Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level

Abstract

In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between the treatments, indicating metal-affinity shifts among isoforms of metal transporters. Most important, we found the zinc treatment to impair both photosynthesis and respiration. A wide range of transcriptional changes including stress-related genes and negative feedback loops emphasize the importance to withhold mineral contents below certain cellular levels which otherwise might lead to agronomical impeding side-effects. By illustrating new mechanisms, genes, and transcripts, this report provides a solid platform towards understanding the complex network of plant mineral homeostasis.

Identification of Circular RNAs from the Parental Genes Involved in Multiple Aspects of Cellular Metabolism in Barley

“…We noticed circular RNAs for the genes that are known to be involved in zinc and iron homeostasis; the circular RNAs of calcium/zinc/iron homeostasis components including ATP-binding cassette AbcI 3 and Cax 2 (Darbani et al, 2013 ) responded to the foliar applications of iron and zinc (Figure 3 ). We have previously reported the interaction between micronutrient homeostasis and respiration and the involvement of auxin and ethylene signaling as well as intracellular protein sorting mechanisms in iron and zinc homeostasis (Darbani et al, 2013 , 2015 ). Involved in the mentioned cellular functions, we accordingly found genes with circular RNAs regulated by the iron and zinc foliar applications (Figure 3 and Supplementary File 1 ).…”

“…In agreement, the circular RNAs of the genes Cox 1, Nad 9, apocytochrome b, and Abc I3 showed regulated cellular levels across tissues and in response to the micronutrients (Figure 3 and Supplementary File 1 ). As respiratory engines, mitochondria are very dependent on micronutrients (Darbani et al, 2013 , 2015 ).…”

“…Divergent primers were also applied to target the circular RNAs in all undigested and digested RNA samples. The geometric average (Vandesompele et al, 2002 ) of two reference genes, barley Gadph and V- ATPase (MLOC_59475 and MLOC_18233; Darbani et al, 2015 ), was used to correct the expression data. To quantify the reference genes in RNaseR enrichment analysis, each reference gene was used to correct the other.…”

Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44

“…The clade was called ETC-clade. This is due to the structural and functional dependency of ETC on the S-adenosylmethionine [ 22 ] as well as iron and heme [ 23 , 24 , 25 ]. Interestingly, the Slc 25A28 and Slc 25A38 also co-localized with the genes coding for ETC and ATP-synthase subunits ( Table 1 ).…”

Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification

“…Like Fe, Zn is toxic when present in excess [264,265]. In barley seed transfer cells, increased Zn loading alone or combined with Fe loading to the grain triggers a major alternation in transcriptome [266]. It is postulated that the metabolic cost associated with such a transcriptomic re-organization may limit the metal translocation to the grains or compromise yield [266].…”