User:Matthew Whiteside/Notebook/Fumigatus Microarray/2009/03/12

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Carbon metabolism

 * 1) possible players: glycogen phosphorylase (Afu1g12920), alcohol dehydrogenase (Afu3g01490), isoamyl alcohol oxidase (Afu3g07410) and NAD-dependent formate dehydrogenase (Afu6g04920).

GABA metabolism

 * 1) Afu5g00710 (GABA permease, putative)
 * 2) * upreg in our study, SreA, and StuA studies.

Nitrogen metabolism

 * AreA & B
 * main repressors in nitrogen repressing system (probably cooperate)
 * e.g. arginine use as N source requires agaA and otaA genes (arginase & ornithine aminotransferase), repressed when ammonium available.
 * PopB
 * deadenalyase (remove polyA tail = +mRNA decay)
 * AreA regulated by Gln (glutamine).
 * Many N metab genes are increased degraded in response to Gln by PopB
 * P-body (cytoplasmic structure) is site of action (mRNA degradation by signalling pathways).

TCA

 * GABA is catabolized to succinate via succinicsemialdehyde. potential bypass outside the classical tricarboxylic acid cycle

A. nidulans Hap complex

 * Heterotrimeric CCAATT-binding complex (CBC). Evo conserved complex of HapB, C & E.
 * A. nidulans has HapX. Repressed by GATA-factor SreA (iron regulation)
 * repressed during iron starvation.
 * Also CBC is modified by Thioredoxin A (trxA). HapC is oxidized by trxA. When reduced HapC locates to cytoplasm, and no transcription.
 * CBC is regulated by post-translation mech (trxA) and transcriptional mech (sreA) for tight control linked to iron.

A. fumigatus SreA

 * iron regulator.
 * Repressor of 49 genes, in response to iron.
 * GATA-factor (common to many ascomyota). Contains putative iron-sensing domain.
 * Repressed genes incl reductive iron assimilation and siderophore-mediated iron uptake.
 * 23 of 49 organized in clusters.
 * Special cases:
 * HapX, iron regulator (see above)
 * mito ornithine carrier (AmcA), supply ornithine.
 * CgrA, ribosome biosynthesis, thermotolerance, virulence.
 * Cluster1 - cell-wall degradation? Afu1g03350 1,3-glucanase.
 * Pep1 - aspartic endopeptidase Afu5g13300, & putative peptidase transporter Afu1g12240. protein degradation. (Pep1 found in sera)
 * carbon metabolism - glycogen phosphorylase (Afu1g12920), alcohol dehydrogenase (Afu3g01490), isoamyl alcohol oxidase (Afu3g07410) and NAD-dependent formate dehydrogenase (Afu6g04920).
 * motif ATCWGATAA
 * source: 1

A. fumigatus LaeA

 * regulator of secondary biosynthesis clusters
 * Seems to act independently of SreA
 * Regulates SidE (some biosynthetic function?), but not other cluster genes (sidC, or D).
 * No homolog in A. nidulans
 * Gliotoxin biosynthesis
 * source: 1

A. fumigatus StuA & BrlA

 * promotors of conidiation (some gene targets overlap)
 * also regulators of secondary biosynthesis (usu related to conidation)
 * StuA 6 biosynthetic clusters
 * BrlA 1 biosynthetic cluster
 * BrlA downregulates rioosomal protein synthesis in response to N limitation (not carbon)
 * seems to be TOR independent
 * source: 2