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( A ) Diagram of the domain organization of the two yeast <t>TLDc</t> domain-containing proteins, Oxr1 <t>and</t> <t>Rtc5,</t> together with two human proteins with a similar domain organization. S. cerevisiae Rtc5 and H. sapiens Meak7 are N-myristoylated proteins, which contain an N-terminal EF-hand-like domain and a C-terminal TLDc domain. S. cerevisiae Oxr1 and the splice variant Oxr1-C of H. sapiens consist mainly of just their TLDc domains. ( B ) A wt strain or strains lacking VMA4, OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing glucose with pH = 5.5, pH = 7.5, or pH = 7.5 and 3 mM ZnCl 2 , 10 mM ZnCl 2 , or 150 mM CaCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4 , OXR1 , RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing glucose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 nm or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates, and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05). ( D , E ) SILAC-based vacuole proteomics of cells lacking either OXR1 ( D ) or RTC5 ( E ) compared with the wt strain. Log10 of the detected protein intensities are plotted against Log2 of the heavy/light SILAC ratios. Significant outliers based on a two-group, two-tailed Student´s t -test are color-coded in red ( P value <1e − 14), orange ( P value <0.0001), or dark blue ( P value <0.05); other identified proteins are shown in light blue. Corresponding experiments performed by switching the heavy and light labeling of the strains are shown in Appendix Fig. S . ( F , G ) Cells in which Subunit C (Vma5) was tagged with msGFP2 were grown in a glucose-containing medium and imaged in the presence of glucose or after shifting them for 20 min to a medium containing galactose as the sole carbon source. The scale bar represents 2 μm. The distribution of Vma5 between the two compartments was quantified by using a ratio between the mean fluorescence intensity in a line along the vacuole membrane and the average of the mean fluorescence intensity in three circular regions in the cytosol. The different colors in the graph indicate independent experiments. The smaller circles represent individual cells, and the bigger circles represent the average for each independent experiment. Statistical comparison was performed using a one-way ANOVA and a Tukey post hoc test among the experimental means within each condition (glucose or galactose, n.s not significant P value >0.05; *** P value <0.001). .

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1) Product Images from "Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase"

Article Title: Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase

Journal: The EMBO Journal

doi: 10.1038/s44318-024-00097-2

( A ) Diagram of the domain organization of the two yeast TLDc domain-containing proteins, Oxr1 and Rtc5, together with two human proteins with a similar domain organization. S. cerevisiae Rtc5 and H. sapiens Meak7 are N-myristoylated proteins, which contain an N-terminal EF-hand-like domain and a C-terminal TLDc domain. S. cerevisiae Oxr1 and the splice variant Oxr1-C of H. sapiens consist mainly of just their TLDc domains. ( B ) A wt strain or strains lacking VMA4, OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing glucose with pH = 5.5, pH = 7.5, or pH = 7.5 and 3 mM ZnCl 2 , 10 mM ZnCl 2 , or 150 mM CaCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4 , OXR1 , RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing glucose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 nm or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates, and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05). ( D , E ) SILAC-based vacuole proteomics of cells lacking either OXR1 ( D ) or RTC5 ( E ) compared with the wt strain. Log10 of the detected protein intensities are plotted against Log2 of the heavy/light SILAC ratios. Significant outliers based on a two-group, two-tailed Student´s t -test are color-coded in red ( P value <1e − 14), orange ( P value <0.0001), or dark blue ( P value <0.05); other identified proteins are shown in light blue. Corresponding experiments performed by switching the heavy and light labeling of the strains are shown in Appendix Fig. S . ( F , G ) Cells in which Subunit C (Vma5) was tagged with msGFP2 were grown in a glucose-containing medium and imaged in the presence of glucose or after shifting them for 20 min to a medium containing galactose as the sole carbon source. The scale bar represents 2 μm. The distribution of Vma5 between the two compartments was quantified by using a ratio between the mean fluorescence intensity in a line along the vacuole membrane and the average of the mean fluorescence intensity in three circular regions in the cytosol. The different colors in the graph indicate independent experiments. The smaller circles represent individual cells, and the bigger circles represent the average for each independent experiment. Statistical comparison was performed using a one-way ANOVA and a Tukey post hoc test among the experimental means within each condition (glucose or galactose, n.s not significant P value >0.05; *** P value <0.001). .

Figure Legend Snippet: ( A ) Diagram of the domain organization of the two yeast TLDc domain-containing proteins, Oxr1 and Rtc5, together with two human proteins with a similar domain organization. S. cerevisiae Rtc5 and H. sapiens Meak7 are N-myristoylated proteins, which contain an N-terminal EF-hand-like domain and a C-terminal TLDc domain. S. cerevisiae Oxr1 and the splice variant Oxr1-C of H. sapiens consist mainly of just their TLDc domains. ( B ) A wt strain or strains lacking VMA4, OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing glucose with pH = 5.5, pH = 7.5, or pH = 7.5 and 3 mM ZnCl 2 , 10 mM ZnCl 2 , or 150 mM CaCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4 , OXR1 , RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing glucose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 nm or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates, and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05). ( D , E ) SILAC-based vacuole proteomics of cells lacking either OXR1 ( D ) or RTC5 ( E ) compared with the wt strain. Log10 of the detected protein intensities are plotted against Log2 of the heavy/light SILAC ratios. Significant outliers based on a two-group, two-tailed Student´s t -test are color-coded in red ( P value <1e − 14), orange ( P value <0.0001), or dark blue ( P value <0.05); other identified proteins are shown in light blue. Corresponding experiments performed by switching the heavy and light labeling of the strains are shown in Appendix Fig. S . ( F , G ) Cells in which Subunit C (Vma5) was tagged with msGFP2 were grown in a glucose-containing medium and imaged in the presence of glucose or after shifting them for 20 min to a medium containing galactose as the sole carbon source. The scale bar represents 2 μm. The distribution of Vma5 between the two compartments was quantified by using a ratio between the mean fluorescence intensity in a line along the vacuole membrane and the average of the mean fluorescence intensity in three circular regions in the cytosol. The different colors in the graph indicate independent experiments. The smaller circles represent individual cells, and the bigger circles represent the average for each independent experiment. Statistical comparison was performed using a one-way ANOVA and a Tukey post hoc test among the experimental means within each condition (glucose or galactose, n.s not significant P value >0.05; *** P value <0.001). .

Techniques Used: Variant Assay, Staining, Fluorescence, Multiplex sample analysis, Two Tailed Test, Labeling, Membrane, Comparison

( A ) Comparison of the AlphaFold model generated for Rtc5 with the available structure of Oxr1, the only two TLDc domain-containing proteins of Saccharomyces cerevisiae . ( B ) A wt strain or strains lacking VMA4 , OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing galactose as the carbon source with pH = 5.5, pH = 7.5, or pH = 7.5 and 6 mM ZnCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4, OXR1, RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing galactose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05).

Figure Legend Snippet: ( A ) Comparison of the AlphaFold model generated for Rtc5 with the available structure of Oxr1, the only two TLDc domain-containing proteins of Saccharomyces cerevisiae . ( B ) A wt strain or strains lacking VMA4 , OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing galactose as the carbon source with pH = 5.5, pH = 7.5, or pH = 7.5 and 6 mM ZnCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4, OXR1, RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing galactose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05).

Techniques Used: Comparison, Generated, Staining, Fluorescence

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Journal: The EMBO Journal

Article Title: Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase

doi: 10.1038/s44318-024-00097-2

Figure Lengend Snippet: ( A ) Diagram of the domain organization of the two yeast TLDc domain-containing proteins, Oxr1 and Rtc5, together with two human proteins with a similar domain organization. S. cerevisiae Rtc5 and H. sapiens Meak7 are N-myristoylated proteins, which contain an N-terminal EF-hand-like domain and a C-terminal TLDc domain. S. cerevisiae Oxr1 and the splice variant Oxr1-C of H. sapiens consist mainly of just their TLDc domains. ( B ) A wt strain or strains lacking VMA4, OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing glucose with pH = 5.5, pH = 7.5, or pH = 7.5 and 3 mM ZnCl 2 , 10 mM ZnCl 2 , or 150 mM CaCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4 , OXR1 , RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing glucose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 nm or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates, and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05). ( D , E ) SILAC-based vacuole proteomics of cells lacking either OXR1 ( D ) or RTC5 ( E ) compared with the wt strain. Log10 of the detected protein intensities are plotted against Log2 of the heavy/light SILAC ratios. Significant outliers based on a two-group, two-tailed Student´s t -test are color-coded in red ( P value <1e − 14), orange ( P value <0.0001), or dark blue ( P value <0.05); other identified proteins are shown in light blue. Corresponding experiments performed by switching the heavy and light labeling of the strains are shown in Appendix Fig. S . ( F , G ) Cells in which Subunit C (Vma5) was tagged with msGFP2 were grown in a glucose-containing medium and imaged in the presence of glucose or after shifting them for 20 min to a medium containing galactose as the sole carbon source. The scale bar represents 2 μm. The distribution of Vma5 between the two compartments was quantified by using a ratio between the mean fluorescence intensity in a line along the vacuole membrane and the average of the mean fluorescence intensity in three circular regions in the cytosol. The different colors in the graph indicate independent experiments. The smaller circles represent individual cells, and the bigger circles represent the average for each independent experiment. Statistical comparison was performed using a one-way ANOVA and a Tukey post hoc test among the experimental means within each condition (glucose or galactose, n.s not significant P value >0.05; *** P value <0.001). .

Article Snippet: Rtc5 is predicted to contain a TLDc domain ( T re2/Bub2/Cdc16, L ysM, d omain c atalytic, Pfam PF07534, InterPro IPR006571, Prosite PS51886, and SMART SM00584).

Techniques: Variant Assay, Staining, Fluorescence, Multiplex sample analysis, Two Tailed Test, Labeling, Membrane, Comparison

Journal: The EMBO Journal

Article Title: Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase

doi: 10.1038/s44318-024-00097-2

Figure Lengend Snippet: ( A ) Comparison of the AlphaFold model generated for Rtc5 with the available structure of Oxr1, the only two TLDc domain-containing proteins of Saccharomyces cerevisiae . ( B ) A wt strain or strains lacking VMA4 , OXR1 or RTC5 , or both OXR1 and RTC5 were spotted as serial dilutions on media containing galactose as the carbon source with pH = 5.5, pH = 7.5, or pH = 7.5 and 6 mM ZnCl 2 . ( C ) Analysis of vacuolar acidity via BCECF staining in a wt strain, a strain lacking VMA4, OXR1, RTC5 , or both RTC5 and OXR1 . The experiments were performed with cultures grown in a medium containing galactose and pH = 5.5. For each strain, at least three independent experiments were performed, each containing three biological replicates. For each sample, the fluorescence emission of BCECF at 538 nm was measured when excited at 440 or 485 nm, and a ratio between these two values was calculated. The ratio was normalized to the average value for the wt strain in that experiment. The different colors in the graph indicate independent experiments, the smaller dots are biological replicates and the larger circles represent the averages of each independent experiment. Statistical analysis was performed with a one-way ANOVA and a Tukey post hoc test. The vma4Δ strain was significantly different from the wt strain (*** P value <0.001), all other strains are not significantly different from the wt strain ( P value >0.05).

Article Snippet: Rtc5 is predicted to contain a TLDc domain ( T re2/Bub2/Cdc16, L ysM, d omain c atalytic, Pfam PF07534, InterPro IPR006571, Prosite PS51886, and SMART SM00584).

Techniques: Comparison, Generated, Staining, Fluorescence

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