A new paper by Susan Lolle, Robbert Pruitt, and collegues at Purdue Univeristy is making some press. The NY Times covered it in a story entitled, Startling Scientists, Plant Fixes Its Flawed Gene. Carl Zimmer has discussed it on his blog: Move Over, Mendel (But Don’t Move Too Far). The paper is entitled, “Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis.” It was quickly published in Nature this week, and is now available as an advanced access publication. I think Nature in its rush to publish cutting edge science has (once again) published a paper of fantastic claims that could use a little more support. I will explain below.
In a 1998 paper, the two main author identified and studied the genes that are involved in organ fusion in Arabidopsis thaliana. They subsequently noticed that one of their genes, hothead (HTH/hth) showed an extremely high rate of reversion from null (hth) to wild-type (HTH). The rate of reversion for several different null alleles, 0.040 - 0.082, was very much higher than expected from typical mutation rates.
They initially suspected that their stocks had been contaminated with wild-type seeds or that their plants were out-crossing with wild-type pollen. However, they genotyped embryos and demonstrated the existence of revertant embryos, which ruled out seed contamination. They next ruled out pollen contamination by demonstrating that pollen from an hth/hth plant can transmit the HTH allele.
Sequencing ruled out the involvement of transposons and repeated sequences. They also tested whether the gene had a higher mutation rate but ruled it out due to lack of silent nucleotide substitutions. They ruled out gene conversion through non homologous recombination because they found no suitable donor sequence in the genome. They also found that molecular markers were genetically unstable (i.e. high mutation rate) in hth/hth plants but not in HTH/HTH plants. This argued for a genome wide effect.
With all these options investigated and ruled out, the authors proposed that genetic information was transmitted not only in the genome but in an additional way. This secondary information was then restoring the HTH allele in some hth/hth individuals. The researchers proposed (double-stranded) RNA as the possible vehicle for this secondary storage.
I think that Lolle et al. missed one important mechanism when they were considering possible explanations: selection. Before I continue, I want to point out what else I think is missing in the study: direct sequencing of male gametophytes to determine their haplotypes, some statistical tests, hth alleles not due to point mutations, knowledge of the rate of silent mutation rates for wild-type hothead genes, and probably a few other things.
I prefer selection over the explanation proposed by the authors, since it is a well established mechanism for changing allele frequencies and it can explain why the reversions only occur in pollen. The selection I’m proposing is the result of pollen competition; i.e. HTH pollen fertilizes ovules better than hth pollen. With pollen having a much larger population size than ovules, there is a greater chance at producing a revertant through mutation, at which point selection can act upon it. HTH could also be important for ovule success, but the lower population size of ovules and less chances for competition would make the effect less likely to show up.
What about the fact that genetic instability was found in other markers in hth/hth individuals? Well, I suspect that the loss of a functioning hothead gene increases the global mutation rate, which affects those markers too. Perhaps this is the reason why HTH pollen is selected for; it puts the mutation rate back in order.
Why didn’t the researchers find silent mutations in revertant HTH? Well, if the revertant HTH is selected because it fixes mutation rates, then individuals that revert sooner than later may be preferred. The fastest way to produce revertant HTH is to reverse the point mutation that produced hth. The researchers might not have had the power to detect silent mutations in revertant HTH because they only sequenced three lines.
What about the fact that HTH/hth heterozygotes produce hth/hth individuals at nearly 25%? Doesn’t that exclude pollen selection? Well, the advantage of HTH pollen over hth pollen may be a paternally influenced trait that only shows up from hth/hth pollen donors. The advantage may also be frequency dependent and only occur when HTH is rare.
The paper by Lolle et al. involves a really interesting system, but I seriously doubt that their proposed explanation will hold up. I think selection, which isn’t discounted by their results, is a better explanation. It is really going to be interesting as more papers and other labs try to figure out what is going on in this system.
- Lolle SJ et al. (2005) Nature 434: 505-509.
- Lolle SJ et al. (1998) Genetics 149: 607-619.