rice domestication. These results provide a foundation for future functional genomic studies of this family in rice.