Functional progress of retrotransposons in plants

Abstract

Retrotransposon is a type of transposable elements (TEs), which can replicate itself and move to other loci through the form of DNA→RNA→DNA intermediated with RNA in the genome, and belongs to the class I type transposon. Basically, retrotransposons can be divided into two mainly categories including LTR (long terminal repeat) and non- LTR (non-long terminal repeat). The LTR retrotransposon can be furtherly divided into two main groups including Ty1/copia and Ty3/gypsy, which have a long terminal repeat structure similar to the retrovirus genome. The LTR usually do not encode proteins, but it can serve as regulator for transcription and termination and so on. Non-LTR retrotransposon includes the LINE (Long interspersed nuclear elements) and SINE (Short interspersed nuclear elements). The SINE retrotransposons do not encode the enzymes required for transposition and cannot complete the retrotransposition autonomously. Retrotransposons are the main components in the genome of most eukaryotic, which are also abundant in higher plants. For example, they account for more than 60 percent of the genome sequence in tomatoes, while nearly 80 percent of the genome sequence is made up of retrotransposons in corn and wheat. As early as 1950s, the famous American geneticist, Barbara McClintock, had discovered the existence of transposon when studying the variation of color spots in corn kernels. However, the function and biological significance of those transposons including retrotransposons have always been controversial. But more and more researches reveal that the retrotransposons play an important role in the regulation of gene expression and evolution of plant genome in recent years. Some activated transcript of retrotransposons can participate the production of non-coding RNAs, such as small RNAs or LncRNAs, and rely on the targeting effect of these non-coding RNAs, and are further involved in the expression regulation of downstream-related genes. The transposition of retrotransposons always influences gene structure and expression of insertion loci and neighborhood. They can act as cis-or trans-acting elements in the upstream or downstream regions of genes, or directly as promoter and terminator and so on to regulate the expression, transcription and function of target genes. Besides, the enzyme system produced by autonomous retrotransposon may also act on the other genes of genome, which may result in the creation of chimeric genes or production of new gene copy. Furthermore, some retrotransposon sequences may have involved in the generation of new functional genes during the long-term evolution of plants. Obviously, they are of great significance to the plants. Moreover, retrotransposon may play a role in physiological changes and stress responses of plants, for instance, the plant growth and development regulation, disease resistance and stress-related response and so on. They can even reprogramming plant cell gene expression or creating a considerable number of natural ecotype variations. Intriguingly, the subtle relationship in the origin and evolution of retrotransposons and retroviruses deserves further exploration. They have too much in common and similarities, which indicate that they must have some evolutionary connections. From the study of retrotransposon, we may obtain some unknown secrets about mammalian retrovirus. In this paper, the function progress of the retrotransposon in plants are briefly summarized from the above aspects, which may lay a good theoretical foundation for further revealing the function and mechanism of retrotransposon in the genome and incite the enthusiasm of researchers to study these elements.