GifOrsay Microarray Platform Using Spotfire to analyse the

Regulation by oxygen Heme is assumed to mediate the “oxygen signal” Regulation by carbon

Experimental flow chart Processing Acquisition -------------------------------------------------------------- Filter and assemble Image Raw data 1 array

NAD metabolism Tryptophan De novo pathway (BNA 1 -BNA 6) Nicotinate ribonucleotide NPT 1

ERG 11 ERG 3 ERG 5 Sterol metabolism ASU 1

30 -40% of yeast genes have no know function

Conclusions • During the anaerobic/aerobic shift one of the major changes is a remodelling

D. Rickman C. J. Herbert M-H. Muchielli B. Guiard A. Glatigny C. Panozzo Gif/Orsay

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Gif/Orsay Microarray Platform Using Spotfire to analyse the regulation of gene expression by oxygen in Saccharomyces cerevisiae

Regulation by oxygen Heme is assumed to mediate the “oxygen signal” Regulation by carbon source Catabolite repression can over-ride regulation by oxygen Carbon sources can require a respiratory metabolism, or use a mixed metabolism “fermentation/ respiration” (diauxic shift)

Regulation by oxygen

FY 167 9 CE N. P K 2 286 Y 7 -1 B DB 303 GW HAP 1 mutation in S 288 c derived strains

Petite production in DBY 7286

Culture conditions

Universal reference

Yeast genome double spotting

Aerobic Shift

Experimental flow chart Processing Acquisition -------------------------------------------------------------- Filter and assemble Image Raw data 1 array = 1 spreadsheet Analysis ------------------------------- Normalize Compare expression data

All clusters

Three phases of expression

Heme biosynthesis HEM 13 HEM 14 COX 15

NAD metabolism Tryptophan De novo pathway (BNA 1 -BNA 6) Nicotinate ribonucleotide NPT 1 NAD salvage pathway Nicotinate

NAD metabolism BNA 1 BNA 4 NPT 1

ERG 11 ERG 3 ERG 5 Sterol metabolism ASU 1

Cell wall DAN PAU TIR

Oxidative stress LYS 7 SOD 2 SOD 1

Respiratory chain

30 -40% of yeast genes have no know function

Late induction YAR 073 w

YAR 073 w profile

YAR 073 w similar profile YAR 073 w

YAR 073 w profile genes YAR 073 w • • 35 genes 18 unknown 11 a. a. and nucleotide biosynthesis 6 translation and vacuole

Transient induction YLR 101 c

YLR 101 c profile

YLR 101 c similar profile YLR 101 c

YLR 101 c profile genes YLR 101 c • • 15 genes 9 unknown 2 named but unknown 1 transcription coregulator • 3 ergosterol biosynthesis

Conclusions • During the anaerobic/aerobic shift one of the major changes is a remodelling of the cell wall and plasma-membrane • There is no strict co-ordinate regulation of biosynthetic pathways, but genes encoding enzymes that use O 2 are subject to a stronger regulation

D. Rickman C. J. Herbert M-H. Muchielli B. Guiard A. Glatigny C. Panozzo Gif/Orsay Micro. CGM, Gif-sur-Yvette Array Platform J. Ouazzani ICSN, Gif-sur-Yvette