Hence, expression of GNC and CGA1 appear to modulate aspects of chloroplast development based on inputs from light and nitrogen, leading to differences in chlorophyll biosynthesis, chloroplast number and starch production. Richter et al., recently reported differences in POR gene expression in transgenic lines with altered GNC and CGA1. We analyzed the expression of these genes as well as expression of the key rate-limiting enzymes HEMA1 and GUN4, which are found upstream in the chlorophyll biosynthetic pathway. These important chlorophyll biosynthesis genes were also found to be modified in correlation with expression levels of GNC and/or CGA1. GUN4 and HEMA1 display BYL719 overlapping spatial and temporal expression with GNC and CGA1 and also exhibit nearly identical circadian oscillations, resulting in a strong level of co-expression. These results validate the systems biology approach that predicted GNC and CGA1 act as part of a network with key chlorophyll biosynthetic genes, specifically GUN4. As seen with GLU1, GNC and CGA1, altering the expression of GUN4 also results in altered chlorophyll biosynthesis. GUN4 has been shown to sustain chlorophyll levels under fluctuating environmental conditions and has been suggested to be involved in retrograde signaling to the nucleus, regulating PORB, PORC and chlorophyll-binding light harvesting complex genes. Because GNC and CGA1 modulate the expression of GLU1 and GUN4, it is likely that changes in gene expression found with changes in their expression will also be altered in GNC and CGA1 transgenics. As such, carbon metabolism-related genes found to be significantly different GNC and CGA1 LY294002 transgenics may be indirectly modified as a consequence of altered chlorophyll biosynthesis. Control of chlorophyll biosynthesis and chloroplast development is vital for plants to optimize photosynthetic capture while maintaining the carbon:nitrogen balance. By increasing the expression of GLU1/Fd-GOGAT as well as key chlorophyll biosynthesis genes, GNC and CGA1 act to increase the flux of assimilated nitrogen towards chlorophyll production. GLU1 accounts for more than 96% of the total GOGAT activity in photosynthetic green leaves and has been verified as the primary nitrogen assimilation enzyme. Altering GLU1 expression has also been shown to result in changes to amino acid production and lead to a cascade of changes gene expression that subsequently influence many aspects of plant development. GLU1 plays a significant role in photorespiration, re-assimilating ammonium produced through this process. Growth in non-photorespiratory conditions recovers the reduced chlorophyll of glu1 mutants. The amount of ammonium released by photorespiration is up to 10 times the amount of nitrogen taken up by the plant.