Tobacco (Nicotiana tabacum) plants expressing a partial ferredoxin-dependent glutamine-2-oxoglutarate aminotransferase (Fd-GOGAT) cDNA in the antisense orientation under the control of the 35S promoter, were used to study the metabolism of amino acids, 2-oxoglutarate and ammonium following the transition from CO2 enrichment (where photorespiration is inhibited) to air (where photorespiration is a major process of ammonium production in leaves). The leaves of the lowest Fd-GOGAT expressors accumulated more foliar glutamine (Gln) and alpha-ketoglutarate (alpha-KG) than the untransformed controls in both growth conditions. Photorespiration-dependent increases in foliar ammonium, glutamine, alpha-KG and total amino acids were proportional to the decreases in foliar Fd-GOGAT activity. No change in endoprotease activity was observed following transfer to air in the Fd-GOGAT transformants or the untransformed controls which has similar activities over a broad range of pH values. We conclude that several pathways of amino acid biosynthesis are modified when NH4+ and Gln accumulate in leaves.