Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Two LEA Proteins Are Boiling-Stable Proteins
2.2. Both LEA Proteins Afford Limited Protection to GLUCOSE-6-PHOSPHATE DEHYDROGENASE against Heat Stress
2.3. Phage Was Retained by Both LEA Proteins
2.4. LEA Protein-Retained Phage Contained Insert
2.5. The Two LEA Protein Homologues Target Discrete Proteins, Some of Which Are Identical
2.6. Proteins Resident in the Cytoplasm and Associated with the Translational Machinery Are Over-Represented among the Retrieved Targets
3. Experimental Section
3.1. Cloning SMP1 and GmPM28
3.2. Recombinant Protein Production and Purification
3.3. Characterization of SMP1 and GmPM28 as Boiling-Stable Proteins
3.4. Determination of Recombinant SMP1 and GmPM28 Capacity to Bind to Microtiter Plate Wells
3.5. GLUCOSE 6 PHOSPHATE DEHYDROGENASE (G6PDH) Protection Assays
3.6. Biopanning
3.7. Titering
3.8. Plaque Isolation, PCR and Sequencing
3.9. Statistical Analysis
4. Conclusions
Supplemental Information
ijms-13-06582-s001.pdfAcknowledgments
References
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In-Frame Hits of SMP1 at 25 °C Using SL1 after 4 Rounds of Panning | ||||
---|---|---|---|---|
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
6 | AT1G15280 | CASC3/Barentsz eIF4AIII binding | 4 | Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
2 | AT1G30610 | EMB88, EMB2279 pentatricopeptide (PPR) repeat-containing protein | 2 | Predictors-iPSORT: plastid; MitoPred: mitochondrion; MultiLoc: plastid; PeroxP: peroxisome; Predotar: plastid; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: nucleus |
1 | AT1G58210 | EMB1674 | kinase interacting family protein | 1 | Predictors-iPSORT: mitochondrion; MitoPred: mitochondrion; MultiLoc: plastid; Predotar: mitochondrion; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: nucleus |
1 | AT3G55170 | Ribosomal L29 family protein | 1 | SUBA MS/MS: cytosol: 17934214; plasma membrane: 19334764 Predictors: LOCtree: plastid; MitoPred: mitochondrion; SubLoc: nucleus; WoLFPSORT: nucleus |
In-Frame Hits of GmPM28 at 25 °C Using SL1 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
7 | AT1G15280 | CASC3/Barentsz eIF4AIII binding | 7 | Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
1 | AT3G63400 | Cyclophilin-like peptidyl-prolyl cis-trans isomerasefamily protein | 1 | Predictors-SubLoc: nucleus |
1 | AT1G30610 | EMB88, EMB2279 | pentatricopeptide (PPR) repeat-containing protein | 1 | Predictors-iPSORT: plastid; MitoPred: mitochondrion; MultiLoc: plastid; PeroxP: peroxisome; Predotar: plastid; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: nucleus |
1 | AT2G02160 | CCCH-type zinc finger family protein | 1 | Predictors-MitoPred: mitochondrion; SubLoc: nucleus; WoLFPSORT: nucleus |
In-Frame Hits of SMP1 at 41 °C Using SL1 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
1 | AT1G30610 | EMB88, EMB2279 pentatricopeptide (PPR) repeat-containing protein | 1 | Predictors-iPSORT: plastid; MitoPred: mitochondrion; MultiLoc: plastid; PeroxP: peroxisome; Predotar: plastid; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: nucleus |
3 | AT2G36640 | ATECP63, ECP63 embryonic cell protein 63 | 2 | Predictors-LOCtree: cytosol SubLoc: nucleus WoLFPSORT: peroxisome |
1 | AT1G55310 | SR33, SCL33, At-SCL33 | SC35-like splicing factor | 1 | Predictors-interchromatin granule, nuclear speck, nucleolus, plasma membrane/TAIR |
1 | AT5G46430 | Ribosomal protein L32e | 1 | SUBA MS/MS: cytosol: 17934214; cytosol: 21166475; plasma membrane: 19334764; plasma membrane: 15574830; Predictors-iPSORT: mitochondrion; LOCtree: mitochondrion; MitoPred: mitochondrion; Mitoprot 2: mitochondrion; MultiLoc: plastid; Predotar: mitochondrion; SubLoc: mitochondrion; TargetP: mitochondrion; WoLFPSORT: cytosol |
2 | AT1G15290 | Tetratricopeptide repeat (TPR)-like superfamily | 1 | SUBA MS/MS: cytosol: 21166475; Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
1 | AT2G31410 | unknown protein | 1 | Predictors-MitoPred: mitochondrion; SubLoc: nucleus; WoLFPSORT: nucleus |
1 | AT1G16610 | SR45, RNPS1 | arginine/serine-rich 45 | 1 | Mitochondria, nucleus plastid/BAR Cell eFP Browser |
In-Frame Hits of GmPM28 at 41 °C Using SL1 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
5 | AT1G30610.1 | EMB88, EMB2279 | pentatricopeptide (PPR)repeatcontaining protein | 4 | Predictors-iPSORT: plastid; MitoPred: mitochondrion; MultiLoc: plastid; PeroxP: peroxisome; Predotar: plastid; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: nucleus |
3 | AT1G15280.1 | CASC3/Barentsz eIF4AIII binding | 2 | Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
In-Frame Hits of SMP1 at 25 °C Using SL2 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
2 | AT1G11630 | Pentatricopeptide repeat-containing protein | 2 | SUBA MS/MS: mitochondrion: 14671022; Predictors-iPSORT: mitochondrion; LOCtree: mitochondrion; MitoPred: mitochondrion; MultiLoc: plastid; Predotar : mitochondrion; SubLoc : nucleus; TargetP : mitochondrion; WoLFPSORT : plastid |
3 | AT1G65090 | unknown protein | 3 | cytosol, mitochondria/BAR Cell eFP Browser |
In-Frame Hits of GmPM28 at 25 °C Using SL2 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
8 | AT5G44120 | CRA1, ATCRA1, CRU1 | RmlC-like cupins superfamily | 1 | SUBA MS/MS: plasma membrane; Predictors-Predotar: endoplasmic reticulum; SubLoc: nucleus; TargetP: extracellular; WoLFPSORT: vacuole |
In-Frame Hits of SMP1 at 41 °C Using SL2 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
3 | AT1G15280.2 | CASC3/Barentsz eIF4AIII binding | 3 | Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
3 | AT1G15290.1 | Tetratricopeptide repeat (TPR)-like superfamily | 1 | SUBA MS/MS: cytosol: 21166475; Predictors-SubLoc: nucleus; WoLFPSORT: nucleus |
1 | AT4G12400.2 | Hop3|stress-inducible protein, putative | 1 | No information |
1 | AT1G54870.1 | NAD(P)-binding Rossmann-fold superfamily protein | 1 | Predictors-MultiLoc: mitochondrion; SubLoc: cytosol; WoLFPSORT: plastid |
1 | AT3G58680.1 | MBF1B, ATMBF1B | multiprotein bridging factor 1B | 1 | GFP: cytosol: 15610358; nucleus: 15610358; Annotators-AmiGO: nucleus; Predictors-LOCtree: cytosol; MitoPred: mitochondrion; Predotar: plastid; SubLoc: nucleus; WoLFPSORT: nucleus |
1 | AT3G01690.1 | alpha/beta-Hydrolases superfamily protein | 1 | Predictors-iPSORT: mitochondrion; SubLoc: nucleus; TargetP: plastid; WoLFPSORT: cytosol |
1 | AT5G52240.1 | MSBP1, ATMP1, AtMAPR5 membrane steroid binding protein1 | 1 | SUBA MS/MS: endoplasmic reticulum: 16618929; plasma membrane: 17317660; plasma membrane: 19334764; plasma membrane: 17644812; Annotators-AmiGO: plasma membrane; Predictors-SubLoc: cytosol; TargetP: extracellular; WoLFPSORT: endoplasmic reticulum |
In-Frame Hits of GmPM28 at 41 °C Using SL2 after 4 Rounds of Panning | ||||
Hits | Locus Identifier | Protein Identity | Independent Clones | Subcellular Residence/Authority |
4 | AT5G18380 | Ribosomal protein S5 domain 2-like superfamily | 3 | Annotators-UniProt : cytosol Predictors-iPSORT: plastid; LOCtree: cytosol; Mitoprot 2: mitochondrion; SubLoc: mitochondrion; WoLFPSORT: cytosol |
2 | AT4G04470 | PMP22| Peroxisomal membrane 22 kDa (Mpv17/PMP22) family protein | 1 | SUBA MS/MS: peroxisome: 18931141; plasma membrane: 19334764; Annotators-TAIR : peroxisome; AmiGO: peroxisome Predictors-iPSORT: mitochondrion; LOCtree: mitochondrion; MitoPred: mitochondrion; Mitoprot 2: mitochondrion; MultiLoc: mitochondrion; PeroxP: no data; Predotar: no data; SubLoc: mitochondrion; TargetP: mitochondrion; WoLFPSORT: plastid |
1 | AT2G19540 | Transducin family protein/WD-40 repeat family protein | 1 | Predictors-SubLoc: cytosol; WoLFPSORT: mitochondrion |
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Kushwaha, R.; Lloyd, T.D.; Schäfermeyer, K.R.; Kumar, S.; Downie, A.B. Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display. Int. J. Mol. Sci. 2012, 13, 6582-6603. https://doi.org/10.3390/ijms13066582
Kushwaha R, Lloyd TD, Schäfermeyer KR, Kumar S, Downie AB. Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display. International Journal of Molecular Sciences. 2012; 13(6):6582-6603. https://doi.org/10.3390/ijms13066582
Chicago/Turabian StyleKushwaha, Rekha, Taylor D. Lloyd, Kim R. Schäfermeyer, Santosh Kumar, and Allan Bruce Downie. 2012. "Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display" International Journal of Molecular Sciences 13, no. 6: 6582-6603. https://doi.org/10.3390/ijms13066582