Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (12): 2523-2537.doi: 10.3864/j.issn.0578-1752.2021.12.004

• TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY·AGRICULTURE INFORMATION TECHNOLOGY • Previous Articles     Next Articles

Identification of 14-3-3 Client Proteins in Rice Grains and Their Response to Exogenous Hormones During the Grain Filling Stage

ZHANG ZhiXing1,2(),MIN XiuMei1,SONG Guo1,CHEN Hua1,XU HaiLong1,LIN WenXiong1,2()   

  1. 1College of Life Science, Fujian Agricultural & Forestry University, Fuzhou 350002
    2Fujian Agriculture & Forestry University/ Fujian Provincial Key Laboratory of Agroecological Processing & Safety Monitoring, Fuzhou 350002
  • Received:2020-08-11 Accepted:2021-01-05 Online:2021-06-16 Published:2021-06-24
  • Contact: WenXiong LIN E-mail:zhangzhixingfz@163.com;wenxiong181@163.com

Abstract:

【Objective】Grain yield and quality of rice mainly depend on grain filling. The family of 14-3-3 proteins is the important regulator of signaling in plant, and plays an important role in plant growth and development. This study was performed to assess the gene expression pattern and to identify client proteins, which would result in important information toward understanding the functional mechanism of 14-3-3 protein during rice grain filling. 【Method】 The expression pattern of each 14-3-3 genes at different grain filling stages were examined by the Real-time RT-PCR (qRT-PCR), and the family members GF14b and GF14e were used for subsequent functional analysis. The function motif of GF14b and GF14e protein were analyzed by using the KEGG database. The amplified open reading frames of GF14b and GF14e were cloned into the PGEX-6P-1 expression vector for production of the N-terminal-tagged fusion proteins GST-GF14b and GST-GF14e. The client proteins of GF14b and GF14e were captured with the affinity chromatography approach and identified by the LC-MS/MS. The protein interaction between client proteins and GF14b and GF14e were validated by the GST Pull-down in vitro. Phosphorylation sites and functions of all client proteins were analyzed using the KinasePhos online website and MapMan software (Version 3.60), respectively. The exogenous hormones (25×10 -6mol·L-1 ABA,10×10-6mol·L-1 IAA,100×10-6mol·L-1 GA,50×10-6mol·L-1 ZR and 2×10-4mol·L-1 BR ) were sprayed on rice grains at 15 days after flowering to investigate the effects of exogenous hormones treatment on the expression of GF14b, GF14e and their interacting genes. 【Result】 Except for the GF14h, the remaining seven 14-3-3 family genes were expressed in rice grains, and the expression of GF14b and GF14e was high and highly variable during grain filling. Two same protein motifs and three differential motifs between GF14b and GF14e were identified with the protein sequence analysis. In total, 59 GF14b- and 72 GF14e-client proteins in rice grains were captured by affinity chromatography on a glutathione-agarose affinity column. Two randomly selected proteins from these client proteins, namely SUS3 and PSA, were further validated by GST Pull-down in vitro, and the results showed that the SUS3 interacted with GF14b and GF14e, whereas PSA specially interacted with GF14e, which confirmed the accuracy of the affinity chromatography assay. Among these client proteins, fourth-three were commonly affinity-identified by the GF14b and GF14e and were predicted to be implicated in the sucrose conversion, starch synthesis, glycolysis and TCA cycle. Meanwhile, it was found GF14b specifically bounded to the nucleotide metabolism and transporters, whilst GF14e tended to interact with the proteins involving C1 metabolism. In addition, most of the identified client proteins possess the phosphorylation sites of Ser or Thr. The present results also showed that the expression of GF14b and GF14e were up-regulated and most of the starch synthesis-related interacting genes (SUS2, AGPS, AGPL, PPDK2, SBE) were down-regulated after exogenous hormones treatment. 【Conclusion】 The magnitude of change in gene expression was greater in GF14b and GF14e than the other 14-3-3 gene family members during grain filling. The GF14b and GF14e could respond the change of hormones concentration and act as a regulator to negatively regulate the expression of starch synthesis related genes through protein-protein interaction, in turn, play an important role in starch synthesis during the grain filling stage.

Key words: rice, grain filling, 14-3-3 protein, protein-protein interactions, hormone

Table 1

qRT-PCR and PCR primers used in this study"

基因
Gene
Accession No. 正向引物序列
Forward primer sequence (5′-3′)
反向引物序列
Reverse primer sequence (5′-3′)
Primer for qRT-PCR
GF14a LOC_Os08g37490 AGCCATGAAGGAGCTGTCGC GCTCATCCTCAGGCTTGGTT
GF14b LOC_Os04g38870 GCTTGAATCCCACCTTGTC AATGTCCTGAGCAGCCTTG
GF14c LOC_Os08g33370 CGTTTGACGAAGCCATCTCC CTAGTAGAACAGGAGAAGAATC
GF14d LOC_Os11g34450 TGCTCTCGCAGATTTGGCTC ATCCCCAGGCTCTTTTGGAG
GF14e LOC_Os02g36974 GATATTGCCCTGGCAGAGTTG GAGATATCGGAAGTCCACAGC
GF14f LOC_Os03g50290 AGCAGCTGAGAACACTCTTG CAGCAATAGCATCGTCGAAC
GF14g LOC_Os01g11110 AGCGACGACCTCGTCTACAT TGACTCTCCTTGCCCTTTGT
GF14h LOC_Os11g39540 TTATGGCCTATCAGGCTTGG TTCTCCTTCAGGAGCTGCAT
AGPS LOC_Os08g25734 TTACTGGGAAGACATTGGTACC CTCCCATGAGTAATGAGTCCTC
AGPL LOC_Os01g44220 GGAAAGATTGAATATTGGGGGC TCAGAGGAAAGAGTTGAACTCC
SBE LOC_Os02g32660 GATCAGTATGAAGGAGGACTGG ACCTACTAATGCTGCAGAATGT
SUS2 LOC_Os06g09450 GGAGAAAACCAAATACCCCAAC CAGTGTGATTCATGGCGATAAG
PPDK2 LOC_Os03g31750 CTAGCGGAATTCTTCTCGTTTG CAAATGCCCACCTCTAAATCAG
β-actin LOC_4333919 CTGCGGGTATCCATGAGACT GCAATGCCAGGGAACATAGT
Primer for PCR
GF14b LOC_Os04g38870 TTTTTTGGATTCATGTCGGCACAGGCGGAGCTTTCC TATATATACTCGAGCTGCCCCTCGCTGGAGTCGCGCTT
GF14e LOC_Os02g36974 TTTCGAATTCATGTCGCAGCCTGCTGAGCTTTCCC TTTCTCGAGCTGTCCATCTCCTGATTCGCCCTTGT
SUS3 LOC_Os07g42490 TCCGAATTCATGGGGGAAACTACTGGAGAACGTGC TTTTCTCGAGTTTGGTGGAGGCCTCTCCCTCAATG
PSA LOC_Os02g12650 GGGGGGGAATTCATGCATGGCTTCTACAGAAGTGTG GAGCTCGAGGTGGTCGTGAGAAATTTCCTTGAGGAC

Fig. 1

Quantitative real the dynamic expression pattern of the 14-3-3 genes during the different stages of rice grain filling DAF: Day after flowering"

Table 2

The functional motif analysis of GF14b and GF14e protein"

功能位点
Functional site
功能位点位置 Functional site location
GF14b GF14e
pf:IFT20 5-55
pf:DUF885 16-149 6-150
pf:14-3-3 9-245 9-245
pf:TPR_12 135-207 135-207
pf:FlaF 192-254

Fig. 2

SDS-PAGE analysis of GF14b and GF14e client proteins in rice grain A:SDS-PAGE analysis of GF14b client proteins; B: SDS-PAGE analysis of GF14e client proteins; Line 1 is the blank control; Line 2 is the negative control; Line 3 and line 4 in Fig. A are the elution protein of affinity chromatography of GF14b; Line 3 and line 4 in Fig. B are the elution protein of affinity chromatography of GF14e; Line 5 in Fig. A is the purified GST-GF14b protein; Line 5 in Fig. B is the purified GST-GF14e protein; Line 6 is the crude protein from developing rice grains; Line 7 is the marker"

Table 3

14-3-3 species GF14b and GF14e client proteins in developing rice grains"

登入号
Accession numbera
蛋白名称
Protein name
细胞定位
Localizationb
预测的磷酸化位点
Predicted phosphorylated sitec
互作结合
Interaction withd
Serine (S) Threonine (T) GF14b GF14e
01 Sugar conversion and starch synthesis
LOC_Os01g44220 ADP-glucose pyrophosphorylase large subunit (AGPL) Chloroplast 0 1 id id
LOC_Os03g28330 Sucrose synthase 1 (SUS1) Cytoplasm 5 4 id id
LOC_Os06g09450 Sucrose synthase 2 (SUS2) Chloroplast 3 4 id id
LOC_Os07g42490 Sucrose synthase 3 (SUS3) Chloroplast 5 5 id id
LOC_Os05g33570 Pyruvate, phosphate dikinase 1 (PPDK1) Chloroplast 5 4 id id
LOC_Os03g31750 Pyruvate, phosphate dikinase 2 (PPDK2) Cytoplasm 7 3 id id
LOC_Os03g55090 Alpha-1,4 glucan phosphorylase (GP) Cytoplasm 12 3 id id
LOC_Os06g51084 1,4-alpha-glucan-branching enzyme (GBE) Chloroplast 12 3 id id
LOC_Os02g32660 Starch branching enzyme (SBE) Chloroplast. 9 2 id id
LOC_Os08g25734 Glucose-1-phosphate adenylyltransferase small subunit (AGPS) Chloroplast 7 1 id id
02 Photosynthesis
LOC_Os01g31690 Oxygen-evolving enhancer protein 1 (OEE1) Chloroplast 3 0 id id
LOC_Os07g04840 PsbP (PSBP) Chloroplast 2 0 id
LOC_Os12g19470 Ribulose bisphosphate carboxylase small chain (RBCS) Chloroplast 4 1 id
LOC_Os10g21268 Ribulose bisphosphate carboxylase large chain (RBCL) Cytoplasm 1 1 id id
LOC_Os12g10580 Ribulose bisphosphate carboxylase large chain (RBCL) Chloroplast 4 2 id
LOC_Os06g04270 Putative transketolase (TK) Chloroplast 7 4 id
03 Glycolysis
LOC_Os01g67860 Fructose-bisphosphate aldolase (FBA) Cytoplasm 4 1 id id
LOC_Os08g02120 Fructokinase-2 (FRK2) Cytoplasm 0 1 id id
LOC_Os05g33380 Fructose-bisphosphate aldolase cytoplasmic isozyme (FBA) Cytoplasm 3 2 id id
LOC_Os03g03720 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) Mitochondrion 0 0 id
LOC_Os08g03290 Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) Mitochondrion 2 2 id id
LOC_Os04g40950 Glyceraldehyde-3-phosphate dehydrogenase 2 (GAPDH2) Mitochondrion 0 2 id id
LOC_Os02g38920 Glyceraldehyde-3-phosphate dehydrogenase 3 (GAPDH3) Cytoplasm 0 2 id id
LOC_Os03g50480 Phosphoglucomutase (PGM) Chloroplast 8 3 id id
LOC_Os06g45710 Phosphoglycerate kinase (PGK) Cytoplasm 3 3 id id
LOC_Os02g07260 Phosphoglycerate kinase (PGK) Mitochondrion 3 4 id id
LOC_Os05g41640 Phosphoglycerate kinase (PGK) Chloroplast 3 1 id id
LOC_Os09g38030 UDP-glucose pyrophosphorylase (UGP) Cytoplasm 3 6 id id
LOC_Os02g02560 UTP--glucose-1-phosphate uridylyltransferase (UGPU) Cytoplasm 5 3 id
04 Amino acid metabolism
LOC_Os01g55540 Aspartate aminotransferase (ASAT) Mitochondrion 2 2 id id
LOC_Os02g14110 Aspartate aminotransferase (ASAT) Chloroplast 1 1 id
LOC_Os10g25130 Alanine aminotransferase (ALAT) Cytoplasm 2 2 id id
LOC_Os12g42876 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 (MLG1) Chloroplast 6 1 id id
登入号
Accession numbera
蛋白名称
Protein name
细胞定位
Localizationb
预测的磷酸化位点
Predicted phosphorylated sitec
互作结合
Interaction withd
Serine (S) Threonine (T) GF14b GF14e
LOC_Os04g55720 D-3-phosphoglycerate dehydrogenase (PGDH) Chloroplast 5 2 id
LOC_Os08g09250 Lactoylglutathione lyase (GLX-I) Cytoplasm 0 1 id
05 nucleotide metabolism
LOC_Os10g41410 Nucleoside diphosphate kinase (NDK) Chloroplast id
06 TCA
LOC_Os10g33800 Malate dehydrogenase (MDH) Cytoplasm 3 1 id id
LOC_Os08g09200 Aconitate hydratase protein (AHP) Chloroplast 5 0 id
07 Fermentation
LOC_Os08g43190 Sorbitol dehydrogenase (SDH) Cytoplasm 4 1 id id
08 Protein synthesis
LOC_Os02g32030 Elongation factor (EF) Nucleus 10 2 id id
LOC_Os01g53900 Elongation factor (EF) Cytoplasm 4 5 id
LOC_Os04g02820 Elongation factor (EF) Nucleus 10 2 id
LOC_Os03g08010 Elongation factor 1-alpha (EFA1) Cytoplasm 2 2 id id
LOC_Os06g37440 Elongation factor 1-gamma 3 (EFG3) Chloroplast id
LOC_Os11g21990 Expressed protein (EP) Nucleus 2 3 id
LOC_Os06g48750 DEAD-box ATP-dependent RNA helicase (DEAD) Nucleus id
LOC_Os01g13430 Importin-alpha re-exporter (IAE) Cytoplasm 30 8 id
LOC_Os09g07510 HEAT repeat family protein (HR) Cytoplasm 9 2 id
LOC_Os08g39140 Heat shock protein 81-1 (HSP81-1) Cytoplasm 5 3 id id
LOC_Os09g30412 Heat shock protein 81-2 (HSP81-2) Cytoplasm 2 2 id id
LOC_Os08g06100 O-methyltransferase 1 (ROMT-9) Cytoplasm 0 2 id id
LOC_Os07g42950 40S ribosomal protein S6 (RPS6) Cytoplasm 6 5 id
LOC_Os02g01280 T-complex protein (TCP) Chloroplast 6 4 id
LOC_Os06g02380 T-complex protein (TCP) Chloroplast 9 3 id
LOC_Os03g64210 T-complex protein (TCP) Chloroplast 0 0 id id
09 Transporters
LOC_Os02g10800 Mitochondrial carrier protein (MCP) Chloroplast 2 2 id
LOC_Os01g25065 Putative ATPase beta subunit (ATPG) Mitochondrion 3 2 id
LOC_Os11g47970 AAA-type ATPase family protein (AAA) Cytoplasm 3 4 id
10 Disease and defense
LOC_Os11g47760 DnaK family protein (DNAK) Cytoplasm 6 7 id id
LOC_Os12g14070 DnaK family protein (DNAK) Chloroplast 7 8 id id
LOC_Os03g16860 DnaK family protein (DNAK) Cytoplasm 6 5 id
LOC_Os02g02410 DnaK family protein (DNAK) Mitochondrion 12 8 id id
LOC_Os08g09770 DnaK family protein (DNAK) Mitochondrion 6 7 id
LOC_Os11g09280 Protein disulfide isomerase-like 1-1 (PDIL1-1) Endoplasmic reticulum 3 3 id
登入号
Accession numbera
蛋白名称
Protein name
细胞定位
Localizationb
预测的磷酸化位点
Predicted phosphorylated sitec
互作结合
Interaction withd
Serine (S) Threonine (T) GF14b GF14e
11 Signal transduction
LOC_Os02g36974 14-3-3-like protein GF14-e (GF14e) Cytoplasm 5 2 id id
LOC_Os03g50290 14-3-3-like protein GF14-f (GF14f) Cytoplasm 2 0 id id
LOC_Os04g38870 14-3-3-like protein GF14-b (GF14b) Cytoplasm 6 2 id id
LOC_Os08g33370 14-3-3-like protein GF14-c (GF14c) Cytoplasm 2 1 id id
LOC_Os08g37490 14-3-3-like protein GF14-a (GF14a) Cytoplasm 2 0 id id
LOC_Os11g34450 14-3-3-like protein GF14-d (GF14d) Cytoplasm 5 1 id
12 Cell growth and division
LOC_Os02g12650 Puromycin-sensitive aminopeptidase (PSA) Cytoplasm 6 2 id
LOC_Os08g30810 Puromycin-sensitive aminopeptidase (PSA) Cytoplasm 5 4 id
LOC_Os02g02890 Peptidyl-prolyl cis-trans isomerase (CYP2) Mitochondrion 3 4 id
LOC_Os01g59790 ADP-ribosylation factor 1 (ARF1) Mitochondrion 0 0 id
LOC_Os03g51600 Tubulin alpha-1 chain (TUBA1) Mitochondrion 6 1 id
LOC_Os05g34170 Tubulin beta-6 chain (TUBB6) Cytoplasm 6 2 id id
LOC_Os06g46000 Tubulin beta-3 chain (TUBB3) Cytoplasm 5 3 id
LOC_Os11g14220 Tubulin alpha-2 chain (TUBA2) Cytoplasm 7 1 id
LOC_Os12g44350 Actin-1 (ACTIN1) Cytoplasm 2 3 id
LOC_Os03g50885 Actin-1 (ACTIN1) Cytoplasm 4 2 id
LOC_Os11g06390 Actin-7 (ACTIN7) Cytoplasm 7 2 id
LOC_Os10g36650 Actin-2 (ACTIN2) Cytoplasm 7 2 id
LOC_Os01g73310 Putative actin (ACTIN) Cytoplasm 5 2 id
LOC_Os05g01600 Actin-97(ACTIN97) Cytoplasm 5 2 id
13 C1-metabolism
LOC_Os09g27420 Formate--tetrahydrofolate ligase (FTL) Chloroplast 10 5 id
LOC_Os06g29180 Formate dehydrogenase 1 (FDH1) Mitochondrion 0 3 id
14 Unknown classification
LOC_Os03g49190 Oleosin 18 kDa (OLE18) Cytoplasm 1 0 id
LOC_Os06g49650 Harpin-induced protein 1 domain containing (HIP1) Nucleus 3 1 id

Fig. 3

GST pull-down validated the identified client proteins of 14-3-3 protein"

Fig. 4

Functional characterization of GF14b and GF14e client proteins"

Fig. 5

Differential analysis between GF14b and GF14e client proteins A: The Venn analysis between GF14b binding proteins and GF14e binding proteins; B: Interaction analysis of respective 14-3-3 isoforms and client proteins. The interaction network was plotted using Cytoscape V3.3. All the abbreviation were showed in Table 3"

Fig. 6

The expression patterns of the GF14b, GF14e and their interacting genes in response to different exogenous hormone treatment"

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