Photoperiodic effect on protein profiles of potato petiole

Photoperiodic effect on protein profiles of potato petiole Shweta Shah 1, Young Jin-Lee 2, David J. Hannapel 3 and A. Gururaj Rao* 1 1 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011 2 Department of Chemistry, Iowa State University, Ames, Iowa 50011 3 Plant Biology Major, Iowa State University, Ames, Iowa 50011 Abstract In potato (Solanum tuberosum), StBEL5 mrna is a mobile RNA that is involved in the signaling system that activates tuber formation. Short-day (SD) conditions induce tuberization and long-day (LD) inhibits the process. The transcriptional source of this mobile RNA is leaf veins and leaf stalks designated, petioles. Transport of StBEL5 RNA is induced by a SD photoperiod that leads to tuber formation. It is likely that the movement of StBEL5 is facilitated by the formation of RNA-protein complex(s). To further understand this proposed mechanism of downstream signaling we have undertaken a detailed proteomic analysis of proteins isolated from potato petioles (PP) grown under LD and SD photoperiod conditions using 2-dimensional gel electrophoresis (2-DE) followed by MALDI MS/MS and/or LC MS/MS. Proteins that were differentially expressed in response to changes in photoperiods were analyzed by Progenesis SameSpots software. Phosphoproteins and RNA-binding proteins were enriched using immobilized metal affinity chromatography and poly(u) Sepharose columns respectively from SD and LD PP protein extracts and similarly analyzed. In addition to establishing a catalog of PP proteins, we have so far identified nearly sixty-seven proteins that are differentially expressed in response to SD or LD photoperiods. Significantly, the RNA-binding protein, elf-5a, has been detected in multiple isoforms specifically under LD conditions. Numerous other poly(u)-binding proteins which contain RNA recognition motifs have also been isolated and identified. This is the first comprehensive proteomics study that examines and catalogs the proteins that are present in the potato petiole and are potentially differentially regulated by photoperiod.

Table 1: Catalogue of differentially expressed proteins of potato petiole extract from plants grown under LD and SD photoperiod. RNA-binding proteins are highlighted in red. Spot # Acession # MW (kda) % coverage # unique peptide Score TAIR accession # Blast E-value 20 gi 61968918 29 11/8 162 AT4G27520 4.00E- 37 TAIR Annotation Plastocyanin-like domain-containing protein Putative function Electron carrier, copper ion binding a Fold Difference LD: 1.6 28 No hit 80 gi 225445166 123.3 9/11 99 AT4G29060 0 Embryo defective RNA binding, translation SD:1.9 2726 elongation factor 95 gi 2241435 106.7 4/2 90 AT4G29060 0 Embryo defective 2726 RNA binding, translation elongation factor SD: 2.1 120 gi 156106716 111.5 3/2 91 AT1G09770 0 Arabidopsis thaliana Cell division cycle 5 DNA binding/ transcription factor LD:2.2 173 gi 3334200 112.9 3/4 229 AT4G33010 0 Glycine decarboxylase P- protein 1 Glycine dehydrogenase, pyridoxal phosphate binding SD:1.9 207 gi 11066033 98 8/4 120 AT2G05710 0 Aconitate hydratase, cytoplasmic, 220 gi 11066033 98 8/4 120 AT2G05710 0 Aconitate hydratase, cytoplasmic, Aconitate hydratase, ATP binding Aconitate hydratase, ATP binding 240 No hit SD: 1:6 272 No hit LD:1.7 342 No hit SD:1.6 482 gi 136739 51.8 23/8 139 AT5G17310 0 UTP--glucose-1- Nucleotidyltransferase LD:2.0 phosphate uridylyltransferase, 484 gi 1488652 53.3 15/6 595 AT2G47510 0 Fumarase 1 Fumarate hydratase LD:1.6 SD:1.6 SD:1.6

gi 116292768 42.8 15/5 482 AT3G51800 3.00E- 170 Aminopeptidase/ metalloexopeptidase 510 gi 1708400 46.7 16/5 301 AT1G65930 0 Isocitrate dehydrogenase, 520 gi 50400860 47 27/8 727 AT3G52880 0 Monodehydroascorba -te reductase, gi 82400134 40.7 8/ 3 216 AT5G43940 0 Sensitive to hot temperatures 5 Metalloexopeptidase Isocitrate dehydrogenase (NADP+), copper ion binding Monodehydroascorbate reductase S-nitrosoglutathione reductase, 564 gi 147794990 46.2 2/1 47 AT1G24120 0 ARG1-LIKE 1 Unfolded protein binding, heat shock protein binding 570 gi 48478827 41.1 17/3 119 AT3G02230 0 Reversibly glycosylated polypeptide 1 Cellulose synthase (UDPforming) 571 gi 1709453 43,2 13/5 488 AT1G59900 0 AT-E1 Alpha Oxidoreductase LD1.8 gi 81074221 50.8 18/8 520 AT4G31990 0 Aspartate aminotransferase 602 gi 26453355 43.9 14/5 334 AT3G63140 7.00E- 170 Chloroplast stemloop binding protein of 41 kda L-aspartate:2- oxoglutarate aminotransferase mrna binding, poly(u) binding 666 gi 145203152 71.1 4/2 105 AT3G12580 0 Heat shock protein 70 ATP binding 707 gi 78191406 25.3 8/3 213 AT2G18110 2.00E- Elongation factor 1- Translation elongation SD:1.6 91 beta, factor gi 3766535 29.3 24/5 893 AT1G78300 9.00E- 130 741 gi 217071540 26 30/5 395 AT3G14290 2.00E- 139 762 gi 24636598 27.4 25/5 488 AT1G07890 2.00E- 126 gi 14594925 27.1 19/4 323 AT2G27020 3.00E- 123 General regulatory factor 2/14-3-3 protein PAE2; endopeptidase Ascorbate peroxidase 1 PAG1; endopeptidase Protein phosphorylated amino acid binding/protein binding Threonine-type endopeptidase L-ascorbate peroxidase Threonine-type endopeptidase LD:1.6 SD:3.6 LD:1.6

765 gi 24636598 27.7 18/3 200 2.00E- 126 776 gi 38112662 27 5/2 293 AT3G55440 4.00E- 128 789 gi 17432522 31.3 39/7 249 AT2G37220 3.00E- 75 807 gi 17380185 24.6 21/4 562 AT3G60820 4.00E- 116 APX1 (ascorbate peroxidase 1) Triose-phosphate isomerase 29 kda ribonucleoprotein PBF1; peptidase 818 gi 76160951 23.5 40/5 149 AT1G75270 8e-89 Dehydroascorbate reductase 2 845 gi 120665 47.4 11/4 189 AT1G42970 0 Glyceraldehyde-3- phosphate dehydrogenase 853 gi 115439527 26 11/4 165 AT4G38510 0 Vacuolar ATP synthase subunit B, 854 gi 115439527 26 3/1 75 AT4G38510 0 Vacuolar ATP synthase subunit B, 879 gi 170773910 21.7 35/3 379 AT3G12390 1.00E- 62 905 gi 75266239 19.7 34/5 604 AT3G20390 2.00E- 65 927 gi 20020 20.3 7/1 93 AT3G27850 1.00E- 53 934 gi 11134035 28.1 7/2 94 AT1G06680 3.00E- 144 939 gi 11134035 28.1 20/5 263 AT1G06680 3.00E- 144 941 gi 11134035 28.1 17/4 229 AT1G06680 3.00E- 144 Nascent polypeptide associated complex alpha chain protein Endoribonuclease L- PSP family protein Ribosomal protein L 12-C subunit P-1 subunit P-1 subunit P-1 L-ascorbate peroxidase Triose-phosphate isomerase RNA binding, poly(u) binding Peptidase/ threonine-type endopeptidase Glutathione binding Glyceraldehyde-3- phosphate dehydrogenase (NADP+) Hydrogen ion transporting ATP synthase Hydrogen ion transporting ATP synthase Involved in response to salt stress Endoribonuclease Structural constituent of ribosome/ translation Poly(U) binding, photosynthesis Poly(U) binding, photosynthesis Poly(U) binding, photosynthesis SD:1.9 SD: 2.1 LD:2.0 LD:2.1 SD: 1.7 LD1.6 SD1.6 SD:2.3

940 gi 11134035 28.1 20/5 263 AT1G06680 3.00E- 144 subunit P-1 Poly(U) binding, photosynthesis 947 gi 82623423 17.9 38/5 753 AT4G39260 GR-RBP8 RNA binding / nucleic acid binding 996 No hit 997 gi 76160941 11.4 22 238 AT3G44590 7.00E- 60S acidic ribosomal Structural constituent of 23 protein P2 ribosome 1001 No hit SD:1.9 1007 gi 76160941 11.4 28 337 AT3G44590 7.00E- 23 60S acidic ribosomal protein P2 Structural constituent of ribosome 1009 gi 76160941 11.4 44 364 AT3G44590 7.00E- 23 60S acidic ribosomal protein P2 Structural constituent of ribosome SD1.6 SD: 2.3 1018 No hit SD:2.1 1046 gi 73808794 16.2 26 110 AT4G09320 2.00E- NDPK1; ATP Nucleoside diphosphate SD:1.9 69 binding / nucleoside diphosphate kinase [ kinase / ATP binding 1071 gi 169786772 20 12/2 160 AT4G35770 3.00E- Senescence 1 Molecular_function SD:3.0 44 unknown 1078 gi 225024 18.1 15/3 142 AT5G21274 4.00E- Calmodulin 6 Calcium ion binding SD:2.7 70 1082 No hit 1089 gi 30039180 8.5 31/2 284 AT1G66240 3.00E- 31 1134 gi 131385 35 11/2 178 AT3G50820 2.00E- 157 1141 gi 115469244 17 15/2 95 AT1G31340 2.00E- 82 535b gi 14031049 39.4 11 196 AT1G71695 2.00E- 130 613b gi 118486419 29.3 6/1 63 AT3G14420 7.00E- 139 Arabidopsis homolog of anti-oxidant1 Subunit O-2 Metal ion binding Oxygen evolving, poly(u) binding SD:2.0 SD:2.0 Related to Ubiquitin 1 Protein binding SD:1.6 Peroxidase 12 Electron carrier LD:1.9 (S)-2-hydroxy-acid oxidase, peroxisomal, Glycolate oxidase

645b gi 83283995 39 15 216 AT2G36460 0 Fructosebisphosphate 684b gi 120666 36.7 4/2 101 AT3G04120 8.00E- 179 792b gi 42795466 33.4 15/3 319 AT4G37800 7.00E- 133 aldolase, Glyceraldehyde-3- phosphate dehydrogenase C subunit1 Xyloglucosyl transferase, 817b gi 2894118 16.4 25/4 630 0 Hypothetical protein (Solanum tuberosum) Fructose-bisphosphate aldolase Glyceraldehyde-3- phosphate dehydrogenase (phosphorylating) Hydrolase 958b No hit SD:1.9 969b gi 225435247 27.6 6/1 86 AT1G56450 1.00E- LD: 1.6 119 PBG1; peptidase/ threonine-type endopeptidase 984b gi 218312 46.7 3/1 109 AT4G20360 0 Rab GTPASE HomologE1B Peptidase / response to cadmium ion, response to salt stress GTP binding, translation elongation factor 1054b gi 19315 26 8/2 64 AT4G11650 4 e-78 Osmotin 34 Response to salt stress LD: 4.1 1186b gi 255547634 27.6 22/3 293 AT5G13120 1.00E- 91 1195b gi 116781417 22.7 14/3 480 AT5G10860 2.00E- 91 Peptidyl-prolyl cistrans isomerase cyclophilin-type family protein CBS domaincontaining protein Isomerase /protein folding LD:1.7 LD:2.1 SD:2.2 SD: 1.8 Response to salt stress LD: 1.7 1203b No hit SD:2.2 1226b gi 1928939 18.3 16/4 172 AT2G16600 3.00E- ROC3; peptidylprolyl Isomerase /protein SD: 1.8 79 cis-trans folding/signal 1356b gi 400851 16.4 16/2 74 AT3G04720 4.00E- 49 a : higher fold expression under indicated condition. isomerase Pathogenesis related 4 transduction Chitin binding/ response to salt stress LD:1.9

Table 2: Catalogue of phosphoproteins enriched from potato petioles extract from plants grown under LD and SD photoperiod. Spot # 5 gi 585201 39.5 8/2 233 AT5G37600 0 ATGSR1 Glutamate-ammonia ligase, copper ion binding 6 gi 118486160 40.1 7/2 101 AT5G11420 4.00E-141 Unknown protein- Molecular function unknown 7 gi 255549002 40.2 10/2 177 AT5G11420 2.00E-174 Unknown protein- Molecular function unknown 8 gi 255549002 40.2 10/2 177 AT5G11420 2.00E-174 Unknown protein- Molecular function unknown 9 gi 255549002 40.2 10/2 177 AT5G11420 2.00E-174 Unknown protein- Molecular function unknown 10 gi 12229803 45 20/4 452 AT5G18170 0 Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 11 gi 12229803 45 19/3 472 AT5G18170 0 Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 12 gi 12229803 45 16/2 344 AT5G18170 0 Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 13 gi 59668640 45 7/1 153 AT5G07440 0 Glutmate dehydrogenase 2 ATP binding /oxidoreductase 14 No hit Accession # MW (kda) % coverage/ # unique peptide MOWSE Score TAIR acession # Blast E-value TAIR Annotation Putative function 1 gi 255549002 40.2 10/2 161 AT5G11420 2.00e-174 Unknown protein- Biological process unknown 2 gi 2213425 32.7 12/3 185 AT1G11840 2.00E-138 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 3 gi 2213425 32.7 12/3 185 AT1G11840 2.00E-138 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 4 gi 1419094 39.3 8/2 242 AT5G37600 0 ATGSR1 Glutamate-ammonia ligase, copper ion binding 15 No hit 16 No hit

17 gi 108711192 17.9 13/2 115 AT1G13950 7.00E-78 Eukaryotic elongation factor 5A-1 Translation initiation factor 18 gi 3024019 17.6 23/3 252 AT1G13950 4.00E-78 Eukaryotic elongation factor 5A-1 Translation initiation factor 19 gi 108711192 17.9 13/2 117 AT1G13950 7.00E-75 Eukaryotic elongation factor 5A-1 Translation initiation factor 20 gi 124226 17.5 13/2 99 AT1G69410 3.00E-79 Eukaryotic elongation factor 5A-3 Translation initiation factor 21 gi 118486160 40.1 7/2 121 AT5G11420 4.00E-141 Unknown protein Molecular function unknown 22 gi 226502202 23.2 5/1 95 AT3G53620 8.00E-99 Arabidopsis thaliana pyrophosphorylase 4 Inorganic diphosphatase 23 No hit 24 No hit 25 no hit 26 gi 1706544 39.8 11/4 208 AT4G16260 2.00E-108-1,3-glucanase1 Hydrolase, hydrolyzing O-glycosyl compounds 27 gi 33517365 44.6 3/1 68 AT1G08450 0 Calreticulin 3 Unfolded protein binding, calcium ion binding 28 gi 42408797 49.8 3/1 70 AT4G38220 9.00E-16 Aminoacylase, Metallopeptidase, hydrolase, protein dimerization 29 gi 225444485 33 16/3 264 AT5G11420 2.00E-163 Unknown protein- Molecular function unknown 30 gi 2213425 32.7 12/3 185 AT1G11840 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 31 gi 2213425 32.7 12/3 186 AT1G11840 2.00E-134 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 32 gi 2213425 32.7 12/3 184 AT1G11840 2.00E-134 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 33 gi 1346172 73.4 10/2 338 AT5G28540 0 BIP1; ATP binding Protein folding, ER-associated protein catabolic process, response to heat

34 gi 16221 61.6 3/1 56 AT3G23990 0 Heat shock protein 60 Chaperone-mediated protein complex assembly 35 gi 38605155 34.2 6/2 87 AT5G13870 2.00E-177 Endoxyloglucan Hydrolase Transferase A4 36 gi 121530 40.3 2/1 71 AT3G14420 0 (S)-2-hydroxy-acid oxidase, peroxisomal, Glycolate oxidase 37 gi 9857712 31.7 7/2 83 AT5G57550 4.00E-146 Xyloglucan endotransglycosylase 3 38 gi 255549002 40.2 10/3 176 AT5G11420 2.00E-174 Unknown protein- 39 gi 255549002 40.2 10/3 142 AT5G11420 2.00E-174 Unknown protein- 40 gi 255549002 40.2 10/3 143 AT5G11420 2.00E-174 Unknown protein- Hydrolase Molecular function unknown Molecular function unknown Molecular function unknown