EMBO/SourceData huggingface dataset:
Figure legend: "(I-L) At the ∼100-cell stage, far fewer SQST-1 aggregates are formed in epg-7 mutants than in atg-3 mutants. (I and K) DAPI images of the embryos shown in J and L, respectively."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(N) Compared with wild-type animals, levels of ZK1053.4::GFP are dramatically elevated in atg-3 and epg-7 mutants."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(O-R) ZK1053.4::GFP is weakly expressed in wild-type embryos (O-P) and sqst-1 mutants (R), but forms a large number of aggregates in epg-7 mutants (Q). (O) DIC image of the embryo shown in P."
NCBI gene IDs:
"epg-7: 180996
sqst-1: 178139"
Figure legend: "(S) Survival curve of L1 larvae under food depletion conditions in wild type, epg-1 mutants, and epg-7 mutants. This experiment was completed once (wild type: n = 2,964; epg-7: n = 602; epg-1: n = 215). Statistical analysis of L1 survival shows that epg-7 mutants exhibit significant difference to wild type and also to epg-1 mutants (log-rank test, P = 0.000)."
NCBI gene IDs:
"epg-1: 176150
epg-7: 180996"
Figure legend: "(T) Loss of function of epg-7 does not ameliorate the degeneration of mec-4::gfp-labeled touch neurons caused by mec-4(u231)."
NCBI gene IDs:
"epg-7: 180996
mec-4: 181728"
Figure legend: "(U) Survival curves of wild type and various mutants. sqst-1;epg-7 mutants have a shortened mean and maximum life span. (P = 0.000 for epg-7 or wild type vs. sqst-1;epg-7 in all three repeats; log-rank test)."
NCBI gene IDs:
"epg-7: 180996
sqst-1: 178139"
Figure legend: "(V) Survival of hydrogen peroxide-treated animals. (In all three repeats, P = 0.000 for epg-7 vs. sqst-1;epg-7; P &gt; 0.2 for wild type vs. sqst-1;epg-7; log-rank test)."
NCBI gene IDs:
"epg-7: 180996
sqst-1: 178139"
Figure legend: "(W) Survival of animals at the indicated time after heat shock treatment. (P &lt; 0.05 for wild type vs. epg-7 or epg-7 vs. sqst-1;epg-7 at 5, 6, and 7 h)."
NCBI gene IDs:
"epg-7: 180996
sqst-1: 178139"
Figure legend: "(X) Dauer formation of daf-2(e1370) mutants in different backgrounds."
NCBI gene IDs:
"daf-2: 175410"
Figure legend: "(D) A large number of SQST-1::GFP aggregates accumulate in epg-7 mutant embryos carrying an epg-7(del Atg11) transgene."
NCBI gene IDs:
"Atg11: 
epg-7: 180996"
Figure legend: "(E and F) No SQST-1 aggregates are detected in epg-7 mutants carrying an epg-7::gfp reporter. (E) DAPI image of the embryo shown in F."
NCBI gene IDs:
"epg-7: 180996"
Figure legend: "(J) Compared with wild-type animals, levels of EPG-7::GFP are dramatically elevated in epg-4 mutants, but remain unchanged in sqst-1 mutants."
NCBI gene IDs:
"epg-4: 176009
sqst-1: 178139"
Figure legend: "(K) The expression level of EPG-7::GFP is dramatically elevated and many EPG-7::GFP aggregates are formed in lgg-1 mutant embryos."
NCBI gene IDs:
"lgg-1: 174050"
Figure legend: "(L and M) No EPG-7 aggregates, detected by anti-EPG-7 antibody, are formed in wild-type embryos. (L) DAPI image of the embryo shown in M. (N) Levels of EPG-7 are dramatically elevated and a large number of EPG-7 aggregates are formed in atg-3 mutants. (O) No EPG-7 aggregates are formed in sqst-1 mutant embryos."
NCBI gene IDs:
"atg-3: 176921
sqst-1: 178139"
Figure legend: "(A) EPG-7 colocalizes with SQST-1 aggregates in epg-8 mutant embryos. Colocalization was defined as two aggregates showing &gt;70% overlap in their fluorescence signals. Insets show a magnified view."
NCBI gene IDs:
"epg-8: 172847"
Figure legend: "(H and I) SQST-1 aggregates accumulate in epg-7 mutant embryos carrying an epg-7(del 531-631)::gfp transgene. (H) DAPI image of the embryo shown in I."
NCBI gene IDs:
"epg-7: 180996"
Figure legend: "(J and K) EPG-7(del 531-631)::GFP is weakly expressed and diffusely localized in epg-7(tm2508) embryos. Its expression is not elevated in lgg-1(RNAi) animals. H-K show embryos carrying the same transgene. Images in J and K were taken using the same exposure time."
NCBI gene IDs:
"epg-7: 180996
lgg-1: 174050"
Figure legend: "(N) Levels of SQST-1(del 26-181)::GFP are dramatically elevated in epg-7 and atg-3 mutants."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(O and P) SQST-1(del 26-181)::GFP is weakly expressed and diffusely localized in sqst-1(ok2892) mutant embryos. (O) DIC image of the embryo shown in P."
NCBI gene IDs:
"sqst-1: 178139"
Figure legend: "(Q and R) SQST-1(del 26-181)::GFP is expressed at dramatically elevated levels and accumulates into a large number of aggregates in lgg-1 (Q) and epg-7 (R) mutants."
NCBI gene IDs:
"epg-7: 180996
lgg-1: 174050"
Figure legend: "(E) Loss of function of epg-7 does not increase levels of LGG-1 and also does not suppress accumulation of LGG-1 in epg-3 mutant embryos."
NCBI gene IDs:
"epg-3: 176712
epg-7: 180996"
Figure legend: "(F-H) Expression of LGG-1 in epg-7 mutant embryos before the ∼100-cell stage (F), at the ∼200-cell stage (G), and at the fourfold stage (H). Images in B-D and F-H were taken using the same exposure time."
NCBI gene IDs:
"epg-7: 180996"
Figure legend: "(I) SQST-1 aggregates are separable from LGG-1 puncta in epg-7 mutant embryos. Insets show a magnified view. (J) In epg-6 mutant embryos, LGG-1 puncta and SQST-1 aggregates are enlarged and colocalized. (K) LGG-1 and SQST-1 aggregates are smaller in size and largely separable in epg-6;epg-7 double mutants. (I-K) DAPI images of the embryos shown in the same row."
NCBI gene IDs:
"epg-6: 189705
epg-7: 180996"
Figure legend: "(L-O) Enlarged LGG-1 and SQST-1 aggregates are colocalized in epg-4 mutants (L and M). Simultaneously depleting epg-7 reduces the size of LGG-1 puncta and SQST-1 aggregates, which become largely separable (N and O). (L and N) DAPI images of the embryos shown in M and O, respectively."
NCBI gene IDs:
"epg-4: 176009
epg-7: 180996"
Figure legend: "(P) In atg-9 mutant embryos, LGG-1 puncta largely colocalize with SQST-1 aggregates at the comma stage. Notably, there are more SQST-1 aggregates than LGG-1 puncta. (Q) SQST-1 aggregates are separable from LGG-1 puncta in atg-9;epg-7 mutants at the comma stage."
NCBI gene IDs:
"atg-9: 178561
epg-7: 180996"
Figure legend: "(R) Percentage of LGG-1 puncta colocalized with SQST-1 aggregates in indicated autophagy mutants. Comma-stage embryos were examined for atg-9 and atg-9;epg-7 mutants. ∼200-cell stage embryos were examined for other autophagy mutants."
NCBI gene IDs:
"atg-9: 178561
epg-7: 180996"
Figure legend: "(I) SQST-1 associates with LGG-1 in vivo. Embryonic extracts from epg-7 mutants show that interaction of SQST-1 with LGG-1 is EPG-7 independent."
NCBI gene IDs:
"epg-7: 180996"
Figure legend: "(L and M) SQST-1(del LGG-1-1+2)::GFP, in which the two LGG-1-binding fragments (amino acids 418-499 and 604-630) are deleted, is weakly expressed and diffusely localized in the cytoplasm in sqst-1(ok2892) mutants. (N and O) Loss of function of lgg-1 dramatically elevates the expression level of SQST-1(del LGG-1-1+2)::GFP, which forms a large number of aggregates. (L and N) DIC images of the embryos shown in M and O, respectively"
NCBI gene IDs:
"lgg-1: 174050
sqst-1: 178139"
Figure legend: "(P) SQST-1(del LGG-1-1+2)::GFP aggregates colocalize with EPG-7 in lgg-1;sqst-1 mutants. Insets show a magnified view."
NCBI gene IDs:
"lgg-1: 174050
sqst-1: 178139"
Figure legend: "Formation of ATG-9 puncta in various autophagy mutants. (A and B) In wild-type embryos, ATG-9::GFP is diffusely localized in the cytoplasm. (A) DIC image of the embryo shown in B. Insets show a magnified view. (C) ATG-9::GFP forms a large number of small, intense puncta in epg-1 mutants. (D and E) Accumulation of ATG-9::GFP puncta in unc-51(D) and epg-1 (E) mutants is independent of lgg-1. (F) The ATG-9::GFP puncta largely disappear in epg-1;epg-7 mutants. (G) ATG-9::GFP accumulates into large punctate structures in epg-6 mutants. (H) Loss of function of lgg-1 suppresses the accumulation of ATG-9::GFP puncta in epg-6 mutants. (I) Loss of function of epg-7 has no effect on the formation of ATG-9::GFP puncta in epg-6 mutants. The ATG-9::GFP puncta are smaller in epg-6;epg-7 mutants than those in epg-6 single mutants. (J-L) ATG-9::GFP accumulates into large punctate structures in epg-4 mutants (J) and the accumulation is suppressed by simultaneously depleting the activity of lgg-1 (K) or epg-7 (L). (M and N) In epg-8 mutants, ATG-9 accumulates into aggregates (M) that are suppressed by loss of lgg-1 activity (N). (O) epg-7 mutants exhibit the same distribution pattern of ATG-9::GFP as wild-type embryos. (P) Percentage of ATG-9::GFP puncta colocalized with EPG-7 and SQST-1 aggregates in indicated autophagy mutants."
NCBI gene IDs:
"epg-1: 176150
epg-4: 176009
epg-6: 189705
epg-7: 180996
epg-8: 172847
lgg-1: 174050
unc-51: 180311"
Figure legend: "(Q-T) The ATG-9::GFP puncta in epg-6 (Q), epg-8 (R), unc-51 (S), and atg-18 (T) mutants colocalize with EPG-7 aggregates."
NCBI gene IDs:
"atg-18: 179246
epg-6: 189705
epg-8: 172847
unc-51: 180311"
Figure legend: "(U and V) ATG-9::GFP puncta in epg-6 (U) and epg-8 (V) mutants colocalize with SQST-1 aggregates. (W and X) In unc-51 (W) and atg-18 (X) mutants, ATG-9::GFP partially colocalizes with SQST-1 aggregates."
NCBI gene IDs:
"atg-18: 179246
epg-6: 189705
epg-8: 172847
unc-51: 180311"
Figure legend: "(A2) Levels of W07G4.5::GFP in wild type, epg-7 mutants, and atg-3 L1 larvae before and after 6 h starvation treatment. (B2) Model for the role of epg-7 in degradation of SQST-1 aggregates. SQST-1 directly interacts with EPG-7 and is recruited into EPG-7 aggregates. EPG-7 also associates with multiple Atg proteins, which may be recruited to the SQST-1-EPG-7 complex in a hierarchical order. IM, isolation membrane. (C2) Hierarchical relationship of the scaffold proteins EPG-2 and EPG-7 and other essential ATG and EPG proteins in the aggrephagy pathway"
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(A and B) C17E4.2::GFP is weakly expressed and diffusely localized in a wild-type embryo. (A) DIC image of the embryo shown in B. (C and D) C17E4.2::GFP is expressed at dramatically elevated levels and accumulates into many aggregates in lgg-1 (C) and epg-7 (D) mutant embryos."
NCBI gene IDs:
"epg-7: 180996
lgg-1: 174050"
Figure legend: "(E and F) W07G4.5::GFP is expressed in the intestine and a few aggregates are formed in a wild-type embryo at the fourfold stage. (E) DIC image of the embryo shown in F. (G and H) W07G4.5::GFP is expressed at dramatically elevated levels and accumulates into a large number of aggregates in atg-3 (G) and epg-7 (H) mutants."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(I) Levels of C33D9.6::GFP and W07G4.5::GFP are dramatically elevated in atg-3 and epg-7 mutant embryos."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996"
Figure legend: "(J and K) C17E4.2 aggregates in atg-3 mutants overlap with EPG-7 aggregates (J), but are separable from SQST-1 aggregates (K). Insets show a magnified view. (L) Colocalization frequency of C17E4.2, C33D9.6, and W07G4.5 aggregates with EPG-7 and SQST-1 aggregates in atg-3 mutants."
NCBI gene IDs:
"atg-3: 176921"
Figure legend: "(M) SQST-1::GFP accumulates in hypodermal cells in epg-7 mutants at the larval stage. (N) SQST-1::GFP aggregates disappear in rheb-1(RNAi);epg-7 mutant larvae. (O) Dramatic accumulation of SQST-1::GFP aggregates in hypodermal cells in atg-3 mutant larvae. (P) SQST-1::GFP aggregates persist in rheb-1(RNAi);atg-3 mutant larvae."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996
rheb-1: 176327"
Figure legend: "(Q-T) At larval stages, W07G4.5::GFP forms aggregates in intestinal cells (Q and R). These aggregates disappear upon RNAi knockdown of let-363 (S and T). (U-X) W07G4.5::GFP aggregates accumulate in intestinal cells in epg-7 mutant larvae (U and V). These aggregates disappear when let-363 is simultaneously depleted (W and X). (Y and Z) In atg-3 mutants, W07G4.5::GFP aggregates accumulate in intestinal cells (Y) and persist after RNAi knockdown of let-363 (Z)."
NCBI gene IDs:
"atg-3: 176921
epg-7: 180996
let-363: 172167"
Figure legend: "D) BDNF decreases mCherry-CLIMP63 co-localization with TRBP, but not with PACT or Ago2. Hippocampal neurons were transfected with GFP and mCherry-CLIMP63 at 7DIV and immunostained three days later, following BDNF or control stimulation. Manders co-localization was measured at the cell soma using GFP as a mask as indicated (p=0.01, t-test type 3, n=4, error bars; s.d.)."
NCBI gene IDs:
"CLIMP63: 362859"
Figure legend: "B) Short BDNF stimulation changes the levels of only a few microRNAs, such as miR-16-5p and miR-551b-5p. Volcano plot of small RNA sequencing data from BDNF- or control-treated cortical neurons (6DIV) was based on differential expression analysis using the edgeR package. Individual points represent the average fold change obtained in three independent experiments for each miRNA, and plotted against obtained p-values. MiRNAs above the red dashed line are significant (p&lt;0.05, t-test type 2, n=3)."
NCBI gene IDs:
"miR-16-5p: 100313997
miR-551b-5p: 100314268"
Figure legend: "C) BDNF stimulation leads to a transient decrease in mature miR-16-5p levels. 6DIV cortical neurons were treated with BDNF for 10 or 20 minutes and mature miRNA levels were measured in rtPCR. Ct values for each miRNA were normalized to U6 and to 20 minutes of control stimulation (n=3, p=0.02, t-test type 3, error bars; s.d.)."
NCBI gene IDs:
"miRNA: 
U6: 
miR-16-5p: 100313997"
Figure legend: "D) BDNF stimulation leads to a transient increase in the levels of pre-miR16 after 10 minutes of BDNF stimulation. Ct values obtained in rtPCR were normalized to U6 and to 20 minutes control stimulation (n=4, t-test type 3, error bars; s.d.)."
NCBI gene IDs:
"U6: 
miR16: 100313997"
Figure legend: "E) BDNF causes a decrease in pre-miR16 binding to TRBP. Cortical neurons were treated with BDNF or vehicle control and RNA IPs were performed using a mouse monoclonal anti-TRBP antibody. Ct values measured in rtPCR were normalized to respective inputs (n=3, p=0.002, t-test type 3, error bars represent s.d.)."
NCBI gene IDs:
"miR16: 100313997"
Figure legend: "A) BDNF changes the canonical isomiR proportion of a subset of miRNAs. IsomiR levels were compared to the total amount of the corresponding miRNA. Shown are the miRNAs that had significant changes in the canonical isomiR (annotated as &apos;0', p&lt;0.05, t-test type 2, n=3). Results are shown in order of decreasing significance. Shown in red are miRNAs of the miR16 family, miR-16-5p and miR-15b-5p. Black squares correspond non-existing isomiRs. Numbers on the top of the table represent the trimming (negative) or addition (positive) of nucleotides to the 3'- or 5'-end of the canonical 5p or 3p isomiRs, respectively. Only templated nucleotide additions and trimmings, which might reflect Dicer-mediated pre-miRNA cleavage, were considered for analysis."
NCBI gene IDs:
"isomiR: 
isomiRs: 
miRNA: 
miRNAs: 
miR-15b-5p: 100314150
miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "B) BDNF stimulation leads to a decrease in the canonical (22 nucleotides) isomiRs of the miR16 family, miR-16-5p (p=0.005) and miR-15b-5p (p=0.02). In both cases, this is accompanied by an increase in the levels of shorter isomiRs; the 19-nucleotide isoform of miR-16-5p (p=0.04) and the 21-nucleotide isoform of miR-15b-5p (p=0.007). The relative isomiRs proportion was calculated as described in A (t-test type 2, n=3, error bars; s.d.)."
NCBI gene IDs:
"isomiRs: 
miR-15b-5p: 100314150
miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "B) Endogenous miR-16-5p activity in developing hippocampal neurons. Hippocampal neurons were transfected with 500ng miR16 or control sensor at 4 DIV and with or without LNA control ('LNA Ctrl') or the anti-sense miR-16-5p inhibitor ('LNA-miR16'). Cells were fixed at 7 DIV and the number of neurons expressing GFP and not dsRed ('GFP-only') was compared to the total number of transfected neurons. LNA-miR16 reduces the amount of repression of the miR16 sensor compared to LNA-Ctrl (n=4, p=0.02, t-test type 2, error bars represent s.d.)."
NCBI gene IDs:
"miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "C) Short-term BDNF stimulation inhibits endogenous miR-16-5p activity. Hippocampal neurons were transfected at 4 DIV and treated with BDNF either 24h or 20 minutes before fixation and neurons were counted as in B. Repression index was obtained by normalizing the miR16 sensor to the control sensor condition in each experiment (n=4, p=0.02, t-test type 3, error bars; s.d.)."
NCBI gene IDs:
"miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "D&amp;E) Inhibition of miR-16-5p increases dendritic complexity and occludes BDNF-induced dendritogenesis. D) Hippocampal neurons were transfected with the control sensor (A), and stimulated with control or BDNF 24 hours before fixation. Pictures were obtained on a confocal microscope and thresholds were set to dsRed signal fluorescence in order to distinguish individual dendrites (scale bars are 10μm). E) To quantify dendritic complexity the total number of dendritic intersections was calculated using Sholl analysis. Values were normalized to LNA-Ctrl and control treatment (n=3, p&lt;0.04, t-test type 3, error bars represent s.d.)."
NCBI gene IDs:
"miR-16-5p: 100313997"
Figure legend: "F&amp;G) Overexpression of miR-16-5p blocks BDNF-induced dendritogenesis. F) Hippocampal neurons were transfected with control sensor and either control miRNA mimic (miR-Ctrl) or a miR-16-5p mimic (miR16) and treated two days later with BDNF or control vehicle. DsRed signal fluorescence was used to set a threshold on images obtained on a confocal microscope (scale bars; 10μm). G) Total number of intersections was quantified in Sholl analysis and values were normalized to miR-Ctrl, control treatment in each experiment (n=4, p=0.02, t-test type 3, error bars; s.d.)."
NCBI gene IDs:
"miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "B) MiR-16-5p targets the 3&apos;UTR of the BDNFmRNA. Cortical neurons were transfected with 100ng pmiRGlo dual-luciferase reporter consisting of the 3&apos;UTR of BDNF (3&apos;UTR WT) or a miR-16-5p-binding site mutant (3&apos;UTR Mut) and either miR-Ctrl or miR-16. The Firefly to Renilla luciferase ratio was measured and values were normalized to the respective reporter expression without miRNA mimic co-transfection (n=3, p=0.02, t-test type 2)."
NCBI gene IDs:
"BDNF: 24225
miR-16: 100313997
MiR-16-5p: 100313997"
Figure legend: "C) BDNFstimulation leads to an increase in the translation of 3&apos;UTR WT (p=0.02, t-test type 3) but not 3&apos;UTR Mut luciferase reporter, which is rescued by miR-16-5p overexpression (p=0.002; t-test type 2). Cortical neurons were transfected as in (B), stimulated with BDNF or vehicle control for 20 minutes, and lysed two hours after stimulation (n=4)."
NCBI gene IDs:
"miR-16-5p: 100313997"
Figure legend: "D) Pre-miR16 is present in the neuronal cell soma and processes of hippocampal neurons. Neurons were plated on compartmentalized chambers and RNA was isolated from the neuronal cell body and processes separately. Pre-miR137 and pre-miR341 were used to assay somatic and neurite enrichment, respectively. Raw Ct values were normalized to GAPDH mRNA in each experiment (n=3)."
NCBI gene IDs:
"GAPDH: 24383
Pre-miR137: 100314031
Pre-miR16: 100313997
pre-miR341: 100313979"
Figure legend: "More Dicer binds to membrane-targeted GFP-TRBP (mGFP-TRBP) compared to GFP-TRBP. HEK293T cells were transfected with GFP, GFP-TRBP or mGFP-TRBP and cell lysates were processed for co-IP using anti-GFP antibody. Dicer binding was normalized to respective input lanes in each condition (n=4, p=0.02; t-test type 2, error bars are s.d.)."
NCBI gene IDs:
"TRBP: "
Figure legend: "B) mGFP-TRBP but not GFP-TRBP blocks the BDNF-induced decrease in miR-16-5p activity in dual-fluorescence sensor assay. Hippocampal neurons were transfected with 200ng miR16- or control-sensor (see Fig 5A) plus 50ng GFP, 400ng GFP-TRBP or 400ng mGFP-TRBP. Neurons were treated with BDNF or vehicle control prior to fixation and immunostained with anti-GFP antibody. BDNF led to a decrease in miR-16-5p activity in GFP-transfected neurons (p=0.03, n=4, t-test type 3), which was significantly different from mGFP-TRBP-expressing neurons (p=0.04, n=4, t-test type 2, error bars are s.d.)."
NCBI gene IDs:
"TRBP: 
miR-16-5p: 100313997
miR16: 100313997"
Figure legend: "A Phenotypes of WT, dja6, dja5, dja6 dja5 and RNAi seedlings on MS medium with 2%  sucrose. Scale bars = 0.5 cm."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "B,C  Phenotypes and chlorophyll fluorescence images of 6-week-old WT, dja6 dja5 and complemented plants (B) on MS medium with 2% sucrose, scale bars = 0.5 cm; WT, dja6, dja5 and RNAi mutants (C) grown on soil,­­­ scale bars = 1 cm. Fluorescences in (B) and (C) were measured with the FluorCam700MF and visualized using a pseudocolor index as indicated on the right."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "D Chlorophyll content of total leaves in 6-week-old WT, dja6, dja5, dja6 dja5  and RNAi seedlings. FW, fresh weight. Data are the means ± SEM (n = 7 biological replicates)."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "E The ultrastructure of plastids from WT, dja6, dja5,  dja6 dja5 and RNAi mutants. T, thylakoids. Scale bars = 0.2 μm."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "A, B Total protein was extracted from 4-week-old WT,  dja6, dja5, dja6 dja5 and RNAi  seedlings, respectively. WT and dja6 dja5 used in (A) were grown on MS medium with 2% sucrose, while WT, dja6, dja5 and RNAi  mutants used in (B) were grown on soil. 10 μg protein was loaded, except for detection with anti-SUFE1 and anti-SUFA antiserum, for which 25 μg were loaded. Specific bands were identified by immunoblotting and by their molecular weight, and are indicated by asterisks. Designations of photosynthetic protein complexes and their diagnostic components are labeled on the left and right, respectively. The Fe-S types of Fe-S proteins are shown in parentheses. Actin  served as controls to normalize protein levels. For each protein, three independent biological replicates were performed and a representative one is shown."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "A-C Metal concentrations in the WT,  dja6 dja5 and RNAi mutants. Fe concentrations in total  leaves (A and B) and total chloroplast (C) from 4-week-old WT, dja6 dja5 and RNAi mutants were quantified by inductively coupled plasma mass spectrometry, and are shown as means ± SEM (n = 3 biological replicates) of μg g-1 dry weight  (DW). WT and RNAi mutants used in (A and C) were grown on soil, while WT and dja6 dja5 seedlings used in (B) were grown on MS medium with 2% sucrose. Similar results were obtained in two additional independent biological experiments. Asterisks indicate significant differences from the value of WT (two-sample Student's t-test; *, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001)."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "D Volcano plot of the result from quantitative transcriptome profiling in WT and dja6 dja5 mutant. Statistical analysis was performed using Student's t-test. Data on the X-axis represent the Log2-ratio of FC (fold change) between the absolute abundances of transcripts identified from dja6 dja5 against WT. The Y-axis represents the Log10 of FDR (false discovery rate). All DEGs (differentially expressed genes) with FDR &lt; 0.01 and FC &gt; 2 are marked in grey, while all iron-related DEGs with FDR &lt; 0.01 and FC &gt; 2 are marked in red. The iron-related DEGs labeled with red dots within the black boxes are referred to in the text. All data are based on three biological replicates."
NCBI gene IDs:
"dja6: 816768
dja5: 830157"
Figure legend: "C Phenotypes and chlorophyll fluorescence images of 6-week-old WT and 35Spro:SynDJA6-FLAG/dja6 dja5 transgenic plants  grown on soil. Scale bars = 1 cm."
NCBI gene IDs:
"FLAG: 
dja6: 816768
DJA6: 816768
dja5: 830157"
Figure legend: "D Expression of FLAG-tagged SynDJA6 in 35Spro:SynDJA6-FLAG/dja6 dja5 transgenic plants. Total leaf  extracts (100 μg proteins) from WT and transgenic  seedlings were loaded. FLAG-tagged SynDJA6 is indicated by asterisk."
NCBI gene IDs:
"dja6: 816768
DJA6: 816768
dja5: 830157"