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.