Four-Dimensional\nData-Independent Acquisition-Based\nProteomic Profiling Combined with Transcriptomic Analysis Reveals\nthe Involvement of the Slym1-SlFHY3-CAB3C Module in Regulating Tomato\nLeaf Color

In green plants, the chloroplast is responsible for light\nenergy\ntransition and organic assimilation. However, the molecular mechanisms\nunderlying chloroplast development in horticultural crops remain unclear.\nHere, four-dimensional data-independent acquisition-based proteomic\nprofiling identified 1,727 differentially expressed proteins between\n“Zhongshu 4” (ZS4) and <i>yellowing mutant</i> (<i>ym</i>) leaves, a considerable proportion of which\nwere down-regulated chloroplast proteins. Functional analysis revealed\nthat light harvesting and chlorophyll biosynthesis were correlated\nwith <i>ym</i> leaf yellowing, validated by RNA sequencing.\nQuantitative PCR confirmed that chlorophyll a/b-binding protein 3C\n(CAB3C) related to light harvesting and NADPH:protochlorophyllide\noxidoreductase 3 (POR3) involved in chlorophyll biosynthesis were\nrepressed in <i>ym</i> leaves. Virus-induced gene silencing\nshowed that suppressing <i>CAB3C</i> and <i>POR3</i> decreased the net photosynthetic rate and chlorophyll content. Additionally,\nthe F-box protein Slym1 negatively regulated the expression of <i>CAB3C</i> by depressing transcription factor SlFHY3 levels.\nOur findings offer insights into the regulatory mechanisms of chloroplast\ndevelopment in tomato.