Genome-wide identification and expression analysis of gibberellin biosynthesis, metabolism and signaling family genes in Phyllostachys edulis / 生物工程学报

Gibberellin is an essential plant hormone that plays an important regulatory role throughout the life cycle of higher plants. A total of 23 genes involved in gibberellin action were identified from Phyllostachys edulis genome, including 8 GA20ox and 1 GA3ox genes involved in the gibberellin biosynthesis, 8 GA2ox genes involved in the metabolism of gibberellin, 2 GID1 genes involved in gibberellin perception, 2 GID2 genes and 2 DELLA genes involved in gibberellin signal transduction. Phylogenetic analysis of these genes from Arabidopsis, Oryza sativa and Phyllostachys edulis revealed that gibberellin biosynthesis, metabolism, and signaling pathways are conserved in these species. Treatment of seeds and seedlings of bamboo with exogenous gibberellin revealed that gibberellin significantly increased seed germination rate and stem elongation of seedlings, and had the best concentration of action. The expression levels of GA20ox and GA3ox genes in the bamboo seedlings were down-regulated and the expression of the active gibberellin-degrading gene GA2ox was up-regulated after GA3 treatment, and the transcriptional level of the gibberellin receptor GID1 and the positive regulatory gene GID2 was significantly increased while the expression of the negative regulatory gene DELLA was decreased. These genes have significant differences in the expression of different spatial locations of bamboo shoot stems, GA20ox, GA3ox, GA2ox, GID1 and GID2 are all expressed in the upper part of bamboo shoots, while the repressor gene DELLA accumulates at the bottom of the shoots and is hardly expressed at the top.

Identification and expression pattern analysis of a Moso Bamboo LTR retrotransposon / 生物工程学报

To develop more active LTR retrotransposons in Phyllostachys edulis, a Ph. edulis LTR retrotransposon (Ph-LTR2) was identified, and the expression pattern of the transposon under stress was systematically analyzed. Ph-LTR2 transposon is 6 030 bp in length and belongs to the Reina subfamily in the Ty3-Gypsy family. With the similarity of 96.41% of both LTR sequences, the Ph-LTR2 transposon inserted the moso bamboo genome about 61.92 thousand years ago. There are 5 copies identified in the genome. The Ph-LTR2 transposon domain includes GAG (gag protein) protein domain, PR (Proteases) protein domain, RT (Reverse transcriptase) protein domain, RH (Ribonuclease H) protein domain, INT (Integrase) protein domain and CHR (Chromatin organization modifier) protein domain. The expression patterns of INT, RT and RH were detected by real-time quantitative PCR. The three domains were found to have specific expression patterns at different tissues of the bamboo. Under the conditions of low/high temperature, methylation inhibitors treatments, irradiation and high salt stress, transcription levels of the three domains of the Ph-LTR2 transposon increased with different degrees. Specifically, after treatment with low/high temperature and methylation inhibitors, the transcription level was up-regulated; after low dose radiation treatment and low concentration of salt solution treatment, the transcription level was also increased, but the expression level decreased with increasing dose of radiation and concentration of salt solution. These results indicate that the expression pattern of the Ph-LTR2 transposon responds to the changes of the external environment, but the exact mechanism is not yet known. The results of this study laid a certain theoretical foundation for the development of the genetic tool based on Ph-LTR2 transposons.

Active miniature inverted-repeat transposable elements transposon in plants: a review / 生物工程学报

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Plant active LTR retrotransposons: a review / 生物工程学报

Long terminal repeat (LTR) retrotransposons are mobile DNA sequences that ubiquitously exist in eukaryotic genomes. They replicate themselves in the genome by copy-paste mechanism with RNA as medium. In higher plants, many active LTR retrotransposons have been applied to analyze molecular marker technology, genetic tagging, insertion mutation and gene function. Here, we systematically review the characteristics of plant active LTR retrotransposons, including their structures, copy numbers and distributions. We further analyzed the gag (group-specific antigen) and pol (polymerase) sequence features of different plants active LTR retrotransposons and the distribution patterns of the cis-acting elements in LTR regions. The results show that autonomous active LTR retrotransposons must contain LTR regions and code Gag, Pr, Int, Rt, Rh proteins. Both LTR regions are highly homologous with each other and contain many cis-regulatory elements; RVT and RNase_H1_RT domain are essential for Rt and Rh protein respectively. These results provide the basis for subsequent identification of plant active LTR retrotransposons and their functional analysis.

Modification and decoration of transposase: a review / 生物工程学报

Transposons are the mobile and autonomic replication DNA fragments in genomes. With more understanding of the structure and function of transposons, numerous transposons have been developed to the genetics tool for gene function analysis, gene transformation and gene therapy. The low transpositional activity of the natural transposons is the main obstacles to the utilization of transposons. Recently, with the progress in bioinformatics and protein engineering methods, researchers have reconstructed and optimized natural transposases to create hyperactive transposases that catalyze the transposition with high efficiency. The resulted hyperactive transposons have been applied to gene-modification and gene-tagging. Meanwhile, transposase chimeras were created by protein fusion technology. The insertion characteristic of transposons were artificially regulated which could be utilized in gene therapy.