Abstract
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.
Highlights
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn
In Arabidopsis, NRAMP1 was shown to be critical for Mn uptake; loss of NRAMP1 function led to severe growth reduction and decreased Mn concentrations[7]
To validate changes observed in the activity of enzymes involved in glucosinolate metabolism at the transcript and protein level, we investigated changes in specific glucosinolates by UPLC-qTOF-MS
Summary
Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. In contrast to other soil-immobile nutrients such as phosphate and Fe for which the mechanisms that re-calibrate cellular homeostasis are relatively well explored, only fragmentary information is available regarding the responses of plants to low Mn supply Such knowledge is of critical importance for the development of Mn-efficient germplasm with improved Mn acquisition and/or increased resource utilization efficiency. Several studies observed only a moderate level of concordance between transcriptomics and proteomics (reviewed by Vogel and Marcotte16), indicating the necessity of integrative studies that cover disparate omics levels
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