HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, United States
- Boston Children's Hospital, Harvard Medical School, United States
- Dana-Farber Cancer Institute, Harvard Medical School, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, United States
- Harvard University, United States
- BioMicro Center, Massachusetts Institute of Technology, United States
Figures
Figure 1
Overview of Ribo-seq and mRNA-seq data.
(A) Illustration of experimental designs. Basophilic erythroblasts (EBs) (S3) from E14.5 FLs of Wt +Fe, Wt –Fe, Hri–/– +Fe and Hri–/– –Fe embryos were sorted and subjected to Ribo-seq and mRNA-seq li…
Figure 2 with 1 supplement
Differentially translated mRNAs in Hri–/– EBs and iron deficiency.
(A) The mRNAs that are significantly differentially translated between Hri–/– and Wt EBs in +Fe or –Fe conditions. (B) Volcano plot of mRNAs that are differentially translated between Hri–/– –Fe and …
Figure 2—figure supplement 1
Translational regulation of ISR mRNAs by HRI.
(A) Increased translation of ISR mRNAs in Wt +Fe EBs compared to Hri–/– +Fe EBs. Red dots on the positive end of the X-axis indicate significantly differentially translated mRNAs that are …
Figure 3 with 3 supplements
Analyses of the mRNAs that are differentially translated between Wt and Hri–/– EBs.
(A) GO analysis of the most highly translated mRNAs in Hri-/– –Fe EBs compared to Wt –Fe EBs. (B) Increased 43S initiation complex, ribosomal protein (RP) synthesis and mitochondrial pathways in Hri–…
Figure 3—figure supplement 1
Differential translation of cytoplasmic and mitochondrial RP mRNAs between Wt and Hri–/– EBs.
(A) The heatmaps of significantly differentially translated 5’ TOP/TOP-like mRNAs, the mTORC1 translational targets. Positive values of Log2(foldchange of TE) indicate upregulated translation in Hri–…
Figure 3—figure supplement 2
Inhibition of mitochondrial protein synthesis by chloramphenicol.
Protein Synthesis assays were performed in DMSO-treated, CHL-treated, CHX-treated and CHX + CHL-treated erythroid cells from the BM of Wt –Fe and Hri–/– –Fe mice. The DMSO-treated control is used to …
Figure 3—figure supplement 3
Inhibition of mitochondrial protein synthesis by INK128.
(A) Protein synthesis in the CHX-treated and CHX + INK128-treated erythroid cells from the BM of Wt –Fe and Hri–/– –Fe mice. In the presence of CHX, only mitochondrial protein synthesis was …
Figure 4 with 1 supplement
Decreased mitochondrial respiration in HRI deficiency.
(A) A representative result for the oxygen consumption rate (OCR) of Wt and Hri–/– erythroid cells. Erythroid cells were isolated from the BM of Wt and Hri-–/– mice in +Fe and –Fe conditions. Five …
Figure 4—figure supplement 1
The relative mitochondrial DNA contents of erythroid cells.
The ratios of mitochondrial DNA (mtDNA) versus genomic DNA (gDNA) were determined by qPCR using the ΔΔCt method for erythroid cells isolated from bone marrow samples. The level in Wt +Fe was defined …
Figure 5
Increased expression of cytoplasmic chaperones, accumulation of unfolded protein inclusions and impaired FL differentiation in Hri–/– erythroid cells.
(A) Venn diagrams depicting the numbers of mRNAs that are significantly differentially expressed between –Fe and +Fe conditions in Wt or Hri–/– EBs. The table on the right lists mRNAs that were …
Figure 6 with 1 supplement
Analyses of differentially expressed mRNAs in iron and HRI deficiencies.
(A) Volcano plots of mRNAs that are differentially expressed between Wt –Fe and Wt +Fe or (B) between Hri–/– –Fe and Wt –Fe EBs. Red dots represent the significantly differentially expressed mRNAs. …
Figure 6—figure supplement 1
Analyses of differentially expressed ISR-target mRNAs.
(A) Heatmaps of ISR-target genes that have a significant difference in expression levels between Hri–/– –Fe and Wt –Fe EBs or between Wt –Fe and Wt +Fe EBs. (B) Expression of Shmt2 in E14.5 FL …
Figure 7 with 3 supplements
Knockdown of Grb10 increases proliferation and inhibits differentiation of FL erythroblasts.
(A) Designs of shRNA knockdown experiments using Lin–Ter119–CD71– FL erythroid progenitors. (B) Proliferation of control and Grb10 knockdown GFP+ cells. Three biological replicas were performed. …
Figure 7—figure supplement 1
Expression of Atf4, Atf5 and Grb10 mRNAs in HRI-ISR defective erythroid cells.
(A) Atf4, Atf5 and Grb10 expression in sorted basophilic EBs as illustrated in Figure 1A. The expression level in Wt +Fe EBs was defined as 1 (n = 3). (B) Grb10 expression at 20 hr and 30 hr of ex …
Figure 7—figure supplement 2
Enrichment of Lin–Ter119–CD71– erythroid progenitors from Wt +Fe E13.5 FLs for ex vivo experiments.
https://doi.org/10.7554/eLife.46976.017
Figure 7—figure supplement 3
Knockdown efficiency of Grb10 in FL cells during ex vivo differentiation.
(A) Knockdown efficiency of Grb10 RNA by shRNA_G3 and shRNA_G7. Grb10 expression in the GFP control at 0 hr of differentiation is defined as 1. (B) Percentages of GFP+ cells during the expansion and …
Figure 8 with 1 supplement
Proposed model of the regulation of erythropoiesis by heme and the HRI-ISR pathway during ID.
Diet-induced systemic ID results in heme deficiency, which activates HRI to phosphorylate its substrate eIF2α. The primary function of eIF2αP is to inhibit general protein synthesis in both the cytop…
Figure 8—figure supplement 1
Expression of Atf4 mRNA in hematopoietic cells.
The plot of Atf4 expression levels in hematopoietic cells of murine bone marrow was obtained from the BloodSpot database (Bagger et al., 2016). The dataset used for ploting the tree was Mouse Normal …
Additional files
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Supplementary file 1
List of diifferentially translated mRNAs by HRI and mTORC1.
Supplementary File 1a. Quality control and mapping of Ribo-seq and mRNA-seq. Supplementary File 1b. Complete gene list of differentially translated mRNAs. Supplementary File 1c. Eif2ak1, Ppp1r15a and Atf4 mRNAs are highly expressed in basophilic erythroblasts. Supplementary File 1d. Higher ribosome occupancy at the AUG of uORF1 in Atf4 mRNA.Supplementary File 1e. Complete gene list of differentially expressed mRNAs.
- https://doi.org/10.7554/eLife.46976.021
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Supplementary file 2
List of mRNAs that are differentially translated between Hri–/– –Fe EBs and Wt –Fe EBs and known mTORC1 targets in the categories of (a) RPs and non-RPs and (b) mitochondrial proteins.
- https://doi.org/10.7554/eLife.46976.022
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Supplementary file 3
List of RNA primers, antibodies and ShRNA oligonucleotides.
Supplementary File 3a. DNA sequence of qPCR primers. Supplementary File 3b. List of antibodies used for western blot analyses. Supplementary File 3c. DNA sequences of shRNA oligonucleotides.
- https://doi.org/10.7554/eLife.46976.023
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Transparent reporting form
- https://doi.org/10.7554/eLife.46976.024
