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Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level.

Darbani B, Noeparvar S, Borg S - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark.

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.

No MeSH data available.


Related in: MedlinePlus

Mapping statistics.On average, 17 million exonic-reads were mapped per replicate. Fe and Zn represent iron and zinc treatments. Samples collected at 6 h and 24 h after the treatments are labeled by 6 and 24. UT is for untreated sample. R1, R2, and R3 represent biological replicates.
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pone.0141398.g001: Mapping statistics.On average, 17 million exonic-reads were mapped per replicate. Fe and Zn represent iron and zinc treatments. Samples collected at 6 h and 24 h after the treatments are labeled by 6 and 24. UT is for untreated sample. R1, R2, and R3 represent biological replicates.

Mentions: Transcriptome sequencing was performed to analyze the cellular response to foliar applications of iron and zinc in transfer cells of immature barley-grains. On average, 44.5% of the reads were mapped onto the barley genome (S1 Table). More than 50% of the 17.2 million exonic single-hit mapped reads evidenced exon-exon junctions per sample-replicate (Fig 1 and S1 Table). The reproducibility measure of slope of inter-replicate regression lines was improved from 0.86 to 0.95 after data correction. Data reproducibility was further checked using a sensitive measure of deviation from perfect reproducibility [16]. The averages of ratios' deviations improved from 55% in uncorrected data to 44% in corrected data. Reference gene-based correction showed no advantage compared to the total exon read count-based correction (Fig 2), revealed by bias structure analysis as introduced in [17]. This is expected from analyzing single cell-type samples.


Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level.

Darbani B, Noeparvar S, Borg S - PLoS ONE (2015)

Mapping statistics.On average, 17 million exonic-reads were mapped per replicate. Fe and Zn represent iron and zinc treatments. Samples collected at 6 h and 24 h after the treatments are labeled by 6 and 24. UT is for untreated sample. R1, R2, and R3 represent biological replicates.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633283&req=5

pone.0141398.g001: Mapping statistics.On average, 17 million exonic-reads were mapped per replicate. Fe and Zn represent iron and zinc treatments. Samples collected at 6 h and 24 h after the treatments are labeled by 6 and 24. UT is for untreated sample. R1, R2, and R3 represent biological replicates.
Mentions: Transcriptome sequencing was performed to analyze the cellular response to foliar applications of iron and zinc in transfer cells of immature barley-grains. On average, 44.5% of the reads were mapped onto the barley genome (S1 Table). More than 50% of the 17.2 million exonic single-hit mapped reads evidenced exon-exon junctions per sample-replicate (Fig 1 and S1 Table). The reproducibility measure of slope of inter-replicate regression lines was improved from 0.86 to 0.95 after data correction. Data reproducibility was further checked using a sensitive measure of deviation from perfect reproducibility [16]. The averages of ratios' deviations improved from 55% in uncorrected data to 44% in corrected data. Reference gene-based correction showed no advantage compared to the total exon read count-based correction (Fig 2), revealed by bias structure analysis as introduced in [17]. This is expected from analyzing single cell-type samples.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Slagelse, Denmark.

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.

No MeSH data available.


Related in: MedlinePlus