Abstract
Copper (Cu) and iron (Fe) constitute fundamental nutrients for plant biology but are often limited due to low bioavailability. Unlike responses to single Cu or Fe deprivation, the consequences of simultaneous Cu and Fe deficiency have not yet been fully deciphered. Previously, it was demonstrated that Cu and Fe deficiency applied in combination imposes transcriptome, proteome, and metabolome changes different from those triggered under each deficiency individually. Here, we evaluated the effect of alternative splicing (AS) on the transcriptome of rosette leaves under single and simultaneous Cu and Fe deficiency. Differentially spliced genes (DSGs) and differentially expressed genes (DEGs) coincided in number (2,600 approx.) although the overlapping fraction was minimal (15%). Functional annotation of changes exclusively detected under simultaneous Cu and Fe deficiency revealed that DEGs participated in general stress responses and translation, while DSGs were involved in metabolic reactions, especially amino acid biosynthesis. Interestingly, transcripts encoding central features for tryptophan (Trp) and asparagine (Asn) synthesis – two significantly altered metabolites under simultaneous Cu and Fe deficiency – underwent exclusive intron retention events under the double deficiency. However, transcript and protein amounts for these enzymes did not correlate with Trp and Asn concentration. In consequence, we propose that AS might act as a regulatory mechanism to modify the stability and/or functionality of the enzymes and therefore fine-tune amino acid production during the combinatorial response to simultaneous Cu and Fe deficiency.
Highlights
Copper (Cu) and iron (Fe) are essential nutrients for plants because they possess suitable redox properties to sustain fundamental processes such as photosynthesis, respiration, and antioxidative defense reactions, among others (Puig et al, 2007; Ravet and Pilon, 2013; Zhang, 2015)
High-throughput profiling and systemic analysis of the transcriptome, proteome, and metabolome of adult rosette leaves grown under double Cu and Fe deficiency for 10 days uncovered an array of molecular changes that were not triggered under single Cu or Fe deficiencies (Garcia-Molina et al, 2020)
With the aim of dissecting the effect of alternative splicing (AS) on metabolic pathways for amino acids exclusively changing under the combinatorial Cu and Fe deficiency, we focused on those for Trp and Asn since they are two significantly altered metabolites (SAMs) and the Mapman bins mapped by CuFe-differentially spliced genes (DSGs) allowed us to extract central features in their biosynthesis
Summary
Copper (Cu) and iron (Fe) are essential nutrients for plants because they possess suitable redox properties to sustain fundamental processes such as photosynthesis, respiration, and antioxidative defense reactions, among others (Puig et al, 2007; Ravet and Pilon, 2013; Zhang, 2015). The transcription factors SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 7 (SPL7) and FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR (FIT1) orchestrate the transcriptional reprogramming under Cu and Fe limitation (Colangelo and Guerinot, 2004; Yamasaki et al, 2009; Bernal et al, 2012). FIT1 promotes FRO4/5 and COPT2 to rely on Cu-depending proteins when Fe is limiting (Colangelo and Guerinot, 2004)
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