Monday, August 11, 2014

Fundamental Plant Biochemical Pathway Origins Traced Back to Ancient Bacteria

Phenylalanine is a precursor for lignin, a compound
that strengthens wood.
Humans are incapable of making half of the amino acids used as protein building blocks.  These are called essential amino acids, because we must obtain them from other sources.  But like the badasses that they are, plants can make all of the amino acids, and supply animals with essential amino acids (Plants are boring? Pshaw).  But a new study reveals that the chemical pathway that plants use to make phenylalanine, an amino acid used to make hundreds of other chemicals, including ones that make wood strong and give red wine its colour, can be traced back to two groups of ancient bacteria.  The origins of many other plant chemical pathways have been traced back to fungi, a group that is fairly evolutionarily close to plants.  But clearly the phenylalanine pathway predates the divergence of fungi from other life.

Phenylalanine is a precursor to Tyrosine, another aromatic amino acids (meaning they contain an aromatic ring).  Aromatic amino acids play a key role in many biochemical pathways.  In humans, phenylalanine is a precursor for dopamine, epinephrine, and norepinephrine.  In plants, up to 30% of photosynthetically fixed carbon is used to produce phenylalanine, which is then used to make anything from pigments, to antibiotics, to alkaloids.  Tyrosine is also important in proteins, because it is often the recipient of phosphate groups which act like an "on" switch.  Plants make phenylalanine using a chemical pathway called the shikimate pathway, which is blocked by common herbicides (like RoundUp).  So you can see how fundamental this pathway is to life on this planet.

To trace the origins of this pathway, the authors examined the sequences of enzymes involved in phenylalanine biosynthesis, including CM (chorismate mutase), PPA-AT (prephenate aminotransferase), and ADT (arogenate dehydratase).  Using the sequences from plants, they were able to probe for similar sequences from other organisms.  By adjusting the parameters of the program, they were able to look at more and more disparate sequences from more distantly related species.  The authors found that CM has eukaryotic origins since it can be traced back to fungi, while homologs of PPA-AT and ADT were present in the bacterial phyla Bacteroidetes and Chlorobi.  The authors were able to purify and test the activities of the two enzymes to prove that they have the same function as the plant enzymes.  This led to the conclusion that PPA-AT and ADT came from an ancient relative of both plants and the two bacterial phyla.  Given their importance, the enzymes have been maintained throughout the evolutionary history of these organisms.  These enzymes are not found in E. coli or yeast, which are the two most commonly studied model microbes. 
Phylogenetic tree showing the evolutionary history of PPA-AT.

By looking at the sequences of more distantly related species, the authors were also able to identify amino acid residues that are key to PPA-AT function.  Mutating out these amino acids either completely or partially eliminated the function of the enzymes, or specificity for a specific substrate. 

This study not only shows the complex evolutionary history of plant biochemical pathways, it also may provide clues about how we can enhance the production of many important plant compounds, including nutrients and medicinal compounds.  These two enzymes, derived from a distantly related single-celled organism, are now found across the plant kingdom, and are absolutely key to plant survival, and in turn, animal survival.

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