13. Spm elements influence gene expression

15.13 Spm elements influence gene expression

Figure 15.26 Spm/En has two genes. tnpA consists of 11 exons that are transcribed into a spliced 2500 base mRNA. tnpB may consist of a 6000 base mRNA containing ORF1 + ORF2.

The Spm and En autonomous elements are virtually identical; they differ at <10 positions. Figure 15.26 summarizes the structure. The 13 bp inverted terminal repeats are essential for transposition, as indicated by the transposition-defective phenotype of deletions at the termini. Transposons related to Spm are found in other plants, and are defined as members of the same family by their generally similar organization. They all share nearly identical inverted terminal repeats, and generate 3 bp duplications of target DNA upon transposition. Named for the terminal similarities, they are known as the CACTA group of transposons.

A sequence of 8300 bp is transcribed from a promoter in the left end of the element. The 11 exons contained in the transcript are spliced into a 2500 base messenger. The mRNA codes for a protein of 621 amino acids. The gene is called tnpA, and the protein binds to a 12 bp consensus sequence present in multiple copies in the terminal regions of the element. Function of tnpA is required for excision, but may not be sufficient.

All of the nonautonomous elements of this family (denoted dSpm for defective Spm) are closely related in structure to the Spm element itself. They have deletions that affect the exons of tnpA.

Two additional open reading frames (ORF1 and ORF2) are located within the first, long intron of tnpA. They are contained in an alternatively spliced 6000 base RNA, which is present at 1% of the level of the tnpA mRNA. The (hypothetical) function containing ORFs 1 and 2 is called tnpB. It may provide the protein that binds to the 13 bp terminal inverted repeats to cleave the termini for transposition.

In addition to the fully active Spm element, there are Spm Vw derivatives that show weaker activity in transposition. The example given in Figure 15.26 has a deletion that eliminates both ORF1 and ORF2. This suggests that the need for TnpB in transposition can be bypassed or substituted.

Spm insertions can control the expression of a gene at the site of insertion. A recipient locus may be brought under either negative or positive control. An Spm-suppressible locus suffers inhibition of expression. An Spm-dependent locus is expressed only with the aid of Spm. When the inserted element is a dSpm, suppression or dependence responds to the trans Vacting function supplied by an autonomous Spm. What is the basis for these opposite effects?

A dSpm-suppressible allele contains an insertion of dSpm within an exon of the gene. This structure raises the immediate question of how a gene with a dSpm insertion in an exon can ever be expressed! The dSpm sequence can be excised from the transcript by using sequences at its termini. The splicing event may leave a change in the sequence of the mRNA, thus explaining a change in the properties of the protein for which it codes. A similar ability to be excised from a transcript has been found for some Ds insertions.

tnpA provides the suppressor function for which the Spm element was originally named. The presence of a defective element may reduce, but not eliminate, expression of a gene in which it resides. However, the introduction of an autonomous element, possessing a functional tnpA gene, may suppress expression of the target gene entirely. Suppression is caused by the ability of TnpA to bind to its target sites in the defective element, which blocks transcription from proceeding.

A dSpm-dependent allele contains an insertion near but not within a gene. The insertion appears to provide an enhancer that activates the promoter of the gene at the recipient locus.

Suppression and dependence at dSpm elements appear to rely on the same interaction between the trans-acting product of the tnpA gene of an autonomous Spm element and the cis-acting sites at the ends of the element. So a single interaction between the protein and the ends of the element either suppresses or activates a target locus depending on whether the element is located upstream of or within the recipient gene.

Spm elements exist in a variety of states ranging from fully active to cryptic. A cryptic element is silent and neither transposes itself nor activates dSpm elements. A cryptic element may be reactivated transiently or converted to the active state by interaction with a fully active Spm element. Inactivation is caused by methylation of sequences in the vicinity of the transcription startpoint. The nature of the events that are responsible for inactivating an element by de novo methylation or for activating it by demethylation (or preventing methylation) are not yet known.