The plant cell cytosol is a dynamic and complex intracellular matrix that, by definition, contains no compartmentalization. Nonetheless, it maintains a wide variety of biochemical networks and often links metabolic pathways across multiple organelles. There have been numerous detailed proteomic studies of organelles in the model plant Arabidopsis thaliana, although no such analysis has been undertaken on the cytosol. The cytosolic protein fraction from cell suspensions of Arabidopsis thaliana was isolated and analyzed using offline strong cation exchange liquid chromatography and LC-MS/MS. This generated a robust set of 1071 cytosolic proteins. Functional annotation of this set revealed major activities in protein synthesis and degradation, RNA metabolism and basic sugar metabolism. This included an array of important cytosol-related functions, specifically the ribosome, the set of tRNA catabolic enzymes, the ubiquitin-proteasome pathway, glycolysis and associated sugar metabolism pathways, phenylpropanoid biosynthesis, vitamin metabolism, nucleotide metabolism, an array of signaling and stress-responsive molecules, and NDP-sugar biosynthesis. This set of cytosolic proteins provides for the first time an extensive analysis of enzymes responsible for the myriad of reactions in the Arabidopsis cytosol and defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding in the cytosol.
AT3G08943, AT3G08947, AT3G07030, AT3G42170, AT4G22285, AT1G24800, AT1G25055, AT1G24881, AT1G25211, AT2G01250, AT2G01690, GSTZ1, AT2G02400, AL6, CAND1, UBC2, GEK1, AT2G03820, CR88, AT2G04390, AT2G04400, AT2G04520, AT2G05220, ACO3, AT2G05920, HEN2, PFD1, AT2G07360, AT2G09990, ABH1, DRP3B, PIP, UGT73B4, NIR1, SQN, AT2G15860, HB1, THY-1, PAP10, MCM4, AT2G16485, ASE1, ROC3, MSI2, UBC23, AT2G16940, TRN1, DSK2, AT2G17280, CPK6, AT2G17360, NTRA, AT2G17930, ATSLY1, EMB2296, PIN1AT, AT2G18110, AT2G18220, COAD, TPS11, AT2G18740, NAP1;2, FVE, CDA1, PRMT1A, PRF1, AT2G20140, CLASP, RPN1A, AT2G20760, AT2G21130, TIM, AT2G21250, UFD1, AT2G21390, CCR2, AT2G22125, AAT, AT2G22420, GEM, SNRK2.9, AT2G23070, PAB4, AT2G23820, SNRNP-G, eIFiso4G2, AT2G24190, AT2G24200, AT2G24590, MAPR2, AT2G25670, AT2G25970, SEH, FUS12, PAG1, CAM5, AGO4, SE, AAO3, PAP12, AT2G27200, BSL3, PGY1, AT2G27710, AT2G27720, AXS1, CPN60A, HIS4, PUM2, PUM1, GSTU7, GSTU6, GSTU5, TUB7, ENOC, PCNA2, AT2G30050, UBA1, AT2G30140, AT2G30200, KIS, GSTF9, GSTF10, AT2G31390, AT2G31610, SAD2, AT2G31670, RABA5d, AT2G32240, AT2G32520, AT2G32730, BGAL9, PKT3, GLTP1, AT2G34040, AT2G34160, AT2G34480, AT2G34840, AT2G34970, GlcNA.1UT2, UBQ7, AT2G35810, AT2G35820, AT2G35840, MMZ3, AT2G36130, AT2G36160, AT2G36460, LOS2, AT2G36580, RPL24A, MAT3, AT2G37020, AT2G37130, AT2G37190, RPS5B, RSZ33, ACT1, AT2G37760, SOUL-1, PDX1.1, FAC1, PRA1.B4, TFIIS, AT2G38580, AT2G38610, AT2G38680, MVD1, AT2G38710, AT2G38730, AT2G38740, EMB2765, RPL23AA, EXPA4, CYT1, EIF2, AT2G40290, AT2G40360, AT2G40510, AT2G40590, AT2G40600, AT2G40660, DPE2, CAM2, AT2G41380, VLN2, AT2G41840, GRF9, RPL16A, CSY3, PP5.2, AT2G42910, ARA4, HOL3, ITPK4, AT2G44060, GDI1, AT2G44120, MTHFR2, AT2G44310, BGLU15, RAB6A, EMB2766, GOS12, MAP1A, AT2G45290, AT2G45300, AT2G45710, PMM, AT2G45810, AT2G46140, TRIP-1, PI4K GAMMA 4, AT2G46520, AT2G46900, ARF1A1C, AT2G47250, UNE5, U1A, AT2G47610, AT2G47640, UXS4, AT2G47970, AT3G03960, GAPC1, AT3G04230, AT3G04600, AT3G04840, DRT102, AT3G04920, ACP1, AT3G05280, ACBP4, RPT5A, AT3G05560, MEE32, CHR11, AT3G06530, REP, GALK, AT3G06610, ACLB-1, IMPA-1, IBR3, MFP2, AT3G07050, ERMO2, GLCAK, AT3G07230, AT3G07590, AT3G07720, AT3G08530, AT3G08590, AT3G09200, ORP3B, AT3G09440, SOX, AT3G09630, ADK1, CDC48, AT3G09890, AT3G10090, SCPL49, AT3G10610, GalAK, GLY2, AT3G10950, AT3G11130, AL2, AT3G11500, AT3G11510, AT3G11630, ATKRS-1, FOLB1, AT3G11830, UBP13, AT3G11964, AT3G12050, RGTB2, BIG, PRMT3, AT3G12290, AT3G12390, NF-YC11, CYSB, HCHIB, HSP70, emb2742, PGK1, SDRB, ECT5, AT3G13235, VCS, ECT2, AT3G13470, SCL30A, BGAL1, EIF4A1, AT3G14067, AT3G14100, AT3G17940, PAE2, AT3G14420, AT3G14600, RHM3, AT3G14990, AT3G15010, mMDH2, RABA1g, AT3G15180, AT3G15460, AT3G15610, PLDALPHA1, AT3G15970, AT3G15980, PDX1.2, UGT88A1, TCTP, AT3G02760, PUM24, LPD1, HS1, MTO3, GRF7, AT3G03920, TPLATE, AT3G02080, VMA10, MS2, AT3G02530, AT3G02360, AT3G02880, VTC4, AT3G01340, RGP1, AT3G02200, DegP7, UNE6, AT3G02560, UGP1, XPL1, WOX1, HAL3A, AT3G18060, RACK1C_AT, AT3G18190, AT3G18600, AT3G18740, ACT2, AT3G18790, AT3G18860, RBP47B, AT3G19400, PEN2, AT3G19990, TCP-1, PUM5, PYRB, UBP14, AT3G20790, UGT71B1, PAC1, POP2, AT3G22230, PBD1, APS1, PKP-ALPHA, AT3G22980, CYN, AT3G23570, RNR2A, AT3G23600, AT3G23620, AT3G23660, AT3G23750, SAHH2, BAM1, AT3G23940, BLI, HSP60, AT3G24090, GR1, SYP32, AT3G24830, ROF1, ATL5, GLYR1, AT3G25545, PP2AA2, LTA2, AT3G26380, ATRZ-1A, GAPA, AT3G26720, UKL2, G6PD5, GC6, AT3G27570, CARA, NQR, AT3G28200, AIG2, AT3G28940, AT3G29320, AHP2, AT3G29360, SUS4, ATMIN7, AAO2, CAM7, ATJ3, NIT2, NIT1, CEF, AT3G44590, AT3G45030, AT3G45930, EXLA3, EXLA1, AT3G46320, UXS5, PUB13, RABA2c, DUT1, PHS2, AT3G47000, AT3G47370, AT3G47560, ALDH10A9, PIMT1, PDE312, CXE12, CXE13, EMB1080, AT3G48990, BBC1, PRXCB, SRp34a, NACA2, BCAT3, ARLA1C, AT3G49910, CKA2, PEN3, SNRK2.2, AT3G50590, AT3G51000, MUR1, PAD1, BAG4, ATG2, ACX4, AT3G52140, SPP2, AT3G52500, UEV1D-4, AT3G52580, AT3G52660, MDAR1, AT3G52930, AT3G52990, STV1, LOS4, AT3G53180, PAL2, AT3G53430, RAB8, PPa4, AT3G53730, AT3G53740, ACT3, AT3G53880, UPP, PAS1, AT3G54150, AT3G54440, AT3G54470, ATVPS33, AT3G55070, AT3G55160, AT3G55200, AT3G55220, HEXO1, MKP1, RPL23AB, TPI, P5CS2, AT3G55750, AT3G56120, EIF3C, AT3G56340, AT3G56460, HIT3, CAM3, UBA2A, NAP57, EIF3E, ADSS, NRPA1, AT3G57890, AT3G58180, PP2A-4, AT3G58510, AT3G58530, AT3G58560, AT3G58610, AT3G58660, AT3G58700, CSY1, AT3G59020, GDI2, MTHFR1, AT3G60245, AT3G60340, AT3G60450, TTN1, AT3G60750, AT3G60770, PBF1, AT3G60860, RS27A, FUS6, AT3G61220, AT3G61240, AT3G61540, RRP41, TUBG1, AT3G62010, AT3G62120, AT3G62130, ARFA1E, AT3G62310, AT3G62560, AUD1, AT3G62840, AT3G62870, AT3G62940, NPL41, AT3G63400, AT3G63460, CUL1, MEE51, AT4G04950, DDB1A, EXO, GRF1, NDPK1, AT4G09520, CPK4, AT4G09670, RPS18C, EMB1691, CYTC-2, AT4G10320, SPT16, NDPK3, TUF, SGT1B, AT4G11380, EIF3A, GPX6, MVA1, AT4G01610, SKU5, AT4G12600, NUDT7, AT4G12780, AT4G13010, AT4G13360, AT4G13370, SAM-2, AT4G13780, SHM4, MEE58, SBP1, AT4G14160, AT4G14300, AT4G14570, ATARD2, ARD1, OASA1, AT4G14930, TUA6, AT4G15000, BAM5, PPDK, AT4G15770, HSBP, AT4G16060, ARA1, IMPA-2, AT4G16155, ECHIA, SPK1, AT4G16440, AT4G16500, AT4G16660, SAR2, MES16, AT4G16720, ACX1, FPS2, AT4G17260, AT4G17390, UCH3, AT4G17520, RAB1C, MOS6, AT4G17620, AT4G17720, AT4G17830, AGD8, AT4G17950, AT4G18100, AT4G18360, AT4G18465, RPL16B, AT4G18740, RABA1d, AT4G18950, AT4G19006, AT4G19150, VPS54, AT4G19880, RABE1b, smB, AT4G20830, TPP2, AT4G20860, DDB1B, AT4G21110, GSTF2, AT4G01400, PPa5, AT4G00830, AT4G02450, SEC15B, AT4G02340, BSL1, AT4G02230, AT4G01810, AT4G02930, MEE49, MPK4, PRL, AT4G02030, AT4G02860, AT4G02840, RPS13A, GLB1, AT4G01897, AT4G21580, AT4G21660, NRPB2, AT4G22350, AT4G22410, AT4G22530, HIP1, AT4G22720, AT4G23050, CDPK6, LACS4, SHD, VEP1, RGTA1, ATR1, AT4G24550, AT4G24800, AT4G24820, AT4G24840, FSD1, AT4G25210, FKBP53, AT4G25740, NAP1;1, AT4G26220, emb1027, AT4G26620, AT4G26630, SUMO1, AT4G26870, ATRBP45C, AT4G27090, PPI1, AT4G27640, AT4G28440, RPT2a, AT4G29120, AT4G29260, PFN2, PRMT11, VIP3, MTO2, VLN4, HA2, RUXF, AT4G30260, AT4G30330, AT4G30550, AT4G30800, AT4G30920, AT4G30990, SKB1, AT4G31180, PBA1, AT4G31480, AT4G31490, SRZ-22, RPS6, AT4G31880, ASP5, PANK2, AT4G32285, SHM3, AT4G32580, AT4G32640, La1, AT4G32760, PFK6, AT4G33070, APM1, AT4G33150, EIF3K, DRP3A, AT4G33670, AGD2, OST1, PAB2, AT4G34150, EDA9, CAD5, AT4G34270, AT4G34412, AT4G34450, CAP1, AT4G34660, AT4G34670, ASE2, ROC5, XDH1, AT4G34920, APX3, CAT2, PSAT, ACO1, AT4G36080, AT4G36195, PAP25, AT4G36590, APP1, ACD2, PCK1, mtHsc70-1, AT4G38370, GRP2, ROC1, MTN1, AT4G38890, AT4G38900, AT4G39150, CCR1, AT4G39280, AT4G39520, AT4G39730, SIR, AT5G04800, AT5G05010, AT5G05340, EIF2 ALPHA, GCP2, RPN8A, DFB, AT5G06060, SNX1, UBA 2, UBP12, PGIP1, PGIP2, AT5G07090, Tudor1, IPK2a, SYP132, AT5G08100, PK3, AT5G08300, AT5G08570, AT5G08670, AT5G08680, AT5G08690, AT5G09510, PPa6, ACT7, EMB2107, AT5G02240, ASN3, EMB3010, GRF6, KAC1, AT5G10540, AT5G10690, ALF4, SPS2F, AT5G11170, AT5G11200, HSC70-1, ASP3, NADP-ME2, AT5G11720, AT5G11810, AT5G11880, AT5G11950, AT5G12040, CYS1, RGTB1, AT5G12240, SEC10, AT5G12410, AT5G13030, AT5G13370, AT5G13420, AT5G13520, AT5G13560, ABO1, SMT1, NACA3, COP13, AT5G14540, ARFA1B, SNL2, AT5G15030, AT5G15200, AT5G15400, AT5G15490, AT5G15520, AT5G15550, RGP2, GRF5, AT5G16070, AT5G16130, ELF9, VAT1, AT5G16300, TRXF2, IPP1, AT5G16510, LRR1, AT5G16760, AT5G16880, AER, AT5G16990, XPO1A, UGP2, GAD, AT5G17380, AT5G17440, ATMS1, AT5G17980, IMPA-9, AT5G03850, RSR4, AT5G02870, AT5G03690, ATMDAR2, GSTL3, UNE18, AT5G02490, AT5G03340, ADK2, DRT101, NCBP, CHR17, AT5G19100, AT5G19440, AT5G19510, ASP2, TUA3, TUA5, emb2734, RPT6A, AT5G20000, RAN-1, RAN2, NUDX19, AT5G20160, SPS1F, AT5G20290, AT5G20400, AT5G20600, CPN20, SUS1, AT5G20890, AT5G20950, B73, AT5G21060, CAM6, AT5G21326, AT5G21990, J2, RIN1, AT5G22440, AT5G22480, AAE17, PFD5, AT5G23400, AT5G23540, SGS3, RPS11-BETA, AT5G24240, AT5G24260, EMB2024, AT5G24710, AT5G25070, AT5G25754, AT5G25757, EIF3B-2, AL4, AT5G26360, PYR6, AT5G26710, AT5G26680, SHM2, AT5G26830, AT5G27120, AT5G27220, GSH2, AT5G27400, MK, AT5G27470, MIRO1, TIF3B1, AT5G27770, AT5G27850, AT5G28050, BIP1, GME, AT5G28850, AT5G28900, AT5G32470, PAP26, AT5G35160, AT5G35180, CAC2, AT5G35530, PAA1, LSP1, AT5G35680, FIM2, AT5G35910, AT5G36160, AT5G36210, AT5G36230, PGLP1, AT5G36790, ACS, BGLU42, AT5G37475, CAM1, OXP1, SOS4, AT5G38130, RAD23D, GRF3, AT5G38830, AT5G38900, AT5G39050, SGR4, AT5G39730, RPL5B, AT5G39850, AT5G40040, AT5G40370, AT5G40490, G6PD6, UK/UPRT1, UBC4, AT5G41520, AT5G41670, AT5G41950, AT5G41970, BIP2, DL1, AT5G42220, AT5G42740, PAF1, AT5G42830, COP8, TRX3, RPT4A, AT5G43060, WPP1, AT5G43310, AT5G43330, AT5G43830, HOT5, CAD1, AT5G44320, TUB4, AT5G44500, AT5G45280, CLPP4, AT5G45620, RABA1c, AT5G45775, APG7, AT5G46020, CUL4, AT5G46430, AT5G46630, AGD9, LBA1, RAB1A, AT5G47690, AT5G47700, FPS1, NSP5, ACAT2, AT5G48480, FKBP15-2, AT5G48650, AT5G48770, HCT, PFD3, XK-2, AT5G49690, MMT, PPOX, ELO3, MAB1, UBC27, CLPC1, PABN1, AT5G51140, EYE, AT5G51530, CPSF160, PGM, AT5G51830, AT5G51970, FIB1, USP, AT5G52580, HSP90.1, AT5G52650, PKP-BETA1, TAP46, BOB1, GLT1, AT5G53480, CB5-E, AT5G53620, AT5G53850, HGO, PHOS32, FQR1, RBP45A, PDC2, RAN3, MAP65-1, AT5G55660, OLI2, HSP81-2, AT5G56350, AT5G56500, PFK7, SYNC1, HAG2, SERAT1;1, AT5G56900, NAP1;3, NMT1, AT5G57290, AT5G57330, GS1, eIFiso4G1, YKT61, TIL, TTL, FHIT, RPT3, AT5G58410, AT5G58420, SNX2a, AT5G58450, AT5G58490, AT5G59140, UXS3, ORP3C, ZEU1, AT5G59690, AT5G59840, AT5G59850, ADF3, AT5G59970, AT5G60160, ALP, AT5G60390, AT5G60670, RABA1f, ECT3, AT5G61170, ATG3, AT5G61510, Tudor2, AT5G61950, AT5G61970, AT5G62300, BAG7, HIR1, AT5G62930, FOLB2, AT5G63680, SAL1, AT5G64250, EXL2, AT5G64270, FKBP12, BETA-UP, AT5G64420, AT5G64460, ASN2, GRF8, AT5G65620, AT5G65760, SNRK2.3, ARLA1D, AT1G05350, RPL10B, AT1G05520, URH2, LEA14, MEE5, TPS7, AT1G06530, PDS1, AT1G06650, AT1G06900, AT1G07070, PCNA1, AT1G07660, AT1G07750, RPS15A, AT1G07820, APX1, AT1G07920, AT1G07930, AT1G07940, AT1G08110, AXS2, AT1G08360, BSL2, AIP3, CSD1, NF-YC9, AMI1, AT1G09010, AT1G09150, IMPA-4, ACLA-3, AT1G09620, RAB11c, AT1G09640, U2A', AT1G09780, PP2A-2, AT1G10590, ARFA1F, ACLA-1, TIF3H1, AT1G10940, PMEPCRA, GLX1, APA1, AT1G12000, AT1G12050, AT1G12270, AT1G12310, UGE1, DET3, GAPA-2, ERF1-2, DIS1, PP2AA3, GAPC2, VIK, SAC52, TWN2, AT1G14680, AT1G14710, AT1G15130, AT1G15290, MBD10, AVP1, TPL, AT1G15790, GOS11, AT1G15930, AT1G15940, CCR1, AT1G16350, PAB1, UBC36, AlaAT1, UBP1B, ATB BETA, AT1G18070, ATARCA, AT1G18470, AT1G18540, AT1G19130, AT1G03220, DHAR1, APS2, FNR2, EMB2719, AT1G20220, AT1G20225, AT1G20260, SMT2, AT1G20370, COR47, ERD10, AT1G20580, CAT1, AT1G20760, AT1G20950, emb1507, AT1G20970, PBC1, AT1G22270, GRF10, AT1G22440, PATL2, PFL, CYTC-1, AT1G22860, AT1G22870, AT1G23190, GGT1, ARF1, SPDS1, AT1G24510, AT1G25141, AT1G25260, OVA9, DCP5, CUL3, EIF2 GAMMA, FUS5, AT1G02080, AXR1, EDA10, PRP39, PRMT10, AT1G04850, AN, emb2386, AT1G04810, AT1G01100, PDH-E1 ALPHA, AT1G04190, KAB1, SAM1, GSTF6, MPK11, AT1G03330, AT1G04410, AT1G02305, AT1G03260, RPS15, PPa1, AT1G27090, TOM20-2, AT1G27400, APT1, NTF2B, AT1G29030, ATS9, AT1G29250, AT1G29850, AT1G29880, CARB, NRPA2, AT1G29965, RPL18AA, PFD6, AT1G30230, AT1G30470, AT1G30580, AT1G30630, AT1G30690, GlcNA.1UT1, IMD3, IMPL1, RUB1, AT1G31440, AT1G31730, AT1G31780, ACBP6, STRS1, PRK, AT1G33030, AT1G33120, PGY2, AT1G33590, AT1G33680, AT1G34030, GF14 PHI, CDPK2, ANNAT1, AT1G36240, AT1G36730, NIA2, AT1G41880, PMI1, GAPB, RP1, AT1G43670, AT1G43690, AT1G44790, AT1G44835, MCM2, PRP40A, AT1G45000, RD21, WPP2, PAF2, AT1G47380, SEC3A, SEC3B, D-CDES, RACK1B_AT, AT1G48830, AT1G48860, AT1G48900, NUC-L1, ACT8, RBP47A, PAB8, MTK, ALATS, AT1G50380, THFS, HIT1, SCL5, AT1G50670, AT1G51010, AT1G51160, AT1G52360, AT1G52380, AT1G52430, AT1G52450, AT1G52730, AT1G52930, AT1G53070, mMDH1, PPC1, MUM4, CYP59, RPT1A, PAE1, UBP1A, ALDH7B4, XRN4, NF-YC3, AT1G55090, AT1G55150, CPN60B, ECT4, UPL1, LOS1, NOP56, AT1G56190, SAR1B, CRT1a, PBG1, AT1G57720, PP2A-1, AT1G59960, AT1G60070, AT1G60080, AT1G60420, ATB2, AT1G60730, HAP13, SNRK2.10, SC3, AT1G61300, AT1G62020, ACO2, AT1G62390, AT1G62740, AT1G62820, NRS/ER, AT1G63290, AT1G63660, AT1G63770, UBC5, AT1G63810, MDAR6, AT1G64190, AT1G64385, RPN12a, GCN3, ILA, AT1G64980, AT1G65050, GTB1, AT1G65700, cICDH, TPX1, AT1G66080, GSR2, CAM4, SAG24, LINC1, AT1G67430, POLA2, AT1G67650, AT1G67680, AT1G67930, XYL1, NUDX1, AT1G69070, UPL2, ARFA1D, AOAT2, AT1G70600, AT1G70730, AT1G70770, SYNC3, LPR2, RSW10, CEL3, AT1G71410, HGPT, PAB5, AT1G71840, PTP1, AT1G71950, PATL1, AT1G72160, ALAAT2, P40, AT1G72550, PSD, CAD1, AT1G73180, AT1G73430, AT1G73980, AT1G74010, AT1G74050, AT1G74060, AT1G74270, NRP1, AT1G74910, ALDH10A8, DHAR2, OTC, AT1G75510, SKP1, AT1G75990, AT1G76010, AT1G76030, AT1G76140, sks5, ERD14, AT1G76550, OPR1, AT1G76810, ADH1, PBC2, AT1G77540, AT1G77550, AT1G77940, AGL67, AT1G78280, GRF2, GSTU19, RHM1, AT1G78830, AT1G78850, VHA-A, AT1G79210, MST1, AT1G79260, NUA, MC4, EMB1135, AT1G79470, AtkdsA1, PGK, AT1G79570, NUDT3, AT1G79870, AT1G79920, HSP91, ATERDJ2A, AT1G79990, SUS2, AT1G80360, EMB2753, NHO1, AT1G80670, AT1G80750, AT1G80930