Photoperiodic effect on protein profiles of potato petiole

Transcription

1 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 Department of Chemistry, Iowa State University, Ames, Iowa Plant Biology Major, Iowa State University, Ames, Iowa 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.

2 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 /8 162 AT4G E- 37 TAIR Annotation Plastocyanin-like domain-containing protein Putative function Electron carrier, copper ion binding a Fold Difference LD: No hit 80 gi /11 99 AT4G Embryo defective RNA binding, translation SD: elongation factor 95 gi /2 90 AT4G Embryo defective 2726 RNA binding, translation elongation factor SD: gi /2 91 AT1G Arabidopsis thaliana Cell division cycle 5 DNA binding/ transcription factor LD: gi /4 229 AT4G Glycine decarboxylase P- protein 1 Glycine dehydrogenase, pyridoxal phosphate binding SD: gi /4 120 AT2G Aconitate hydratase, cytoplasmic, 220 gi /4 120 AT2G Aconitate hydratase, cytoplasmic, Aconitate hydratase, ATP binding Aconitate hydratase, ATP binding 240 No hit SD: 1:6 272 No hit LD: No hit SD: gi /8 139 AT5G UTP--glucose-1- Nucleotidyltransferase LD:2.0 phosphate uridylyltransferase, 484 gi /6 595 AT2G Fumarase 1 Fumarate hydratase LD:1.6 SD:1.6 SD:1.6

3 gi /5 482 AT3G E- 170 Aminopeptidase/ metalloexopeptidase 510 gi /5 301 AT1G Isocitrate dehydrogenase, 520 gi /8 727 AT3G Monodehydroascorba -te reductase, gi / AT5G Sensitive to hot temperatures 5 Metalloexopeptidase Isocitrate dehydrogenase (NADP+), copper ion binding Monodehydroascorbate reductase S-nitrosoglutathione reductase, 564 gi /1 47 AT1G ARG1-LIKE 1 Unfolded protein binding, heat shock protein binding 570 gi /3 119 AT3G Reversibly glycosylated polypeptide 1 Cellulose synthase (UDPforming) 571 gi ,2 13/5 488 AT1G AT-E1 Alpha Oxidoreductase LD1.8 gi /8 520 AT4G Aspartate aminotransferase 602 gi /5 334 AT3G E- 170 Chloroplast stemloop binding protein of 41 kda L-aspartate:2- oxoglutarate aminotransferase mrna binding, poly(u) binding 666 gi /2 105 AT3G Heat shock protein 70 ATP binding 707 gi /3 213 AT2G E- Elongation factor 1- Translation elongation SD: beta, factor gi /5 893 AT1G E gi /5 395 AT3G E gi /5 488 AT1G E- 126 gi /4 323 AT2G E- 123 General regulatory factor 2/ 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

4 765 gi / E gi /2 293 AT3G E gi /7 249 AT2G E gi /4 562 AT3G E- 116 APX1 (ascorbate peroxidase 1) Triose-phosphate isomerase 29 kda ribonucleoprotein PBF1; peptidase 818 gi /5 149 AT1G e-89 Dehydroascorbate reductase gi /4 189 AT1G Glyceraldehyde-3- phosphate dehydrogenase 853 gi /4 165 AT4G Vacuolar ATP synthase subunit B, 854 gi /1 75 AT4G Vacuolar ATP synthase subunit B, 879 gi /3 379 AT3G E gi /5 604 AT3G E gi /1 93 AT3G E gi /2 94 AT1G E gi /5 263 AT1G E gi /4 229 AT1G E- 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

5 940 gi /5 263 AT1G E- 144 subunit P-1 Poly(U) binding, photosynthesis 947 gi /5 753 AT4G39260 GR-RBP8 RNA binding / nucleic acid binding 996 No hit 997 gi AT3G E- 60S acidic ribosomal Structural constituent of 23 protein P2 ribosome 1001 No hit SD: gi AT3G E S acidic ribosomal protein P2 Structural constituent of ribosome 1009 gi AT3G E S acidic ribosomal protein P2 Structural constituent of ribosome SD1.6 SD: No hit SD: gi AT4G E- NDPK1; ATP Nucleoside diphosphate SD: binding / nucleoside diphosphate kinase [ kinase / ATP binding 1071 gi /2 160 AT4G E- Senescence 1 Molecular_function SD: unknown 1078 gi /3 142 AT5G E- Calmodulin 6 Calcium ion binding SD: No hit 1089 gi /2 284 AT1G E gi /2 178 AT3G E gi /2 95 AT1G E b gi AT1G E b gi /1 63 AT3G E- 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

6 645b gi AT2G Fructosebisphosphate 684b gi /2 101 AT3G E b gi /3 319 AT4G E- 133 aldolase, Glyceraldehyde-3- phosphate dehydrogenase C subunit1 Xyloglucosyl transferase, 817b gi / Hypothetical protein (Solanum tuberosum) Fructose-bisphosphate aldolase Glyceraldehyde-3- phosphate dehydrogenase (phosphorylating) Hydrolase 958b No hit SD: b gi /1 86 AT1G E- LD: PBG1; peptidase/ threonine-type endopeptidase 984b gi /1 109 AT4G Rab GTPASE HomologE1B Peptidase / response to cadmium ion, response to salt stress GTP binding, translation elongation factor 1054b gi /2 64 AT4G e-78 Osmotin 34 Response to salt stress LD: b gi /3 293 AT5G E b gi /3 480 AT5G E- 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: b No hit SD: b gi /4 172 AT2G E- ROC3; peptidylprolyl Isomerase /protein SD: cis-trans folding/signal 1356b gi /2 74 AT3G E- 49 a : higher fold expression under indicated condition. isomerase Pathogenesis related 4 transduction Chitin binding/ response to salt stress LD:1.9

7 Table 2: Catalogue of phosphoproteins enriched from potato petioles extract from plants grown under LD and SD photoperiod. Spot # 5 gi /2 233 AT5G ATGSR1 Glutamate-ammonia ligase, copper ion binding 6 gi /2 101 AT5G E-141 Unknown protein- Molecular function unknown 7 gi /2 177 AT5G E-174 Unknown protein- Molecular function unknown 8 gi /2 177 AT5G E-174 Unknown protein- Molecular function unknown 9 gi /2 177 AT5G E-174 Unknown protein- Molecular function unknown 10 gi /4 452 AT5G Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 11 gi /3 472 AT5G Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 12 gi /2 344 AT5G Glutmate dehydrogenase 1 ATP binding/ oxidoreductase 13 gi /1 153 AT5G 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 /2 161 AT5G e-174 Unknown protein- Biological process unknown 2 gi /3 185 AT1G E-138 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 3 gi /3 185 AT1G E-138 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 4 gi /2 242 AT5G ATGSR1 Glutamate-ammonia ligase, copper ion binding 15 No hit 16 No hit

8 17 gi /2 115 AT1G E-78 Eukaryotic elongation factor 5A-1 Translation initiation factor 18 gi /3 252 AT1G E-78 Eukaryotic elongation factor 5A-1 Translation initiation factor 19 gi /2 117 AT1G E-75 Eukaryotic elongation factor 5A-1 Translation initiation factor 20 gi /2 99 AT1G E-79 Eukaryotic elongation factor 5A-3 Translation initiation factor 21 gi /2 121 AT5G E-141 Unknown protein Molecular function unknown 22 gi /1 95 AT3G E-99 Arabidopsis thaliana pyrophosphorylase 4 Inorganic diphosphatase 23 No hit 24 No hit 25 no hit 26 gi /4 208 AT4G E-108-1,3-glucanase1 Hydrolase, hydrolyzing O-glycosyl compounds 27 gi /1 68 AT1G Calreticulin 3 Unfolded protein binding, calcium ion binding 28 gi /1 70 AT4G E-16 Aminoacylase, Metallopeptidase, hydrolase, protein dimerization 29 gi /3 264 AT5G E-163 Unknown protein- Molecular function unknown 30 gi /3 185 AT1G11840 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 31 gi /3 186 AT1G E-134 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 32 gi /3 184 AT1G E-134 Glyoxalase I homolog Lactoylglutathione lyase, metal ion binding 33 gi /2 338 AT5G BIP1; ATP binding Protein folding, ER-associated protein catabolic process, response to heat

9 34 gi /1 56 AT3G Heat shock protein 60 Chaperone-mediated protein complex assembly 35 gi /2 87 AT5G E-177 Endoxyloglucan Hydrolase Transferase A4 36 gi /1 71 AT3G (S)-2-hydroxy-acid oxidase, peroxisomal, Glycolate oxidase 37 gi /2 83 AT5G E-146 Xyloglucan endotransglycosylase 3 38 gi /3 176 AT5G E-174 Unknown protein- 39 gi /3 142 AT5G E-174 Unknown protein- 40 gi /3 143 AT5G E-174 Unknown protein- Hydrolase Molecular function unknown Molecular function unknown Molecular function unknown