The structure of plant polyadenylation signals
A primary area of research focus in this lab is that of mRNA 3' end formation
(or polyadenylation) in plants. We have conducted functional analyses of three
different plant polyadenylation signals (1,2,3), including detailed studies
of one (3,4,5). From these studies, we have arrived at a general model for the
structure of a plant polyadenylation signal. Briefly, each poly(A) site in a
plant gene is defined by the action of three different cis elements:
the poly(A) site itself (the Cleavage/ polyadenylation Site, or CS), an element
located some 13-30 nts upstream from the poly(A) site (the Near-Upstream Element,
or NUE), and an element located farther upstream (as far as 90 nts) from the
poly(A) site (the Far-Upstream Element, or FUE). As far as can be determined,
these different cis elements are interchangeable. (More information about
these elements can be found here.)
Plant genes almost always come with more than one poly(A) site (6). Each of these sites is accompanied by separate CSs and NUEs, but several sites may be, and usually are, controlled by a single FUE. There seem to be rather strict spacing constraints between NUEs and CSs, and there is some evidence that spacing between NUEs and FUEs may affect the functioning of a given site (7); however, FUEs can clearly be situated as far as 70 nts from associated NUEs, and no one has really found a situation where functioning of a poly(A) site has been quantitatively eliminated by increasing the spacing between FUE and NUE. The best model to accommodate the results from different labs is one where FUEs can function over large distances (defined as nts) but work better when in close proximity to an associated NUE.
As far as consensus sequences are concerned, there are no sharply-defined consensus sequences for any of these three elements in plants. This is in contrast to the case with mammalian genes, in which the sequence AAUAAA is nearly ubiquitous. However, yeast genes resemble plant genes in the lack of a consensus poly(A) signal. The current thinking for plant consensus signals is: for CSs, a YA dinucleotide situated within a U-rich region (6); for NUEs, an A-rich region of between 6 and 10 nts (5) situated between 13 and 30 nts upstream from a CS; and for FUEs, some combination of rather nebulous UG motifs (4) and/or the sequence UUGUAA (8). This model is consistent with large-scale sequence analyses of Arabidopsis genes (9).
1. Hunt, A. G. and MacDonald, M. (1989). Deletion analysis of the polyadenylation
signal of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene. Plant
Mol. Biol. 13, 125-138.
2. MacDonald, M. H., Mogen, B., and Hunt, A. G. (1991). Characterization of the polyadenylation signal of the T-DNA-encoded octopine synthase gene. Nuc. Acids Res. 19, 5575-5581.
3. Mogen, B., Graybosch, R., MacDonald, M., and Hunt, A. G. (1990). Upstream sequences other than AAUAAA are required for efficient mRNA 3' end formation in plants. Plant Cell 2, 1261-1272.
4. Mogen, B. D., MacDonald, M. H., Leggewie, G., and Hunt, A. G. (1992). Several distinct types of sequence elements are required for efficient mRNA 3' end formation in a pea rbcS gene. Mol. Cell. Biol. 12, 5406-5414.
5. Li, Q. and Hunt, A. G. (1995) A near upstream element in a plant polyadenylation signal consists of more than six bases. Plant Mol. Biol. 28, 927-934.
6. Hunt, A. G. (1994) Messenger RNA 3' end formation in plants. Ann. Rev. Plant Physiol. Plant Mol. Biol. 45, 47-60.
7. Wu, L., Ueda, T., and Messing, J. (1994) Sequence and spatial requirements for the tissue- and species- independent 3'-end processing mechanism of plant mRNA. Mol. Cell. Biol. 14, 6829-6838.
8. Sanfacon, H., Brodmann, P., and Hohn, T. (1991) A dissection of the cauliflower mosaic virus polyadenylation signal. Genes. Develop. 5, 141-149.
9. Graber, J. H., Cantor, C. R., Mohr, S. C., and Smith, T. F. (1999) In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species. Proc. Natl. Acad. Sci. USA 96, 14055-60.