A diverse family of phenylalanine ammonia-lyase genes expressed in pine trees and cell cultures

My first first-author paper. Accidental discovery. Told the story the way I wanted to tell it.

I was trying to clone and sequence a short stretch of DNA from the phenylalanine ammonia-lyase (PAL) gene from the Jackpine tree (Pinus banksiana) to complete the sequencing of the full gene. Foreshadowing: It was accepted at the time, that angiosperms (flowering plants) had multiple genes encoding the PAL protein, whereas gymnosperms (e.g. conifers) had only a single gene for PAL. When I compared the first bit of sequence (importantly, obtained using PCR primers that bound evolutionarily conserved regions) to what we already had, there were differences, so I assumed I had grabbed DNA from a different Pinus by accident. I repeated this, ensuring I had the right DNA sample, and found a third version of the sequence! What felt like grabbing the wrong sample tube turned into a legit research project and my first first-author paper that changed the dogma. Gymnosperm PAL is also encoded by a multigene family.

Oh yeah, and one of the two reviews came back as a hand-written note saying no corrections were needed prior to publication.

PAL is my favourite gene because it lured me to bioinformatics in the late 90's.

Look! When you align the amino acid sequences of PAL proteins from dicot and monocot plants, you can see conserved regions of similarities and differences! I wonder if those have something to do with enzyme function ;-)

What?! Histidine ammonia-lyases that occur in animals and bacteria (and not plants or yeasts) appear to have evolved from a common ancestor with phenylalanine ammonia lyases that occur in plants and yeasts (and not animals or bacteria)!

I even have an email from Russell Doolittle to support that hunch.

Once I realized I could learn more about PAL, and faster, by comparing sequences from free public databases, I was hooked. I even started a database of gymnosperm intron lengths (in ink on a single piece of paper). I knew I needed to “do” bioinformatics from then on, and used this grassroots experience to talk my way into a job in a bioinformatics core facility with Francis Ouellette.