But there’s a lot of be happy about! I’m done teaching for a long time. As much as I enjoyed working with the kids in my class, the other responsibilities of teaching (grading, sitting through lectures without the chance to break in for the discussions and arguments that make academia so fun, grading, designing assignments, grading) were really starting to wear me down.

And I’m only three weeks (June 22nd) from either passing my qualifying exam or becoming a beaten and broken shell of a man. For three hours four professors will question me on everything I’ve learned (or should have learned but didn’t) in my education up to this point, and everything I propose to spend the next few years of my life doing. This may not sound like a good thing, but it is. Because my qualifying exam has been hanging over my head all semester,

The lab has a new paper in press, having run the sequential gauntlets of Peer Review, Editorial Evaluation, and finally (and perhaps most dreaded) Your-Figures-Aren’t-High-Resolution-Enough e-mails from the journal’s publication department. But more on the details of that whenever the paper actually shows up.

But what was the point of this entry again? Oh yeah. Transposons. I have a soft spot from transposons (I’m guessing most people who work with maize genetics do). Today we may know that transposons are found in practically every genome under the sun, but they were discovered first in maize using old school genetics (breeding plants together and counting traits in the offspring), before DNA sequencing was a gleam in its inventor’s eye.

And on top of that, some delightfully high-copy number transposons are in the middle of proving a major scientific point for me, so I figured the least I could do was devote a week to them here on the site.

If you’re not a geneticist, should you still care about transposons? Absolutely! Transposons are one of the best arguments, not for why genetic engineering is safe, but for why, if anyone worried about hypothetical unintended consequences of genetic engineering should be worried about any food with DNA in it (and as far as I know, that’s all food.) To paraphrase a seinfield character: “No food for you!”

The week’s schedule:

• Tuesday: An introduction to transposons. Selfish (not junk) DNA.
• Wednesday: Transposon mutagenesis. In which we learn what happens when selfish DNA (transposons) goes head to head with DNA that has learned to cooperate with other DNA to build whole organisms (genes).
• Thursday: Transposons and gene regulation. How tiny transposons are changing the way rice genes respond to stress and where orange cauliflower comes from.
• Friday: Franken-gene! The terrifying (actually awesome) story of a new gene stitched together from pieces of lesser genes by (you guessed it) a transposon!

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise.

Plants are not like people. The list of differences goes on and on, but today the difference we’re concerned about is where amino acids come from. Amino acids are the building blocks of proteins, the same way Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are the building blocks of DNA. Both our bodies and plants (and almost every other living thing) use the same twenty amino acids to build proteins. Our bodies can make ~12 of the twenty animo acids for themselves, but there are at least eight amino acids that the human body cannot produce (called essential amino acids). Our only source of these amino acids is from protein in our food.

It’s all well and good for us to get amino acids from our food, but plants don’t eat. They’re made of pretty much nothing more than water, sunlight and air. And trust me, none of those things are a good source of protein.

Unlike us, plants have to be able to make all twenty amino acids from scratch. That means they need whole biochemical pathways* that aren’t found in animals. But a biochemical pathway is like an assembly line. Break one of the steps in the middle and the whole thing falls apart. That’s what glyphosate/round-up does.

This part of the story starts with an enzyme called 5-enolpyruvylshikimate-3-phosphate synthase (or EPSPS for short). Do you don’t have to understand what EPSPS does specifically**, what is important is that its job is an important step in making the three amino acids Tryptophan, Phenylalanine, and Tyrosine***.  When EPSPS can’t do its job, the next protein in the biochemical pathway won’t get the parts it needs to do its job, and in short order the whole pipeline shuts down, none of those three amino acids get produced, and the plant dies.

How does glyphosate keep EPSPS from doing it’s job? It imitates one of the the chemical building blocks EPSPS normally works with, so EPSPS proteins will bind to it like they would to the actual chemical compound. But since glyphosate isn’t the compound EPSPS actually work with, it sticks in the protein. If it helps you can think of this as feeding the wrong sort of paper into a printer, causing a paper jam. Lots of individual molecules of glyphosate get into each plant cell. They stick in EPSPS proteins floating within the cell, which keeps EPSPS from doing its job, and once EPSPS stops working, the plant cell can’t make the amino acids it needs to survive, and dies.

Glyphosate is very good at doing what it does: killing plants. And as weed-killers go, it’s a lot less nasty for animals since it works by breaking a protein animals don’t need or even have. But there is one problem. Some weeds are becoming less effected by the herbicide, able to survive larger and large doses.  There are a number of ways plants can evolve to survive large doses of glyphosate. Let’s talk about three:

1. The first, and probably most obvious, is to change the shape of the EPSPS protein so glyphosate can no longer jam the mechanism. As it turns out mutations that change which amino acid is used at one specific point can produce a version of the EPSPS gene that is less likely to be broken by glyphosate. Think of it as changing the design of a print so paper that would jam the mechanism either won’t fit in the printer at all or passes through harmlessly. This method of getting “superweed” powers has been used by malaysian goose-grass and and australian ryegrass.
2. A second way for plants to become superweeds is to stop transporting glyphosate around the plant. I don’t have a good printer metaphor for this one. Cells in the leaves of plants are mostly completely grown and don’t need to make as many new proteins as the rapidly dividing cells in meristems and newly developing leaves. When a farmer sprays glyphosate it will mostly land on the mature leaves of the plant. If plants can keep the herbicide in those leaves and keep it from traveling throughout the rest of the plants, they stand a better chance of survival, and that’s exactly what has been found in resistant stiffstalk rye and pigweed.
3. The first two methods are all well and good, but I probably wouldn’t have bother to write this post if it wasn’t for the method of resistance discovered in Amaranthus palmeri (one of the many species that share the common name pigweed). Palmer amaranth’s approach to resisting glyphosate is charming in its brute force. Resistant plants have duplicated the gene for EPSPS many times (up to 160 copies in some plants!). All those extra genes mean the plants produce a lot more EPSPS protein, so no matter how many individual EPSPSs get jammed by glyphosate molecules, there are still plenty more working EPSPSs to keep doing the job, and the biochemical pathway never stops. Sure a problem with paper jams can be fixed by more advanced printers, or more strict controls on what kind of paper is allowed into the building… but Palmer amaranth’s solution was simply to build a lot more printers.

Potentially there’s potentially a fourth way to develop glyphosate resistance, which would be for the resistant version of the EPSPS protein engineered into glyphosate resistant crops**** to be introgressed into wild relatives allowing those wild crop relatives to become herbicide resistant “super weeds”. This gets talked about a lot and clearly the risk is going to depend on a lot of factors*****. In researching this post I couldn’t find any papers describing herbicide resistant weeds that owe their resistance to a gene from an herbicide resistant crop. And given how much ink has been spilled on the subject, I would expect any such papers to makes a big splash.

*Biochemical pathways are just a bunch of steps needed to get from some molecule an organism already has, to some other molecule the organism wants. Usually each individual chemical change is performed by some specific protein, like workers on an assembly line. (Sometimes its even arranged like an assembly line with intermediate molecules being passed directly from one protein to another, although it isn’t always that way)

**Although if you’re interested you can read more about the details of the EPSPS protein here.

***The first two are certainly essential amino acids. Our bodies can produce our own tyrosine, but all we do is modify phenylalanine. We can’t make it from scratch.

****Weeds that resist glyphosate are “super weeds”, but I can’t imagine ever hearing the crops that resist the exact same herbicide called “super crops” .

*****How the crop reproduces, whether its being grown near any wild ancestors, how weedy those wild ancestors are to begin with, which crop alleles are in close linkage with the resistance gene (crop-like traits tend to make weeds much less successful).

Gaines, T., Zhang, W., Wang, D., Bukun, B., Chisholm, S., Shaner, D., Nissen, S., Patzoldt, W., Tranel, P., Culpepper, A., Grey, T., Webster, T., Vencill, W., Sammons, R., Jiang, J., Preston, C., Leach, J., & Westra, P. (2009). Gene amplification confers glyphosate resistance in Amaranthus palmeri Proceedings of the National Academy of Sciences, 107 (3), 1029-1034 DOI: 10.1073/pnas.0906649107

POWLES, S., & PRESTON, C. (2006). Evolved Glyphosate Resistance in Plants: Biochemical and Genetic Basis of Resistance Weed Technology, 20 (2), 282-289 DOI: 10.1614/WT-04-142R.1

Photo: ekpatterson, flickr (click photo to see in original context)

There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution).

On the other hand, two unrelated human beings, members of the same species, have more than four times as many genetic differences as two unrelated heirloom tomatoes.

Genetic Diversity:

Corn vs. Corn > Human vs. Chimpanzee >> Human vs. Human >> Heirloom Tomato vs. Heirloom Tomato

Now the fact that any two human beings are more closely related to each other than either is to a chimpanzee should be obvious to anyone who gives it a moments thought.

I plan to poll my sections tomorrow to see how many of them would put corn and heirloom tomatoes in the opposite positions, but many have figured out my feelings about corn, so they’ll probably guess it’s a trap.

The helitron captured fragments are copied from real genes (often multiple pieces are captured from different genes) which is why many gene annotation programs (trained to recongize the difference between genes and non-coding DNA) will identify the fragments being genes themselves.

What if some of those fragments actually are genes? By combining pieces from completely different genes, helitrons could be a whole new source of crazy new genes that natural selection could act upon.

That is the question the authors of this poster are trying to get at, by identifying more helitron fragments and checking to see if those fragments were actually expressed in the genome.

Allison Barbaglia et al. “Accessing the transcriptional activity of Helitron-captured genes of maize” Poster #243 2010 Maize Meeting

Last november when the maize genome was published, one of the companion papers looked at genes where a different number of copies were found in different breds of maize (this is called Copy Number Variation) and genes found in B73 (the variety of maize that was sequenced) but completely missing from the genomes of other varietes. There’s a great post on that paper written up by Mary at OpenHelix.

A few months later, it sounds like this dataset has grown substantially. Over XXXX B73 genes (that’s X% of the filtered B73 gene set!) that appear to be lost (or have sequences so different they no longer register) in at least some varities of maize. And because the new dataset incorporates data from XX different maize breds and XX different teosinte* lines they’re able to identify some of the losses as older because they’re found in multiple comparisons, while some appear to be lost in only a single breed, and might represent more recent losses.

As you can imagine I’d love to get my hands on this dataset myself, but the next best thing will be to take furious notes when Nathan Springer talks about the project on Friday morning**, and being sure to swing by Steven Eichten’s poster soak in the awesomeness.

Ruth A. Swanson-Wagner et al. “Combined Analysis of genomic structural variation and gene expression variation between maize and teosinte populations” Talk #1 2010 Maize Meeting (Presented by Nathan Spinger)

Steven R. Eichten et al. “Extenisve Copy Number Variation Among Maize Lines” Poster #139 2010 Maize Meeting

*Teosinte is the wild species from which maize/corn was domesticated.

**And he’s talking at 8:30 AM on a day when I still plan on being heavily jet lagged.

Plants, like animals, possess two complete genome copies, one from each parent. They’ll only pass on one copy (mixtures of pieces from each parent) to their offspring. Any given sequence has a 50% chance of being passed on which seems fair given the plant is passing on 50% of its total genetic material. But abnormal chromosome ten cheats (using those extra centromere-like sequences I mentioned earlier). It has up to an 83% chance of being passed on.

Since the breed of corn (B73) the maize genome was based on has the normal version of chromosome 10, we know very little about the extra DNA found in abnormal chromosome 10. The authors of this poster are going to correct that oversight, by sequencing the region, figuring out how (and how long ago) abnormal chromosome 10 came into being, and hopefully identifying the genes within the region that make chromosome-knobs act like centromeres.

*Knobs are dense segments of DNA that scientists have been able to spot visually within chromosomes since before we knew for sure that chromosomes carried genetic information.

**Centromeres are the part of the chromosomes that bind together during cell division (the center of the X in the traditional drawing of a chromosome). They’re also the place where the molecular machinery that pulls chromosomes apart at the end of the process of cell division.

Lisa Kanizay and Kelly R. Dawe “Uncovering the sequence and structure of maize abnormal chromosome 10″ Poster #165 2010 Maize Meeting.

The relationships of the four grass species with sequenced genomes. The branches are NOT to scale with how long ago the species split apart. Green stars represent whole genome duplications. The most important one to notice in the one in the ancestry of maize/corn. That duplication means that every region in sorghum, rice, or brachypodium is equivalent to two different places in the maize genome, one descended from each of the two copies of the genome that existed after the duplication.

And this morning the dataset I drew that example from, 464 classical maize genes mapped onto the maize genome assembly plus syntenic orthologs in up to four grass species: sorghum, rice, brachypodium, and the other region of the maize genome created by the maize whole genome duplication (technically syntenic homeologs since we started in maize to begin with, by the principle is the same), went out to the maize genetics community (thank you MaizeGDB!).

A postdoc in our lab tells me more people have visited CoGe today than any day on record (and we hit that mark before noon!).

Anyway, thank you guys, it’s great to feel appreciated!

Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth).

More interesting, at least to me, is the fact that there is NO gene equivalent to colored aleurone1 and purple plant1 in the region we’d expect to find such a gene in Brachypodium (the only other grass species with a sequenced genome)*. From all the genes that line up perfectly on either side we can predict the exact location the gene equivalent to colored aleurone1 and purple plant1 should be found in the Brachypodium genome. But the gene isn’t there…

The GEvo panel shown here can be regenerated at: http://tinyurl.com/yddlwor

The original version of this image had Pl1 mislabeled as C1. This version corrects that error.

For a couple more examples of comparisons between the four sequences grass genomes check out the Cogepedia post I spent this morning pulling together.

*The publication of which I celebrated just a little while ago.

I mention all this to explain why I was so excited to learn that her post this week sings the praises of a group of species near and dear to my heart, the grasses. The whole post is definitely worth a read. Even if you don’t learn something you didn’t already know, read it as a source of inspiration for telling OTHER people how cool grasses are. And the closing is truly excellent:

We usually talk of our domestication of grasses, and the ways in which we have evolved them: we have made plants with bigger, more nutritious seeds that don’t fall to the ground, for example.But their effect on us has been far more profound. Our domestication of grasses, 10,000 years ago or so, allowed the building of the first cities, and marks the start of civilization as we know it. Grasses thus enabled the flowering of a new kind of evolution, a kind not seen before in the history of life: the evolution of human culture.

Some of the comments are heart warming to read as well, although a bunch of people have fallen prey to the maize/corn confusion. (Explained in detail here)

*Speaking of cool science that most of the general public doesn’t know about: We’ve known for more than four years that mutations of the gene talpid2 in chickens cause chicken embyros to develop teeth, something we thought birds had lost the ability to do 60-80 million years ago (around the same time grass was bursting onto the world stage.) Don’t worry too much about getting bitten by a sabertoothed turkey, the toothed embryos have other problems that mean they don’t survive.

**There’s also a three-part video series based on the book that I can best describe as … odd.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

• A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
• Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
• They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
• While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
• That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.