Autophagy induced by rapamycin and carbon‐starvation have distinct proteome profiles in Aspergillus nidulans

Abstract

It is hypothesized that autophagy, a global catabolic pathway which is highly conserved from yeast to man, plays an important role in many bioprocesses. Though autophagy is known to be induced by either nutrient starvation or treatment with the drug rapamycin, it is not clear whether the two modes of induction have the same long-term impact in the cell, particularly in the biotechnologically important filamentous fungi. Here, we compare the overall proteomes from the carbon-starved (G-) and rapamycin treated (R+) model fungus Aspergillus nidulans. From about 1,100 visualized protein spots, we conservatively selected a total of 26 proteins with significant different expression. To highlight, increased levels of glucosidases and decreased levels of N-acetylglucosamine pyrophosphorylase were observed, suggesting degradation of the fungal cell wall as an alternate carbon source for both modes of induction. Cdc37 was reduced in expression while 14-3-3 ArtA was increased, implying regulation of polar growth, while also potentially regulating autophagy negatively via PKA or Tor. Other proteins included aspartate transaminase, tryptophan synthase B (TrpB), glycylpeptide N-tetradecanoyltransferase (Nmt1), and aldehyde dehydrogenase (aldA). More interestingly, the majority of the identified proteins (16 of 26) were uniquely expressed in elevated levels in G-. A novel predicted protein from AN8223 which has no sequence homology to other organisms is also implicated to be involved in carbon-starvation. Thus, proteomic data here show that in A. nidulans, rapamycin-induced autophagy and carbon-starvation induced autophagy share some effectors for cell survival, but predominantly involve different long-term effectors.

Transcriptome changes initiated by carbon starvation in Aspergillus nidulans

“…In recent experiments, we found that a DchiB DengA double mutant grew significantly slower in surface cultures than its control strain on culture media containing weak carbon sources (Szilágyi et al, 2012). All these data suggest that fungi not only split their own cell wall polysaccharides but also utilize them, as has also been suggested by Kim et al (2011) in their proteome study.…”

“…In our experiments, among these proteins/genes, only four, aldA, AN8223, AN7298 and AN4102 (Table S2), behaved similarly to those observed by Kim et al (2011). This significant difference may be explained by the fact that Kim et al (2011) studied older (14 h) cultures than us (4 h).…”

“…During the proteome analysis of A. nidulans cultures, Kim et al (2011) identified 10 proteins characteristically upregulated and five proteins characteristically downregulated in carbon-starved cultures. In our experiments, among these proteins/genes, only four, aldA, AN8223, AN7298 and AN4102 (Table S2), behaved similarly to those observed by Kim et al (2011). This significant difference may be explained by the fact that Kim et al (2011) studied older (14 h) cultures than us (4 h).…”

“…Upregulation of the putative b-glucosidase-encoding genes bglM (Table 2) and AN4102 (Table S2) might also be related to the degradation of the fungal cell wall, and was in good accordance with the observed elevated b-glucosidase activity found previously under carbon starvation (Szilágyi et al, 2010). The AN4102 gene product was also recorded in a proteome analysis performed on carbon-starved cultures by Kim et al (2011). Induction of the putative glucosamine-6-phosphate isomerase and N-acetylglucosamine-6-phosphate deacetylase, as well as the activation of several potential high-affinity carbohydrate transporters, including mstA and hxtA (Tables 2 and S2), were also observable.…”

“…mycotoxins, antibiotics, antimycotics, pigments), hydrolytic enzymes (e.g. proteinases, chitinases, glucanases, nucleases), and antifungal and antibacterial enzymes/ proteins, as well as the initiation of asexual, sexual and parasexual cycles (White et al, 2002;Fischer & Kües, 2006;Keller et al, 2005;Emri et al, 2008;Kim et al, 2011). Some of these processes have been investigated in detail (Fischer & Kües, 2006;Keller et al, 2005), but only a few studies have applied a holistic approach to understand the global changes caused by carbon starvation.…”