Proteomics and transcriptomics of broccoli subjected to exogenously supplied and transgenic senescence-induced cytokinin for amelioration of postharvest yellowing

Abstract

Transgenic broccoli harboring senescence-associated-gene (SAG) promoter-triggered isopentenyltransferase (ipt), which encodes the key enzyme for cytokinin (CK) synthesis and N(6)-benzylaminopurine (BA) CK treated broccoli both showed retardation of postharvest senescence during storage. The mechanisms underlying the two treatments were compared. The combination of proteomic and transcriptomic evidences revealed that the 2 treatments conferred common and distinct mechanisms in delaying senescence of broccoli florets. We propose a long-term acclimation of metabolism and protection systems with ipt-transgenic treatment of broccoli and short-term modulation of metabolism and establishment of a protection system with both BA and ipt-transgenic treatments in delaying senescence of broccoli florets. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Chlamydospore Specific Proteins of Candida albicans

“…Specifically, SWATH MS mode was utilized for optimization of quadrupole settings in the instrument [15][16][17][18][19][20]. Samples were spiked from each treatment (chlamydospores and yeast phase cells) to produce the SWATH spectral library, and were analyzed via LC-MS/MS by information dependent acquisition (IDA) (Figure 1b, Supplementary Tables 1-17).…”

“…Samples were spiked from each treatment to produce the SWATH spectral library and analyzed via LC-MS/MS by information-dependent acquisition (IDA) in duplicate [17][18][19][20]. In brief, a digested protein sample (4 µg) was injected into a Eskigent C18-RP HPLC column (100 × 0.3 mm, 3 µm, 120 Å) and then separated using a 95-min gradient of 3 to 35% ACN (acetonitrile) for IDA run and (1 µg) for SWATH run [17][18][19][20].…”

“…For all fragment-ion scans in high-sensitivity mode accumulation time (dwell time) of 100 ms was used. For 100 ms each SWATH-MS cycle a survey scan in high-resolution mode was also acquired resulting in a duty cycle of 3.4 s [17][18][19][20]. A spectral library was generated from IDA run using Protein pilot software version 4 by analyzing data against yeast database.…”

“…SWATH runs of control and test were uploaded in SWATH processing window with 5 min RT window, 50 ppm mass error and 99% confidence. Processed SWATH file was exported to marker view software [17][18][19][20].…”

“…Data was normalized by Total sum normalization. Processed SWATH runs were grouped as control and test and compared using t-test [17][18][19][20]. Protein expression data was generated, and proteins with p-value < 0.05 and fold change ≥2 fold were considered as differentially expressed proteins in test with respect to control [11,12].…”