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Table 2 Common upstream motifs in the genes involved in cytoplasmic protein synthesis

From: Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level

Presence of regulatory motif

  

COG general functional category

COG pathway/system

Subcellular localization

GOC number

ORF name

Gene description

Genes identified experimentally to be regulated by Rap1

rap1

-

-

EH

E7

-

COG0028

YLR044C

PDC1 pyruvate decarboxylase, isozyme 1

rap1

-

-

G

G1

-

COG0469

YAL038W

CDC19 pyruvate kinase

RAP1

-

-

G

G2

-

COG0126

YCR012W

PGK1 phosphoglycerate kinase

RAP1

-

-

G

G2

-

COG0057

YGR192C

TDH3 glyceraldehyde-3-phosphate dehydrogenase 3

RAP1

-

-

G

G2

-

COG0588

YKL152C

GPM1 phosphoglycerate mutase

rap1

-

-

G

G2

-

COG0148

YHR174W

ENO2 enolase II (2-phosphoglycerate dehydratase)

rap1

-

-

G

G2

-

COG0057

YJR009C

TDH2 glyceraldehyde-3-phosphate dehydrogenase 2

RAP1

RRPE

-

J

-

-

COG2238

YOL121C

RPS19A 40S small subunit ribosomal protein S19.E

RAP1

-

-

J

-

-

COG2238

YNL302C

RPS19B 40S small subunit ribosomal protein S19.E

rap1

-

PAC

J

-

-

COG2451

YPL143W

RPL33A ribosomal protein L35A.E.C16

rap1

-

-

J

-

-

COG2451

YOR234C

RPL33B ribosomal protein L35A.E.C15

RAP1

-

-

J

J2

-

COG1190

YDR037W

KRS1 lysyl-tRNA synthetase, cytosolic

rap1

RRPE

-

J

J2

-

COG0008

YOR168W

GLN4 glutaminyl-tRNA synthetase

RAP1

RRPE

PAC

J

J3

-

COG0199

YDL061C

RPS29B ribosomal protein S29.E.B

RAP1

RRPE

PAC

J

J3

-

COG0092

YNL178W

RPS3 ribosomal protein S3.E

RAP1

RRPE

PAC

J

J3

-

COG0522

YPL081W

RPS9A ribosomal protein S9.E.A

RAP1

RRPE

-

J

J3

-

COG0103

YDL083C

RPS16B ribosomal protein S16.E

RAP1

RRPE

-

J

J3

-

COG2004

YIL069C

RPS24B 40S small subunit ribosomal protein S24.E

RAP1

RRPE

-

J

J3

-

COG0052

YLR048W

RPS0B 40S ribosomal protein P40 HOMOLOG B

RAP1

RRPE

-

J

J3

-

COG0185

YOL040C

RPS15 40S small subunit ribosomal protein

RAP1

-

PAC

J

J3

-

COG0052

YGR214W

RPS0A 40S ribosomal protein P40 HOMOLOG A

RAP1

-

-

J

J3

-

COG0186

YBR048W

RPS11B ribosomal protein S11.E.B

RAP1

-

-

J

J3

-

COG2125

YBR181C

RPS6B ribosomal protein S6.E

RAP1

-

-

J

J3

-

COG0522

YBR189W

RPS9B ribosomal protein S9.E.B

RAP1

-

-

J

J3

-

COG0100

YCR031C

RPS14A 40S ribosomal protein S14.E

RAP1

-

-

J

J3

-

COG0184

YDR064W

RPS13 ribosomal protein

RAP1

-

-

J

J3

-

COG1383

YDR447C

RPS17B ribosomal protein S17.E.B

RAP1

-

-

J

J3

-

COG0099

YDR450W

RPS18A ribosomal protein S18.E.C4

RAP1

-

-

J

J3

-

COG2004

YER074W

RPS24A 40S small subunit ribosomal protein S24.E

RAP1

-

-

J

J3

-

COG0098

YGL123W

RPS2 40S small subunit ribosomal protein

RAP1

-

-

J

J3

-

COG0048

YGR118W

RPS23A 40S small subunit ribosomal protein S23.E

RAP1

-

-

J

J3

-

COG0051

YHL015W

RPS20 ribosomal protein

RAP1

-

-

J

J3

-

COG1471

YHR203C

RPS4B ribosomal protein S4.E.C8

RAP1

-

-

J

J3

-

COG0096

YJL190C

RPS22A ribosomal protein S15A.E.C10

RAP1

-

-

J

J3

-

COG0049

YJR123W

RPS5 ribosomal protein S5.E

RAP1

-

-

J

J3

-

COG1471

YJR145C

RPS4A ribosomal protein S4.E.C10

RAP1

-

-

J

J3

-

COG2051

YKL156W

RPS27A ribosomal protein S27.E

RAP1

-

-

J

J3

-

COG1890

YLR441C

RPS1A ribosomal protein S3A.E

RAP1

-

-

J

J3

-

COG1890

YML063W

RPS1B ribosomal protein S3A.E

RAP1

-

-

J

J3

-

COG2125

YPL090C

RPS6A ribosomal protein S6.E

rap1

RRPE

-

J

J3

-

COG0100

YJL191W

RPS14B 40S small subunit ribosomal protein S14.E.B

rap1

RRPE

-

J

J3

-

COG2053

YOR167C

RPS28A 40S small subunit ribosomal protein S28.E.C15

rap1

-

-

J

J3

-

COG2007

YBL072C

RPS8A ribosomal protein S8.E

rap1

-

-

J

J3

-

COG0186

YDR025W

RPS11A ribosomal protein S11.E

rap1

-

-

J

J3

-

COG2007

YER102W

RPS8B ribosomal protein S8.E

rap1

-

-

J

J3

-

COG0048

YPR132W

RPS23B 40S small subunit ribosomal protein S23.E

RAP1

RRPE

-

J

J4

-

COG2058

YDL130W

RPP1B 60S large subunit acidic ribosomal protein L44PRIME

RAP1

RRPE

-

J

J4

-

COG0093

YER117W

RPL23B ribosomal protein L23.E

RAP1

RRPE

-

J

J4

-

COG0081

YGL135W

RPL1B 60S large subunit ribosomal protein

RAP1

RRPE

-

J

J4

-

COG0097

YGL147C

RPL9A ribosomal protein L9.E

RAP1

RRPE

-

J

J4

-

COG0198

YGR034W

RPL26B 60S large subunit ribosomal protein

RAP1

RRPE

-

J

J4

-

COG1631

YHR141C

RPL42B ribosomal protein L36A.E

RAP1

RRPE

-

J

J4

-

COG1552

YIL148W

RPL40A ubiquitin

RAP1

RRPE

-

J

J4

-

COG0091

YJL177W

RPL17B 60S large subunit ribosomal protein L17.E

RAP1

RRPE

-

J

J4

-

COG1358

YLL045C

RPL8B 60S large subunit ribosomal protein L7A.E.B

RAP1

RRPE

-

J

J4

-

COG1632

YLR029C

RPL15A 60S large subunit ribosomal protein L15.E.C12

RAP1

RRPE

-

J

J4

-

COG2058

YOL039W

RPP2A acidic ribosomal protein P2.BETA

RAP1

RRPE

-

J

J4

-

COG1727

YOL120C

RPL18A 60S large subunit ribosomal protein S18.E

RAP1

RRPE

-

J

J4

-

COG1841

YPL198W

RPL7B 60S large subunit ribosomal protein

RAP1

-

PAC

J

J4

-

COG2147

YBL027W

RPL19B 60S large subunit ribosomal protein L19.E

RAP1

-

PAC

J

J4

-

COG0197

YLR075W

RPL10 60S large subunit ribosomal protein

RAP1

-

-

J

J4

-

COG0093

YBL087C

RPL23A 60S large subunit ribosomal protein L23.E

RAP1

-

-

J

J4

-

COG2147

YBR084C-A

RPL19A 60S large subunit ribosomal protein L19.E

RAP1

-

-

J

J4

-

COG2139

YBR191W

RPL21A ribosomal protein L21.E

RAP1

-

-

J

J4

-

COG0255

YDL191W

RPL35A 60S large subunit ribosomal protein

RAP1

-

-

J

J4

-

COG0080

YDR418W

RPL12B 60S large subunit ribosomal protein L12.E

RAP1

-

-

J

J4

-

COG2126

YDR500C

RPL37B ribosomal protein L.37.E

RAP1

-

-

J

J4

-

COG1911

YGL030W

RPL30 60S large subunit ribosomal protein L30.E

RAP1

-

-

J

J4

-

COG1841

YGL076C

RPL7A 60S large subunit ribosomal protein L7.E.A

RAP1

-

-

J

J4

-

COG0200

YGL103W

RPL28 60S large subunit ribosomal protein L27A.E

RAP1

-

-

J

J4

-

COG0094

YGR085C

RPL11B ribosomal protein

RAP1

-

-

J

J4

-

COG1358

YHL033C

RPL8A 60S large subunit ribosomal protein L7A.E.A

RAP1

-

-

J

J4

-

COG0090

YIL018W

RPL2B 60S large subunit ribosomal protein L8.E

RAP1

-

-

J

J4

-

COG2174

YIL052C

RPL34B ribosomal protein L34.E

RAP1

-

-

J

J4

-

COG2167

YJL189W

RPL39 60S large subunit ribosomal protein L39.E

RAP1

-

-

J

J4

-

COG2163

YKL006W

RPL14A ribosomal protein

RAP1

-

-

J

J4

-

COG0244

YLR340W

RPP0 acidic ribosomal protein L10.E

RAP1

-

-

J

J4

-

COG0198

YLR344W

RPL26A 60S large subunit ribosomal protein

RAP1

-

-

J

J4

-

COG0102

YNL069C

RPL16B 60S large subunit ribosomal protein

RAP1

-

-

J

J4

-

COG1631

YNL162W

RPL42A ribosomal protein L36A.E

RAP1

-

-

J

J4

-

COG0089

YOL127W

RPL25 ribosomal protein L23A.E

RAP1

-

-

J

J4

-

COG2157

YOR312C

RPL20B 60S large subunit ribosomal protein

RAP1

-

-

J

J4

-

COG1358

YOR369C

RPS12 40S small subunit acidic ribosomal protein S12

RAP1

-

-

J

J4

-

COG2139

YPL079W

RPL21B ribosomal protein L21

RAP1

-

-

J

J4

-

COG0256

YPL131W

RPL5 60S large subunit ribosomal protein L5.E

RAP1

-

-

J

J4

-

COG1997

YPR043W

RPL43A ribosomal protein L37A.E

RAP1

-

-

J

J4

-

COG0094

YPR102C

RPL11A ribosomal protein L11.E

rap1

RRPE

-

J

J4

-

COG2058

YDR382W

RPP2B 60S large subunit acidic ribosomal protein

rap1

RRPE

-

J

J4

-

COG1727

YNL301C

RPL18B 60S large subunit ribosomal protein L18.E

rap1

RRPE

-

J

J4

-

COG0087

YOR063W

RPL3 60S large subunit ribosomal protein L3.E

rap1

-

-

J

J4

-

COG1717

YBL092W

RPL32 60S large subunit ribosomal protein L32.E

rap1

-

-

J

J4

-

COG2097

YDL075W

RPL31A 60S large subunit ribosomal protein L31.E

rap1

-

-

J

J4

-

COG0080

YEL054C

RPL12A 60S large subunit ribosomal protein L12.E

rap1

-

-

J

J4

-

COG2075

YGL031C

RPL24A 60S large subunit ribosomal protein L24.E.A

rap1

-

-

J

J4

-

COG2075

YGR148C

RPL24B 60S large subunit ribosomal protein L24.E.B

rap1

-

-

J

J4

-

COG2163

YHL001W

RPL14B ribosomal protein

rap1

-

-

J

J4

-

COG0102

YIL133C

RPL16A 60S large subunit ribosomal protein

rap1

-

-

J

J4

-

COG1552

YKR094C

RPL40B ubiquitin

rap1

-

-

J

J4

-

COG2126

YLR185W

RPL37A ribosomal protein L37.E

RAP1

RRPE

PAC

K

-

-

COG0724

YGR159C

NSR1 nuclear localization sequence binding protein

RAP1

RRPE

PAC

K

K1

-

COG0202

YPR110C

RPC40 DNA-directed RNA polymerase I, III 40 kD

      

subunit

  

Genes not identified experimentally to be regulated by rap1

RAP1

RRPE

-

E

-

-

COG0421

YLR146C

SPE4 spermine synthase

-

RRPE

-

E

-

-

COG0031

YGR155W

CYS4 cystathionine beta-synthase

-

-

PAC

E

-

-

COG0833

YGR191W

HIP1 histidine permease

-

-

-

E

-

-

COG0531

YGL077C

HNM1 choline permease

-

-

-

E

-

-

COG0367

YGR124W

ASN2 asparagine synthetase

-

-

-

E

-

-

COG0367

YPR145W

ASN1 asparagine synthetase

-

RRPE

-

E

E7

MIT

COG0059

YLR355C

ILV5 ketol-acid reducto-isomerase

-

-

-

E

E7

MIT

COG0473

YIL094C

LYS12 homoisocitrate dehydrogenase

-

-

-

E

H7

-

COG0722

YBR249C

ARO4 2-dehydro-3-deoxyphosphoheptonate aldolase, tyrosine-inhibited

-

-

-

E

H7

-

COG0082

YGL148W

ARO2 chorismate synthase

-

-

-

EH

E7

-

COG0028

YGR087C

PDC6 pyruvate decarboxylase 3

-

-

-

EH

E7

-

COG0028

YLR134W

PDC5 pyruvate decarboxylase, isozyme 2

-

RRPE

-

F

F2

-

COG0503

YML022W

APT1 adenine phosphoribosyltransferase

-

-

PAC

F

F2

-

COG0005

YLR017W

MEU1 multiple enhancer of UAS2

-

RRPE

PAC

F

F3

-

COG0504

YBL039C

URA7 CTP synthase 1

-

RRPE

-

F

F3

-

COG0167

YKL216W

URA1 dihydroorotate dehydrogenase

-

RRPE

-

F

F3

-

COG0461

YML106W

URA5 orotate phosphoribosyltransferase

-

-

-

F

F3

-

COG0563

YDR226W

ADK1 adenylate kinase, cytosolic

-

-

-

F

F3

-

COG0284

YEL021W

URA3 orotidine-5'-phosphate decarboxylase

-

-

-

F

F3

-

COG0563

YKL024C

URA6 uridine-monophosphate kinase

-

-

-

F

F3

-

COG0418

YLR420W

URA4 dihydroorotase

-

RRPE

-

FE

F1

-

COG0462

YHL011C

PRS3 ribose-phosphate pyrophosphokinase

-

RRPE

-

FE

F1

-

COG0462

YKL181W

PRS1 ribose-phosphate pyrophosphokinase

-

RRPE

-

G

G1

-

COG0205

YGR240C

PFK1 6-phosphofructokinase, alpha subunit

-

-

-

G

G1

-

COG0205

YMR205C

PFK2 6-phosphofructokinase, beta subunit

-

-

-

G

G2

-

COG0166

YBR196C

PGI1 glucose-6-phosphate isomerase

-

-

-

G

G2

-

COG0149

YDR050C

TPI1 triose-phosphate isomerase

-

-

-

G

G2

-

COG0057

YJL052W

TDH1 glyceraldehyde-3-phosphate dehydrogenase 1

-

-

-

G

G2

-

COG0191

YKL060C

FBA1 fructose-bisphosphate aldolase

-

-

-

G

G2

-

COG0158

YLR377C

FBP1 fructose-1,6-bisphosphatase

-

RRPE

PAC

G

G3

-

COG0120

YOR095C

RKI1 D-ribose-5-phosphate ketol-isomerase

-

RRPE

PAC

G

G3

-

COG0021

YPR074C

TKL1 transketolase 1

-

RRPE

-

H

-

-

COG0499

YER043C

SAH1 S-adenosyl-l-homocysteine hydrolase

-

-

-

H

-

-

COG0192

YDR502C

SAM2 S-adenosylmethionine synthetase 2

-

-

-

H

-

-

COG0192

YLR180W

SAM1 S-adenosylmethionine synthetase 1

-

RRPE

PAC

J

-

-

COG1889

YDL014W

NOP1 fibrillarin

-

RRPE

PAC

J

-

-

COG1499

YHR170W

NMD3 nonsense-mediated mRNA decay protein

-

RRPE

PAC

J

-

-

COG1498

YLR197W

SIK1 involved in pre-rRNA processing

-

RRPE

PAC

J

-

-

COG0144

YNL061W

NOP2 nucleolar protein

-

RRPE

PAC

J

-

-

COG1498

YOR310C

NOP58 required for pre-18S rRNA processing

-

RRPE

PAC

J

-

-

COG1374

YPL211W

NIP7 required for efficient 60S ribosome subunit biogenesis

-

RRPE

PAC

J

-

-

COG0030

YPL266W

DIM1 rRNA (adenine-N6, N6-)-dimethyltransferase

-

RRPE

-

J

-

-

COG0293

YCL054W

SPB1 required for ribosome synthesis, putative methylase

-

RRPE

-

J

-

-

COG0689

YGR095C

RRP46 involved in rRNA processing

-

RRPE

pac

J

-

-

COG3277

YHR089C

GAR1 nucleolar rrna processing protein

-

RRPE

-

J

-

-

COG2519

YJL125C

GCD14 translational repressor of GCN4

-

RRPE

-

J

-

-

COG0349

YOR001W

RRP6 similarity to human nucleolar 100K polymyositis-scleroderma protein

-

-

PAC

J

-

-

COG0009

YGL169W

SUA5 translation initiation protein

-

rrpe

PAC

J

-

-

COG1097

YHR069C

RRP4 3' → 5' exoribonuclease required for 3' end formation of 5.8S rRNA

-

-

PAC

J

-

-

COG1736

YKL191W

DPH2 diphtheria toxin resistance protein

-

-

PAC

J

-

-

COG1798

YLR172C

DPH5 diphthamide methyltransferase

-

-

-

J

-

-

COG2123

YDR280W

RRP45 rRNA processing protein

RAP1

RRPE

-

J

J1

-

COG2092

YAL003W

EFB1 translation elongation factor eEF1beta

-

RRPE

-

J

J1

-

COG1503

YBR143C

SUP45 translational release factor

-

RRPE

-

J

J1

-

COG0480

YOR133W

EFT1 translation elongation factor EEF2

-

RRPE

-

J

J1

-

COG1601

YPL237W

SUI3 translation initiation factor EIF2 beta subunit

-

-

-

J

J1

-

COG0480

YDR385W

EFT2 translation elongation factor EEF2

-

-

-

J

J1

-

COG0361

YMR260C

TIF11 translation initiation factor EIF1A

-

RRPE

PAC

J

J2

-

COG0215

YNL247W

Cysteinyl-tRNA synthetase

-

RRPE

-

J

J2

-

COG0423

YBR121C

GRS1 glycine-tRNA ligase

-

RRPE

-

J

J2

-

COG0008

YGL245W

Strong similarity to glutamine-tRNA ligase

-

RRPE

-

J

J2

-

COG0017

YHR019C

DED81 asparaginyl-tRNA-Synthetase

-

RRPE

-

J

J2

-

COG0008

YOR168W

GLN4 glutaminyl-tRNA synthetase

-

-

-

J

J2

-

COG0172

YDR023W

SES1 seryl-tRNA synthetase, cytosolic

RAP1

-

-

J

J3

-

COG2051

YHR021C

RPS27B ribosomal protein S27.E

-

RRPE

-

J

J3

-

COG0199

YLR388W

RPS29A ribosomal protein S29.E.A

-

RRPE

-

J

J3

-

COG2053

YOR167C

RPS28A 40S small subunit ribosomal protein S28.E.C15

-

-

-

J

J3

-

COG1998

YLR167W

RPS31 ubiquitin/40S small subunit ribosomal protein

-

-

-

J

J3

-

COG2053

YLR264W

RPS28B 40S small subunit ribosomal protein S28.E.C12

-

-

-

J

J3

-

COG0096

YLR367W

RPS22B ribosomal protein S15A.E.C12

-

RRPE

PAC

J

J4

-

COG0244

YKL009W

MRT4 mRNA turnover 4

-

RRPE

PAC

J

J4

-

COG2075

YLR009W

Similarity to ribosomal protein L24.E.B

-

RRPE

-

J

J4

-

COG0088

YBR031W

RPL4A ribosomal protein

-

RRPE

-

J

J4

-

COG0088

YDR012W

RPL4B ribosomal protein L4.E.B

-

-

-

J

J4

-

COG2058

YDL081C

RPP1A 60S large subunit acidic ribosomal protein A1

-

-

-

J

J4

-

COG1632

YMR121C

RPL15B 60S large subunit ribosomal protein L15.E.C13

-

-

-

J

J4

-

COG2157

YMR242C

RPL20A 60S large subunit ribosomal protein

-

-

-

J

J4

-

COG0097

YNL067W

RPL9B ribosomal protein L9.E.C14

-

-

-

J

J4

-

COG0081

YPL220W

RPL1A ribosomal protein

-

RRPE

-

JE

J1

-

COG0050

YDR172W

SUP35 eukaryotic peptide chain release factor GTP-binding subunit

-

RRPE

-

JE

J1

-

COG0050

YER025W

GCD11 translation initiation factor EIF2 gamma chain

-

RRPE

PAC

K

-

-

COG0571

YMR239C

RNT1 double-stranded ribonuclease

-

RRPE

PAC

K

-

-

COG0724

YPL043W

NOP4 nucleolar protein

-

RRPE

-

K

-

-

COG0724

YER165W

PAB1 mRNA polyadenylate-binding protein

-

-

-

K

-

-

COG0724

YDR429C

TIF35 translation initiation factor EIF3 (P33 subunit)

-

-

-

K

-

-

COG0724

YOR361C

PRT1 translation initiation factor EIF3 subunit

-

RRPE

PAC

K

K1

-

COG2012

YBR154C

RPB5 DNA-directed RNA polymerase I, II, III 25 kD subunit

-

-

PAC

K

K1

-

COG1761

YNL113W

RPC19 DNA-directed RNA polymerase I, III 16 kD subunit

-

-

-

K

K1

-

COG0202

YIL021W

RPB3 DNA-directed RNA-polymerase II, 45 kDA

-

-

-

K

K1

-

COG1644

YOR210W

RPB10 DNA-directed polymerase I, II, III 8.3 subunit

-

-

-

K

K1

-

COG1758

YPR187W

RPO26 DNA-directed RNA polymerase I, II, III 18 kD subunit

-

RRPE

PAC

L

-

-

COG1643

YGL120C

PRP43 involved in spliceosome disassembly

-

RRPE

PAC

L

-

-

COG1643

YMR128W

ECM16 similarity to helicases

-

RRPE

PAC

LKJ

-

-

COG0513

YGL078C

DBP3 putative RNA helicase required for pre-rRNA processing

-

RRPE

PAC

LKJ

-

-

COG0513

YGL171W

ROK1 ATP-dependent RNA helicase

-

RRPE

PAC

LKJ

-

-

COG0513

YJL033W

HCA4 can suppress the U14 snoRNA rRNA processing function

-

RRPE

PAC

LKJ

-

-

COG0513

YKR024C

DBP7 RNA helicase required for 60S ribosomal subunit assembly

-

RRPE

PAC

LKJ

-

-

COG0513

YLL008W

DRS1 RNA helicase of the DEAD box family

-

RRPE

-

LKJ

-

-

COG0513

YKR059W

TIF1 translation initiation factor 4A

-

-

PAC

LKJ

-

-

COG0513

YJL138C

TIF2 translation initiation factor EIF4A

-

RRPE

-

O

-

-

COG0545

YLR449W

FPR4 strong similarity to peptidylprolyl isomerase FPR3P

-

RRPE

-

O

-

-

COG0443

YNL209W

SSB2 heat shock protein of HSP70 family, cytosolic

-

-

-

O

-

-

COG0443

YHR064C

PDR13 regulator protein involved in pleiotropic drug resistance

  1. The first list comprises those genes known to be targeted by Rap1 [18] and the second one those that are not. In the presence of motif columns, '-' means that no motif was identified. Regulatory motifs in uppercase correspond to those found by our computational analysis, those in lowercase correspond to motifs found by others [10,18]. The genes are ordered by their functional category.