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 which 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 which show that the chemical make-up, or “composition”, of glyphosate-tolerant crops is equivalent to 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% dwt, tryptophan amounts were 0.65 and 0.63% dwt, and phenylalanine amounts were both 0.49% 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 to organically-grown crops, likely because these are no requirements for regulatory studies/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, there was a large influence of environment and variety on the nutrient content. So, based on the data that shows compositional equivalence between glyphosate-tolerant crops to conventional counterparts, and the data that shows 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 to 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 looking out in 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 towards up towards 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 doesn’t grow upright, may be very stunted in growth, and may have multiple stems growing (instead of just one). One example of what you might see can be found at this link: https://news.uns.purdue.edu/html4ever/031002.Johal.corn.html.
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