Table 2. Classification into functional families of ORFs whose transcripts are induced at least 2-fold after alkaline pH stress. The asterisks denote that the intensity of the hybridisation signal was out of the linear range of detection and, therefore, induction might be stronger than that presented here. The «Time» column indicates the kinetic of response. Genes showing the highest induction after 5 min at alkaline pH are denoted by «E» (Early). «I» (Intermediate) indicates a peak at 25 min and «L» (Late) corresponds to genes that shows the highest induction after 45 min at alkaline pH. Functional categories were assigned based on information provided by MIPS (Mewes et al., 1999). Boldface indicates genes identified as responsive to a wide variety of stresses (Gasch et al., 2000; Causton et al., 2001)

 

 

ORF

Gene

-Fold

Time

Function

 

Carbohydrate Metabolism / Energy

 

YOR374W

ALD4

6.8

E

Mitochondrial aldehyde dehydrogenase

YPL061W

ALD6

5.0 (*)

I

Acetaldehyde dehydrogenase

YOR095C

RKI1

3.3

I

Ribose-5-phosphate ketol-isomerase

YEL071W

DLD3

3.9 (*)

I

D-lactate dehydrogenase

YIL162W

SUC2

4.6

E

Sucrose utilization

YDR178W

SDH4

2.4

E

Subunit succinate dehydrogenase complex

YCR005C

CIT2

4.1

I

Peroxisomal citrate synthase

 

Phosphate transport / metabolism

 

YBR296C

PHO89

3.2

E

High-affinity Na+-phosphate symporter

YHR215W

PHO12

2.2

L

Inducible, secreted acid phosphatase

YML123C

PHO84

12.7

L

H+/phosphate permease

YJL012C

VTC4

2.9

I

Putative polyphosphate synthetase

YPL019C

VTC3

2.2

L

Putative polyphosphate synthetase

YER072W

VTC1

2.5

L

Putative polyphosphate synthetase

 

Other metabolism

 

YLR303W

MET17

2.2

I

Methionine biosynthesis

YKL001C

MET14

4.2

I

Sulfate assimilation

YGL037C

PNC1

2.3

E

Pyridine nucleotide cycle

YML106W

URA5

5.0

I

Pyrimidine biosynthesis

YPL057C

SUR1

2.2

I

Sphingolipid metabolism

YLR056W

ERG3

2.1

L

Sterol metabolism

YOL165C

AAD15

2.8

I

Hypothetical aryl-alcohol dehydrogenase

YCR107W

AAD3

2.5

I

Putative aryl-alcohol dehydrogenase

YFL056C

AAD6

2.5

I

Probable aryl alcohol dehydrogenase

 

Ion transport & homeostasis / Other transports

 

YBR158W

CST13

4.2

I

Cu2+ ion homeostasis (putative

YLR214W

FRE1

7.4

I

Iron and copper homeostasis

YOR382W

FIT2

6.6

L

Possibly involved in iron uptake

YPL135W

ISU1

2.3

I

Iron homoestasis

YEL065W

ARN3

5.4

I

Ferrioxamine B permease

YHL040C

ARN1

2.4

L

Transport of ferrichromes.

YHL047C

ARN2

3.9

L

Triacetylfusarinine C transporter

YMR058W

FET3

2.6

L

Cell surface ferroxidase

YPR124W

CTR1

2.5

I

Required for high-affinity uptake of copper

YDR038C

ENA5

2.5

E

Na(+) ATPase

YDR040C

ENA1

2.0

E

Na(+) ATPase

YCR011C

ADP1

2.1

I

Putative ATP-dependent permease

YDR011W

SNQ2

3.1

I

Putative ATP-dependent permease

YGL077C

HNM1

2.2

E

Choline permease

YGR121C

MEP1

2.0

E

Ammonia permease

YHR092C

HXT4

2.3

E

Moderate- to low-affinity hexose transporter

YIL170W

HXT12

2.7

E

Hexose transporter

 

Transcription & RNA processing

 

YBR112C

CYC8

2.9

I

General repressor

YBR154C

RPB5

7.2

I

Shared subunit of RNA pol. I. II. III

YCL066W

HMLa1

2.3

I

Activates alpha-specific genes

YJR063W

RPA12

2.1

I

RNA polymerase I subunit

YKR025W

RPC37

2.0

I

RNA polymerase III 37 kDa subunit

YPR110C

RPC40

2.3

I

Shared subunit of RNA pol. I and III

YLR136C

TIS11

4.6

I

Pol II transcription

YDR395W

SXM1

2.3

I

mRNA export. nuclear protein targeting

YHR170W

NMD3

2.2

I

mRNA decay

YKL009W

MRT4

2.6

I

mRNA decay

YOL123W

HRP1

2.0

E

Nuclear polyA RNA-binding protein

YDR083W

RRP8

2.9

I

Ribosomal RNA processing

YHR169W

DBP8

2.1

I

RNA helicase

YJL116C

NCA3

9.7

I

RNA processing/modification

YDR087C

RRP1

3.8

I

rRNA processing

YJL033W

HCA4

3.5

I

rRNA processing

YOL142W

RRP40

2.2

I

rRNA processing

YDL051W

LHP1

2.3

I

tRNA processing

 

Stress response

 

YMR174C

PAI3

4.5

I

Osmotic stress response

YJR104C

SOD1

2.1

I

Copper-zinc superoxide dismutase

YKR066C

CCP1

2.6

I

Cytochrome-c peroxidase

YCR021C

HSP30

2.0

L

Heat shock protein

YDR513W

GRX2

2.3

I

Glutaredoxin

YDR353W

TRR1

4.6 (*)

I

Thioredoxin reductase

YBR111C

YSA1

2.1

I

Nucleoside diphosphate-sugar hydrolase

YMR175W

SIP18

2.1

I

Induced by osmotic stress

 

Protein degradation / synthesis / modification

 

YER012W

PRE1

2.1

I

20S proteasome subunit C11(beta4)

YGR135W

PRE9

2.2

I

20S proteasome subunit Y13 (alpha3)

YLR120C

YPS1

2.7

E

GPI-anchored aspartyl protease

YPL154C

PEP4

2.1

E

Vacuolar aspartyl protease

YDR037W

KRS1

2.2

I

tRna synthetase. lysyl

YDR041W

RSM10

2.0

E

Mitochondrial ribosomal small subunit

YDR418W

RPL12B

2.2 (*)

I

Ribosomal protein L12B

YNL002C

RLP7

2.0

I

Similarity to ribosomal proteins

YOL127W

RPL25

3.7

L

Ribosomal protein L25

YMR060C

TOM37

3.1

L

Outer membrane translocase

YBR110W

ALG1

5.3

I

Beta-1.4-mannosyltransferase

YBR205W

KTR3

3.0

I

Putative alpha-1.2-mannosyltransferase

YMR101C

SRT1

2.0

L

Cis-prenytransferase (putative)

 

Other

 

YAL059W

ECM1

2.0

I

Cell wall biogenesis

YGR008C

STF2

2.3

E

Cell wall maintenance

YKL096W

CWP1

2.2

E

Mannoprotein of the cell wall

YBR160W

CDC28

2.4

I

Cyclin-dependent protein kinase

YNL307C

MCK1

2.2

E

Member of the GSK-3 family of protein kinases

YOR242C

SSP2

3.7

L

Sporulation

YCR052W

RSC6

2.9

I

Chromatin remodeling complex subunit

YCR009C

RVS161

2.1

I

Actin-binding protein

YBR179C

FZO1

3.4

E

Mitochondrial membrane GTPase

YIR012W

SQT1

2.5

I

Ribosome biogenesis. putative

YNL036W

NCE103

7.6

E

Secretion

YBR109C

CMD1

2.8

I

Calmodulin. Ca+ binding

YGR023W

MTL1

2.3

L

Morphogenesis

YKL043W

PHD1

3.1

E

Transcription factor involved in filamentous growth

 

Unknown

 

YAL049C

 

2.6

I

YAL053W

 

2.0

L

YBL108W

 

3.2

L

YBR004C

 

2.2

E

YBR207W

FTH1

2.6

I

YBR287W

 

3.7

E

YCL059C

KRR1

2.3

I

YCR054C

CTR86

3.0

I

YDL046W

 

4.6

E

YDL167C

 ARP1

2.6

I

YDL213C

 

3.7

I

YDR161W

TCI1

2.0

I

YDR370C

 

5.0

I

YDR372C

 

2.7

I

YDR516C

 

2.3

E

YDR534C

 

2.5

L

YER150W

SPI1

2.7

E

YGL039W

 

2.0

I

YGL183C

 

5.0

I

YGR187C

HGH1

2.0

I

YGR211W

ZPR1

2.0

I

YGR213C

RTA1

3.4

E

YGR243W

 

2.5

E

YHL021C

 

2.1

E

YHR052W

 

2.2

I

YHR087W

 

2.4

E

YHR138C

 

2.6

E

YJL171C

 

2.4

E

YKL071W

 

13.8

I

YKL175W

ZRT3

2.3

L

YLR108C

 

2.3

I

YLR186W

 

2.3

I

YLR205C

 

2.2

I

YLR327C

 

5.2

E

YLR405W

 

2.1

L

YLR414C

 

2.5

E

YML058C-A

 

2.1

L

YML059C

 

2.1

L

YML128C

MSC1

3.0

E

YML131W

 

2.9

I

YMR031C

 

2.9

E

YMR173W

DDR48

5.4

I

YMR173W-A

 

5.9

I

YMR251W-A

HOR7

9.2

E

YMR304C-A

 

2.3

E

YMR316W

DIA1

2.8

E

YMR318C

 

2.8

I

YNL013C

 

2.6

L

YNL134C

 

2.7

I

YNL149C

 

2.3

I

YNL208W

 

2.2

I

YNL300W

TOS6

2.2

L

YOL150C

 

3.0

I

YOL151W

GRE2

4.1

I

YOR049C

 

3.7

E

YOR161C

 

2.4

E

YPL183C

 

2.3

L