The stacked cotton line MON88913 x MON15985 expresses several novel proteins: the delta-endotoxins the Cry1Ac and Cry2Ab which confer resistance to lepidopteran pests, and EPSPS (5-enolpyruvylshikimaete-3-phosphate synthase) that confers tolerance to the herbicide glyphosate.

The cry1Ac gene and the cry2Ab gene from Bacillus thuringiensis subsp. kurstaki conferring resistance to lepidopteran pests, and the epsps gene encoding 5-enolpyruvylshikimaete-3-phosphate synthase that confers tolerance to the herbicide glyphosate. gene from Agrobacterium tumefaciens strain CP4.

The cry1Ac and cry2Ab genes, isolated from the common soil bacterium Bacillus thuringiensis (Bt) strain subsp. kurstaki, produce the insect control proteins (delta-endotoxins) Cry1Ac and Cry2Ab. Cry proteins, of which these are only two among many, act by selectively binding to specific sites localized on the lining of the midgut of susceptible insect species. Following binding, pores are formed that disrupt midgut ion flow, causing gut paralysis and eventual death due to bacterial sepsis. There are no binding sites for the delta-endotoxins of B. thuringiensis on the surface of mammalian intestinal cells, therefore, livestock animals and humans are not susceptible to these proteins.

The line also contains a form of the plant enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) that allows the plant to survive the otherwise lethal application of glyphosate. The glyphosate-tolerant EPSPS gene was isolated from the CP4 strain of the common soil bacterium Agrobacterium tumefaciens.

Glyphosate specifically binds to and inactivates the enzyme EPSPS, which is part of an important plant biochemical pathway called the shikimate pathway. The shikimate pathway is involved in the biosynthesis of the aromatic amino acids tyrosine, phenylalanine and tryptophan, as well as other aromatic compounds. When conventional plants are treated with glyphosate they cannot produce the aromatic amino acids essential to their survival. The modified maize line permits farmers to use glyphosate-containing herbicides for weed control in the cultivation of maize. The EPSPS enzyme is present in all plants, bacteria and fungi, but not in animals, which do not synthesize their own aromatic amino acids. Thus, EPSPS is normally present in food derived from plant and microbial sources.