Journal: Nature

Article Title: Root microbiota drive direct integration of phosphate stress and immunity

doi: 10.1038/nature21417

Figure Lengend Snippet: a , Venn diagram (left) showing the overlap between genes up-regulated and down-regulated in Col-0 and phr1 phl1 in response to phosphate starvation. Gene ontology enrichment (right) analyses indicate that defense-related genes are up-regulated exclusively in phr1 phl1 . The complete enrichment results are shown in . Color key (white to red) represents the gene ontology enrichment significance shown as -log 2 (FDR). White means no enrichment. b , Fold-change of genes differentially expressed in Col-0, phr1 phl1 or in both genotypes in response to phosphate starvation. Columns on the right indicate whether each gene is also up-regulated by MeJA or BTH/SA. Arabidopsis plants were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi for 7 d in a vertical position and then transferred to the same medium containing 1 % sucrose either alone or supplemented with 1 mM Pi for 12 d. c , Venn diagram showing the overlap among genes up-regulated in Col-0 and phr1 phl1 during a typical PSR (from a) and the defense genes up-regulated in phr1 phl1 in response to the SynCom (from ; clusters c3 and c8). The red ellipse indicates 113 defense genes that were up-regulated in phr1 phl1 during classical PSR and during PSR triggered by the SynCom; yellow ellipse indicates the 14 genes up-regulated genes under the same conditions. p -values refer to enrichment results using hypergeometric tests. d phr1 phl1 exhibits enhanced transcriptional activation of 251 genes differentially expressed following chronic flg22 exposure. Averaged from six biological replicates. e phr1 exhibits enhanced disease resistance to the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis isolate Noco2. Infection classes were defined by the number of asexual sporangiophores (Sp) per cotyledon and displayed as a color gradient from green (more resistant) to red (more susceptible); the mean number of sporangiophores per cotyledon is noted above each bar. Col-0 and Ws-2 represent susceptible and resistant controls, respectively. More than 100 cotyledons counted per genotype; the experiment was performed at least five times with similar results. f phr1 mutants exhibit enhanced disease resistance to the hemibiotrophic bacterial pathogen Pseudomonas syringae DC3000. The coi1-16 (n= 9 (day zero), 13 (day three)) and sid2-1 (n= 16, 20) mutants were controls for resistance and susceptibility, respectively. Col-0 (n=16, 20), phr1 (n=17, 20), phr1 phl1 (n=16, 20) and control plants were inoculated under typical experimental conditions: phosphate replete in non-axenic potting soil . The experiment includes at least 9 biological replicates from three independent experiments. Statistical comparisons among genotypes were one-way ANOVA tests followed by a post-hoc Tukey analysis; genotypes with the same letter above the graph are statistically indistinguishable at 95 % confidence.

Article Snippet: The ChIP-seq data will be fully presented in de Lorenzo, et al . . For the transcriptional analysis under conditions typically used to study PSR (axenic growth with sucrose present; no microbiota involved), with Methyl Jasmonate (MeJA) and the 22-amino acid flagellin peptide (flg22), plants were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi for 7 d in a vertical position and then transferred to 1 mM Pi and 5 µM Pi media containing 1 % sucrose either alone or supplemented with 10 µM MeJA (Sigma) or 1 µM flg22 (Sigma) for 12 d. For growth inhibition assays, seedlings were grown on Johnson medium (1 % Sucrose) in 1 mM Pi and 5 µM Pi conditions for 5 d, transferred to 1 mM Pi and 5 µM Pi media supplemented or not with 10 µM MeJA for 5 d. Main root length was then measured using ImageJ software .

Techniques: Activation Assay, Infection

Journal: Nature

Article Title: Root microbiota drive direct integration of phosphate stress and immunity

doi: 10.1038/nature21417

Figure Lengend Snippet: a , Total number of differentially expressed genes (FDR ≤ 0.01 and minimum of 1.5X fold-change) in Col-0 and phr1 phl1 with respect to low Pi (50 µM Pi), flg22 treatment (1 µM) and MeJA (10 µM). In this experiment, plants were grown for 7 days in Johnson medium containing 1 mM Pi, and then transferred for 12 days to low (50 µM Pi) and high Pi (625 µM Pi) conditions alone, or in combination with each treatment. Sucrose was added to the medium at a final concentration of 1 %. b , Venn diagram showing the overlap among genes that were up-regulated by chronic exposure to flg22 in Col-0 and in phr1 phl1 and a literature-based set of genes that were up-regulated by acute exposure (between 8 to 180 min) to flg22 . The red ellipse indicates the 251 chronic flg22-responsive genes defined here. c , Venn diagram showing the overlap among genes that were up-regulated by chronic exposure to MeJA in Col-0 and in phr1 phl1 in this work and a set of genes that were up-regulated by MeJA treatment of Arabidopsis seedlings (between 1 and 8 hours). The red ellipse indicates the intersection of JA-responsive genes identified in both experiments. d , Col-0 and phr1 phl1 exhibit similar transcriptional activation of 426 common JA-marker genes (c) independent of phosphate concentration. As a control we used coi1-16 , a mutant impaired in the perception of JA. The gene expression results are based on six biological replicates per condition. e , Growth inhibition of primary roots by MeJA. Root length of wild-type Col-0 (n= 125 (+ Pi - MeJA), 120 (+ Pi + MeJA), 126 (− Pi - MeJA), 125 (− Pi + MeJA)), phr1 phl1 (n=85, 103, 90, 80) and the JA perception mutant coi1-16 (n= 125, 120, 124, 119) was measured after 4 days of growth in the presence or not of MeJA with or without 1 mM Pi. Letters indicate grouping based on multiple comparisons from a Tukey post-hoc test at 95 % confidence. In agreement with the RNA-seq results, no difference in root length inhibition was observed between Col-0 and phr1 phl1 .

Article Snippet: The ChIP-seq data will be fully presented in de Lorenzo, et al . . For the transcriptional analysis under conditions typically used to study PSR (axenic growth with sucrose present; no microbiota involved), with Methyl Jasmonate (MeJA) and the 22-amino acid flagellin peptide (flg22), plants were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi for 7 d in a vertical position and then transferred to 1 mM Pi and 5 µM Pi media containing 1 % sucrose either alone or supplemented with 10 µM MeJA (Sigma) or 1 µM flg22 (Sigma) for 12 d. For growth inhibition assays, seedlings were grown on Johnson medium (1 % Sucrose) in 1 mM Pi and 5 µM Pi conditions for 5 d, transferred to 1 mM Pi and 5 µM Pi media supplemented or not with 10 µM MeJA for 5 d. Main root length was then measured using ImageJ software .

Techniques: Concentration Assay, Activation Assay, Marker, Mutagenesis, Expressing, Inhibition, RNA Sequencing Assay

Journal: Frontiers in Plant Science

Article Title: Extracellular Alkalinization as a Defense Response in Potato Cells

doi: 10.3389/fpls.2017.00032

Figure Lengend Snippet: Comparison of the alkalinization effect of various elicitors on the potato and Arabidopsis suspension cells.

Article Snippet: Flg22 (22 amino acids flagellin peptide), Elf26 (conserved amino terminus of bacteria elongation factor EF-Tu) and AtPEP (plant elicitor peptides from Arabidopsis ) were synthesized by GenScript, Inc. (Piscataway, NJ, USA).

Techniques: Comparison, Suspension, Concentration Assay

Journal: Frontiers in Plant Science

Article Title: Extracellular Alkalinization as a Defense Response in Potato Cells

doi: 10.3389/fpls.2017.00032

Figure Lengend Snippet: Elicitors- and pathogens-induced reactive oxygen species (ROS) accumulation in potato cells. (A) Time-dependent ROS production in the presence of elicitors (10 μM of Flg22, Elf26, or chitin 6-mer; 0.5 mM of ATP or 1 μM Systemin). (B) Time-dependent ROS production in the presence of pathogens (1 × 10 5 spores/mL of V. dahliae, C. coccodes , or P. infestans ; or 1 × 10 5 spore balls/mL of S. subterranea ). Data show photon counts in 1.0 s at each time point with mean ± SE ( n = 6).

Article Snippet: Flg22 (22 amino acids flagellin peptide), Elf26 (conserved amino terminus of bacteria elongation factor EF-Tu) and AtPEP (plant elicitor peptides from Arabidopsis ) were synthesized by GenScript, Inc. (Piscataway, NJ, USA).

Techniques:

Journal: Cell reports

Article Title: Selective clearance of aberrant membrane proteins by TORC1-mediated micro-ER-phagy

doi: 10.1016/j.celrep.2025.115282

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: pHS12-mCherry Encodes mitochondrially targeted preCox4 (22amino acid)-mCherry under ADH1 promoter, Leu2 , Amp r , , Addgene Plasmid #25444.

Techniques: Virus, Recombinant, Protease Inhibitor, Plasmid Preparation, Software