Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots

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

Examination of the role of iron deficiency response in the accumulation of Cd by rice grown in paddy soil with variable irrigation regimes

Background and aims: Cd uptake has been shown to increase during conditions of Fe deficiency. This study tested the hypothesis that Fe-deficiency-responsive genes, particularly OsNRAMP1, play a role in the increased Cd uptake that occurs when rice is grown in aerobic soil conditions. Methods: Plants were grown in aerobic or flooded soil conditions. Uptake of Cd was compared to levels of expression of candidate metal transporters and to metal ion availability in soil. Results: Plants grown with intermittent soil flooding experienced a predominantly aerobic root environment and had the highest plant Cd uptake. Stronger upregulation of OsNRAMP1 was detected in plants grown in unflooded soil than in flooded soil. However, these transcriptional responses were not linked to an increase in Cd uptake. Overexpression of OsNRAMP1 was not found to increase the uptake of Cd in rice in soil or solution culture. In contrast, there were large differences in availability of Cd, Fe and Mn between flooded and aerobic soils, which were linked to changes in Cd uptake. Conclusions: Aerobic soil conditions favour Cd uptake through increased Cd availability and decreased competition between Cd and Fe rather than through the increased expression of the Fe transporters themselves. © 2013 Springer Science+Business Media Dordrecht.Matthew S. Rodda, Robert J. Rei

Cadmium uptake and distribution in Arabidopsis thaliana exposed to low chronic concentrations depends on plant growth

This study tested the hypothesis that Cd uptake is correlated with the shoot or root growth of Arabidopsis thaliana ecotype Columbia cultivated hydroponically at environmentally relevant Cd concentrations: 20, 100 and 350 nmol L-1. Growth of both roots and shoots were delayed at 350 nmol L-1. The rate of Cd uptake determined by spiking the nutrient solution with Cd-109 for 24 h, was significantly correlated with the root growth rate. The fraction of Cd absorbed that was allocated to shoots was constant with time but decreased with increasing exposure to Cd. Autoradiography and gamma counting showed that Cd was preferentially allocated to developing leaves. Hence, the quantity of Cd in shoots depended both on the root growth, which probably governed the uptake, and on the maturity of the leaves, which may have determined the Cd allocated to shoots through changes in the transpiration stream