adaptive phase at day 1 of carbon starvation. The encoded proteins include two predicted metacaspases and a Poly poly merase homologue. Four proteins shar ing NACHT domains combined with ankyrin or WD40 domain except repeats and three proteins with a NB ARC domain were upregu lated as well. As implied by the enrichment results for both GO and KEGG pathway annotations, carbon starvation coor from RNA polymerase I promoter, ribosome biogenesis, translation, secretion and respiration. Pfam domain and KEGG pathway enrichment results are summarized in the supplemental data. Although the three annotations have di?erent sources, structures and levels of complexity, the indi vidual enrichment results con?rm each other. Only in a few cases, Pfam domain and KEGG pathway enrich ment analyses provided additional information beyond the GO enrichment results.

For example, among the upregulated genes at day 1, 3 and 6, those having a puta tive sugar transporter domain were strongly enriched. In consideration of the severe carbon limitation, it can be assumed that these predicted sugar trans porters comprise high a?nity sugar transporters. Indeed, mstA and mstF encoding two high a?nity sugar H symporters were signi? cantly upregulated at day 1 and 3 as well as day 1, 3 and 6, respectively. Furthermore, the cytochrome P450 domain was signi?cantly enriched among genes upreg ulated at day 1. The biochemical roles of the majority of cytochromes P450 are unknown but many are expected to dinately induced the expression of genes involved in autophagic processes.

To date, more than 30 autophagy genes have been identi?ed for Saccharomyces cere visiae and other fungi, 23 of which have a pre dicted orthologue in A. niger. All except one were detected as signi?cantly upregulated during at least one of the starvation time points. The expression level of atg8, encoding a lipid conjugated ubiquitin like protein that controls the expansion of pre autophagosomes, was the highest among all atg genes. At day 3 it reached 75% of the actin expression level during exponential growth. Despite this concerted induc tion during carbon starvation, it is clearly evident from the expression data that autophagic processes also play an important role during exponential growth, because atg gene expression levels ranged from 0. 6% to 24% when compared with the actin gene expression level.

The induction of hydrolases, including proteases and glycosyl hydrolases, has been proposed as a key event in aging fungal cultures. During carbon starva tion, glycosyl hydrolases are involved in both the lib eration of GSK-3 carbon from fungal cell wall polymers and cell wall remodeling. We identi?ed inhibitor licensed those upregulated genes that putatively encode glycosyl hydrolases active on fungal cell wall polymers such as chitin, glucan and mannan by mining publicly accessible data. The expression pro?les allow a general classi ?cation into early and late response genes. In agree ment with literature, the chitinolytic genes chiB and

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