A comparative proteomic analysis provides insights into pigment biosynthesis in brown color fiber

A comparative proteomic analysis was performed to identify the differences between brown cotton fiber and a white near-isogenic line, and 78 differential spots were identified at three time points (12-, 18-, and 24-day post-anthesis [DPA]) using MALDI-TOF/TOF. Our data illustrate several aspects of pigment synthesis and fiber development in brown color fiber (BCF). First, 21 spots were associated with secondary metabolism; 15 of these with high abundance in BCF were involved in flavonoid biosynthesis. Second, several spots with lower abundance in BCF were found. Thirteen spots were related to energy/carbohydrate metabolism; in particular, spots related to the glycolytic pathway exhibited lower abundance in 12 DPA BCF. Several spots related to redox homeostasis, cytoskeleton, and protein metabolism also showed lower abundance in BCF, including proteins that are critical for fiber development, such as ascorbate peroxidase, superoxide dismutase, actin, annexin and heat shock protein. Third, several proteins such as leucine aminopeptidase preprotein and progesterone-5-beta-reductase were newly identified proteins in cotton fibers. These findings demonstrated the presence of a complicated metabolic network in BCF and advanced our understanding of the molecular mechanisms of pigment biosynthesis in colored cotton, which will provide new insight for the development of new color types by genetic manipulation.