Figure 2.

Characterization of the nsi Knockout Lines and Quantitative Lys Acetylome Analysis.

(A) The left panel represents the gene model of NSI based on TAIR10. Positions of T-DNA insertions in each line are marked with arrows. Sand colored boxes represent 5′- and 3′-UTR regions, orange boxes exons, and black lines introns. The right panel shows the absence of NSI mRNA verified with end-point RT-PCR. ACTIN2 was used as a control of cDNA quality.

(B) Phenotypes of 5-week-old wild type and nsi mutant lines grown in short day (8 h light/16 h dark), PPFD 100 µmol m⁻² s⁻¹, 50% humidity, and 23°C.

(C) and (D) Volcano plots representing quantitative Lys acetylome (C) and proteome (D) analyses of the nsi knockout lines (nsi-1 and nsi-2) compared with the wild type. Sums indicate numbers of quantified Lys acetylation sites and proteins, respectively. For statistical analyses, nsi-1 and nsi-2 were treated as group (defect in NSI) and tested against the wild type. Values had to be present in at least six out of the eight biological replicates. All replicate values are listed in the Supplemental Data Sets1 and 2. Green (plastid localization) and blue (nonplastid localization) circles illustrate significant data points with log₂ fold changes ≥0.5 or ≤−0.5 and false discovery rate corrected P value ≤ 0.05 (LIMMA). Proteins involved in state transitions have been marked with text in the figure. 1, KEA1/2 K168/K170 (AT1G01790.1/AT4G00630.2); 2, unknown protein K62 (AT2G05310.1); 3, FER1 K134 (AT5G01600.1); 4, LHCB6 K220 (AT1G15820.1); 5, plastid-lipid associated protein PAP K225 (AT3G26070.1); 6, ATPF K119 (ATCG00130.1); 7, SOUL heme binding family protein K320 (AT5G20140.1); 8, SBPase K307 (AT3G55800.1); 9, ENH1 K233 (AT5G17170.1); 10, PSBH (ATCG00710.1); 11, ARM repeat superfamily protein (AT5G48120.1); 12, FAD6 (AT4G30950.1).