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A Late Form of Nucleophagy in Saccharomyces cerevisiae

Mijaljica, Dalibor, Prescott, Mark, Devenish, Rodney J.·2012·PLoS ONE
DOI 10.1371/journal.pone.0040013PMC PMC3386919
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Figure 1 Delivery of n-Rosella to the vacuole of nitrogen-starved wild type cells. (A) Wild type (BY4741) cells expressing n-Rosella were subjected to nitrogen starvation and then sampled at selected time points (0, 6, 24, 48 and 72 hours after commencement of nitrogen starvation). Accumulation of diffuse red fluorescence in the vacuole was taken as evidence of nucleophagy. (B) The percentage of cells showing accumulation of diffuse red fluorescence in the vacuole at various time points is shown. (C) Cells expressing n-Rosella were starved in SD(-N) medium for 0, 3, 6, 9, 12, 15, 18, 21, 24, 48 and 72 hours, and the increase in processed degradation product (free GFP) levels was monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. (D) Staining with Hoechst 33258 was performed to confirm the targeting of n-Rosella (red and green fluorescence) to the nucleus 24 hours after commencement of nitrogen starvation. (E) Staining with the vacuolar lumen dye, CMAC-Arg was performed to confirm the delivery of n-Rosella (diffuse red fluorescence) to the vacuole (24 hours after commencement of nitrogen starvation).
Figure 1 Delivery of n-Rosella to the vacuole of nitrogen-starved wild type cells. (A) Wild type (BY4741) cells expressing n-Rosella were subjected to nitrogen starvation and then sampled at selected time points (0, 6, 24, 48 and 72 hours after commencement of nitrogen starvation). Accumulation of diffuse red fluorescence in the vacuole was taken as evidence of nucleophagy. (B) The percentage of cells showing accumulation of diffuse red fluorescence in the vacuole at various time points is shown. (C) Cells expressing n-Rosella were starved in SD(-N) medium for 0, 3, 6, 9, 12, 15, 18, 21, 24, 48 and 72 hours, and the increase in processed degradation product (free GFP) levels was monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. (D) Staining with Hoechst 33258 was performed to confirm the targeting of n-Rosella (red and green fluorescence) to the nucleus 24 hours after commencement of nitrogen starvation. (E) Staining with the vacuolar lumen dye, CMAC-Arg was performed to confirm the delivery of n-Rosella (diffuse red fluorescence) to the vacuole (24 hours after commencement of nitrogen starvation).CC BY · PubMed Central
Figure 2 The diffuse red fluorescence (NAB35-DsRed.T3) accumulated in the vacuole is delivered directly from the nucleus. Wild type (BY4741) and atg6Δ cells expressing cyto-GFP alone (A), or co-expressing cyto-GFP and NAB35-DsRed.T3 (B), under growing (SS+D) and nitrogen starvation conditions (SD-N) were sampled after 24 hours. Staining with the vacuolar lumen staining dye, CMAC-Arg was used to confirm delivery of fluorescent reporters to the vacuole.
Figure 2 The diffuse red fluorescence (NAB35-DsRed.T3) accumulated in the vacuole is delivered directly from the nucleus. Wild type (BY4741) and atg6Δ cells expressing cyto-GFP alone (A), or co-expressing cyto-GFP and NAB35-DsRed.T3 (B), under growing (SS+D) and nitrogen starvation conditions (SD-N) were sampled after 24 hours. Staining with the vacuolar lumen staining dye, CMAC-Arg was used to confirm delivery of fluorescent reporters to the vacuole.CC BY · PubMed Central
Figure 3 Wild type cells co-expressing Nvj1-EYFP and NAB35-DsRed.T3 nuclear reporters show temporal separation of nucleophagic events. (A) Wild type (BY4741) cells co-expressing both nuclear reporters were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions (3 and 24 hours after commencement of nitrogen starvation), respectively. The appearance of Nvj1p-EYFP-derived vesicles (PMN vesicles) in the vacuole is highlighted by white arrows, whereas accumulation of NAB35-DsRed.T3-derived fluorescence (diffuse red fluorescence) is indicated by yellow arrows. (B) Percentage of cells showing accumulation of fluorescence in the vacuole over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (C) Accumulation of both Nvj1p-EYFP-derived vesicles (PMN vesicles) and accumulation of NAB35-DsRed.T3-derived diffuse red fluorescence in the same cells 24 hours after commencement of nitrogen starvation. The appearance of vacuolar vesicles containing both nuclear reporters is indicated by white arrows.
Figure 3 Wild type cells co-expressing Nvj1-EYFP and NAB35-DsRed.T3 nuclear reporters show temporal separation of nucleophagic events. (A) Wild type (BY4741) cells co-expressing both nuclear reporters were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions (3 and 24 hours after commencement of nitrogen starvation), respectively. The appearance of Nvj1p-EYFP-derived vesicles (PMN vesicles) in the vacuole is highlighted by white arrows, whereas accumulation of NAB35-DsRed.T3-derived fluorescence (diffuse red fluorescence) is indicated by yellow arrows. (B) Percentage of cells showing accumulation of fluorescence in the vacuole over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (C) Accumulation of both Nvj1p-EYFP-derived vesicles (PMN vesicles) and accumulation of NAB35-DsRed.T3-derived diffuse red fluorescence in the same cells 24 hours after commencement of nitrogen starvation. The appearance of vacuolar vesicles containing both nuclear reporters is indicated by white arrows.CC BY · PubMed Central
Figure 4 The inactivation of the NVJ1 and VAC8 genes required for PMN does not abrogate the delivery of n-Rosella to the vacuole. nvj1Δ (A) and vac8Δ (B) cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (C) The percentage of nvj1Δ and vac8Δ cells showing accumulation of diffuse red fluorescence in the vacuole under growing (SS+D) and nitrogen starvation (SD-N) conditions (24 hours after commencement of nitrogen starvation). (D) Wild type, nvj1Δ and vac8Δ cells expressing n-Rosella were starved in SD(−N) medium for 0 and 24 hours, and the levels of the free GFP degradation product monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. (E) vac8Δ cells co-expressing the two nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (3 and 24 hours after commencement of nitrogen starvation), respectively. The accumulation of NAB35-DsRed.T3-derived fluorescence (diffuse red fluorescence) is indicated by white arrow. (F) Percentage of vac8Δ cells showing accumulation of fluorescence in the vacuole over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red.
Figure 4 The inactivation of the NVJ1 and VAC8 genes required for PMN does not abrogate the delivery of n-Rosella to the vacuole. nvj1Δ (A) and vac8Δ (B) cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (C) The percentage of nvj1Δ and vac8Δ cells showing accumulation of diffuse red fluorescence in the vacuole under growing (SS+D) and nitrogen starvation (SD-N) conditions (24 hours after commencement of nitrogen starvation). (D) Wild type, nvj1Δ and vac8Δ cells expressing n-Rosella were starved in SD(−N) medium for 0 and 24 hours, and the levels of the free GFP degradation product monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. (E) vac8Δ cells co-expressing the two nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (3 and 24 hours after commencement of nitrogen starvation), respectively. The accumulation of NAB35-DsRed.T3-derived fluorescence (diffuse red fluorescence) is indicated by white arrow. (F) Percentage of vac8Δ cells showing accumulation of fluorescence in the vacuole over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red.CC BY · PubMed Central
Figure 5 Detection of nuclear-derived intra-vacuolar puncta in atg15Δ and pep4Δ cells. (A) atg15Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). Staining with Hoechst 33258 was performed to confirm the targeting of n-Rosella (red and green fluorescence) to the nucleus and nucleus-derived vesicles/puncta observed in the vacuole. (B) atg15Δ cells co-expressing the nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). White arrow highlights Nvj1p-EYFP labeled vesicle whereas yellow arrow highlights NAB35-DsRed.T3 labeled vesicle/puncta, respectively. (C) Percentage of cells showing accumulation of reporter fluorescence over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (D) pep4Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (E) pep4Δ cells co-expressing the nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). The appearance of Nvj1p-EYFP-derived vesicles (PMN blebs and/or vesicles) in the vacuole is highlighted by white arrows, whereas accumulation of NAB35-DsRed.T3-derived vesicles/puncta is indicated by yellow arrows. (F) Staining with the vacuolar lumen dye, CMAC-Arg confirmed the delivery of NAB35-DsRed.T3 (red fluorescence) and Nvj1-EYFP (green fluorescence) to the vacuole.
Figure 5 Detection of nuclear-derived intra-vacuolar puncta in atg15Δ and pep4Δ cells. (A) atg15Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). Staining with Hoechst 33258 was performed to confirm the targeting of n-Rosella (red and green fluorescence) to the nucleus and nucleus-derived vesicles/puncta observed in the vacuole. (B) atg15Δ cells co-expressing the nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). White arrow highlights Nvj1p-EYFP labeled vesicle whereas yellow arrow highlights NAB35-DsRed.T3 labeled vesicle/puncta, respectively. (C) Percentage of cells showing accumulation of reporter fluorescence over time: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (D) pep4Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (E) pep4Δ cells co-expressing the nuclear reporters, Nvj1-EYFP and NAB35-DsRed.T3 were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). The appearance of Nvj1p-EYFP-derived vesicles (PMN blebs and/or vesicles) in the vacuole is highlighted by white arrows, whereas accumulation of NAB35-DsRed.T3-derived vesicles/puncta is indicated by yellow arrows. (F) Staining with the vacuolar lumen dye, CMAC-Arg confirmed the delivery of NAB35-DsRed.T3 (red fluorescence) and Nvj1-EYFP (green fluorescence) to the vacuole.CC BY · PubMed Central
Figure 6 The deletion of the ATG6 or ATG11 genes does not abrogate the delivery of n-Rosella to the vacuole. (A) atg11Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions (0, 24, 48 and 72 hours after commencement of nitrogen starvation). (B) atg11Δ cells co-expressing both nuclear reporters were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions and the percentage of cells showing accumulation of fluorescence over time determined: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (C) Wild type, atg6Δ, atg11Δ, atg8Δ and atg10Δ cells expressing n-Rosella were starved in SD(-N) medium for 0 and 24 hours, and degradation product (free GFP) levels were monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal.
Figure 6 The deletion of the ATG6 or ATG11 genes does not abrogate the delivery of n-Rosella to the vacuole. (A) atg11Δ cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions (0, 24, 48 and 72 hours after commencement of nitrogen starvation). (B) atg11Δ cells co-expressing both nuclear reporters were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions and the percentage of cells showing accumulation of fluorescence over time determined: ♦ green (Nvj1p-EYFP) only; • red (NAB35-DsRed.T3) only; ▾ green and red. (C) Wild type, atg6Δ, atg11Δ, atg8Δ and atg10Δ cells expressing n-Rosella were starved in SD(-N) medium for 0 and 24 hours, and degradation product (free GFP) levels were monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal.CC BY · PubMed Central
Figure 7 Deletion of the ATG3 gene abrogates the delivery of n-Rosella to the vacuole and influences nuclear morphology. (A) atg3Δ and (B) atg3Δ + ATG3 cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (C) Electron microscopy images of wild type (BY4741), atg3Δ and atg3Δ + ATG3 cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions. Nitrogen-starved cells were sampled for imaging after 12 and 24 hours. Examples of contacts between the nucleus and vacuoles as well as alterations in nuclear morphology are presented. N, nucleus; V, vacuole. Bar, 2 µm. (D) Wild type, atg3Δ and atg4Δ cells expressing n-Rosella were starved in SD(−N) medium for 0 and 24 hours, and the levels of free GFP degradation product monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. **indicates non-specific degradation product observed only in growing cells (0 hours).
Figure 7 Deletion of the ATG3 gene abrogates the delivery of n-Rosella to the vacuole and influences nuclear morphology. (A) atg3Δ and (B) atg3Δ + ATG3 cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation). (C) Electron microscopy images of wild type (BY4741), atg3Δ and atg3Δ + ATG3 cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD-N) conditions. Nitrogen-starved cells were sampled for imaging after 12 and 24 hours. Examples of contacts between the nucleus and vacuoles as well as alterations in nuclear morphology are presented. N, nucleus; V, vacuole. Bar, 2 µm. (D) Wild type, atg3Δ and atg4Δ cells expressing n-Rosella were starved in SD(−N) medium for 0 and 24 hours, and the levels of free GFP degradation product monitored by immunoblotting as described in Materials and Methods. Cytosolic PGK was detected as a loading control. *indicates the presumptive degradation product of n-Rosella lacking the NAB35 nuclear targeting signal. **indicates non-specific degradation product observed only in growing cells (0 hours).CC BY · PubMed Central
Figure 8 The absence of a functional ATG4 gene product abrogates the delivery of n-Rosella to the vacuole and influences nuclear morphology. atg4Δ (A), atg4Δ + ATG4 (B), and atg4Δ + Atg4C159A (C) cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation).
Figure 8 The absence of a functional ATG4 gene product abrogates the delivery of n-Rosella to the vacuole and influences nuclear morphology. atg4Δ (A), atg4Δ + ATG4 (B), and atg4Δ + Atg4C159A (C) cells expressing n-Rosella were imaged under growing (SS+D) and nitrogen starvation (SD−N) conditions (24 hours after commencement of nitrogen starvation).CC BY · PubMed Central

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Metadata

Authors
Mijaljica, D., Prescott, M., & Devenish, R. J.
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-06-29
Volume
7
Issue
6
Pages
e40013
ISSN
1932-6203
DOI
10.1371/journal.pone.0040013
PMC
PMC3386919
Cited by
50
References
2
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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