Thank you for your question, and I have to admit, I am a little excited that someone is asking about auxin! As a graduate student, I studied how auxin (a plant growth regulator, also called a phytohormone) is made in sweet corn, so I am happy that the knowledge I gained might be of some help here.
As you seem well aware, there is an enzyme in plants and bacteria (called EPSPS) that catalyzes a reaction necessary for the synthesis of some amino acids, specifically the amino acids that have a chemical structure known as an “aromatic ring.” These “aromatic amino acids” are precursors to other important plant compounds, including the ones you list in your question (auxin, phytoalexins, folic acid, lignin, plastoquinones). Glyphosate works by binding to the EPSPS enzyme and prevents it from catalyzing the reaction, thus affecting the synthesis of the aromatic amino acids and potentially the downstream plant compounds. In glyphosate-tolerant crops, a version (from naturally occurring bacteria) of this enzyme is expressed that has a slightly different shape. This slightly different shape prevents glyphosate from binding, rendering the plant resistant to glyphosate’s effects, and allows normal rates of amino acid synthesis.
There are a lot of data published in peer-reviewed journals that show that the chemical makeup, or composition, of glyphosate-tolerant crops is equivalent to that of conventional counterparts. A good example of how aromatic amino acid (tyrosine, tryptophan and phenylalanine) amounts are not affected in glyphosate-tolerant crops, compared to a conventional comparator, can be found in Lundry et al. (2013). The data show that tyrosine amounts were 0.31 and 0.30 percent dwt, tryptophan amounts were 0.65 and 0.63 percent dwt and phenylalanine amounts were both 0.49 percent dwt in glyphosate-tolerant and conventional corn, respectively. We can see from this data that glyphosate tolerance does not decrease aromatic amino acid amounts, and that aromatic amino acid amounts, like all compounds, can vary due to natural causes like environment or background genetics. There is less information on comparisons of conventionally grown crops with organically grown crops, likely because these are no requirements for regulatory studies or approvals of crops based on input systems. One study available in corn (Rohlig and Engel, 2010) showed that input system (conventional vs. organic) had little effect on composition, but, as expected, environment and variety largely influenced the nutrient content. So, based on the data that show compositional equivalence between glyphosate-tolerant crops and conventional counterparts, and the data that show little effect of input system on composition, it stands to reason that GM crops would not have lower levels of aromatic amino acids and the other compounds that you mention, compared with organic counterparts.
For some of the compounds that you mention, if there were significantly lower amounts in glyphosate-tolerant plants, the plants would not look physiologically normal. You would be able to see these abnormalities just by looking out into a field. Auxin, for example, helps plants grow and develop normally (similar to hormones in other species, which is why it is called a phyto, or plant, hormone). It helps enable plants to respond to light (which is why plants grow up toward the sun), as well as plant responses to gravity (why roots grow down into the ground), as well as individual cell growth and multiplication. If there were lower levels of auxin in glyphosate-tolerant corn, you would be able to look out into the field and see corn that didn’t grow upright, might be very stunted in growth and might have multiple stems growing (instead of just one). One example of what you might see can be found here.
I hope this answers your question. If not, or if you need help falling asleep at night, I have a 400-page thesis that might help.
- Lundry, DR; Burns, JA; Nemeth, MA; and Riordan, SG. 2013. Journal of Agricultural and Food Chemistry 61: 1991-1998. http://pubs.acs.org/doi/pdf/10.1021/jf304005n
- Röhlig, R.M. and Engel, K.-H. Influence of the Input System (Conventional versus Organic Farming) on Metabolite Profiles of Maize (Zea mays) Kernels J. Ag. Food Chem. 2010, 58 (5), 3022–30: http://pubs.acs.org/doi/full/10.1021/jf904101g