DOI: 10.5061/dryad.6djh9w19t
title: Genetic analysis of SnRK1β3 subunit of peach and the functional identification of overexpression transformed tomato

description: The sucrose non-fermentation-related kinase 1 (SnRK1) protein complex in
 plants plays an important role in energy metabolism, anabolism, growth,
 and stress resistance. This protein complex typically consists of an α
 subunit, three β subunits, one or two βγ subunits, and a γ subunit.
 Studies on plant SnRK1 have primarily focused on the functional α subunit,
 with the β regulatory subunit remaining relatively unexplored. The present
 study aimed to elucidate the evolutionary relationship, structural
 prediction, and interaction with the core α subunit of peach SnRK1β3
 (PpSnRK1) subunit. In addition, we produced transgenic tomato plants
 overexpressing PpSnRK1 (OEPpSnRK1). We mainly tested the growth index and
 drought resistance of transgenic tomato plants.The results showed that
 PpSnRK1 has a 354 bp encoded protein sequence (cds), which is mainly
 located in the nucleus and cytoplasm. Phylogenetic tree analysis showed
 that PpSnRK1β3 has similar domains to other woody plants. Transcriptome
 analysis of OEPpSnRK1β3 showed that PpSnRK1β3 is widely involved in plant
 physiological regulation processes and stress response. Functional
 analyses of these transgenic plants revealed prolonged growth periods,
 enhanced growth potential, improved photosynthetic activity and superior
 drought stress tolerance.
description: <em>Phylogenetic tree analysis</em>
   Protein sequences of SnRK1β3 were
 gathered from the NCBI database for 14 plant species
 ([https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/)), which
 included *Arabidopsis thaliana*,* Populus trichocarpa*,* Prunus persica*,*
 Vitis vinifera*,* Malus domestica*,* Prunus avium*,* Ananas comosus*,*
 Nicotiana attenuata*,* Carya illinoinensis*,* Durio zibethinus*,*
 Mangifera indica*,* Pyrus x bretschneideri*,* Triticum aestivum*, and
 *Gossypium hirsutum*. These sequences were analyzed using MEGA7 software
 to construct an evolutionary tree using the neighbor-joining method with
 1000 bootstrap copies [1]. Structural domains were analyzed using Pfam
 ([http://pfam-legacy.xfam.org/](http://pfam-legacy.xfam.org/)) [2].
 Protein sequence alignment was performed using DNAMAN software
 [3].   <em>Yeast
 two-hybrid (Y2H) assay</em>  
 The PpSnRK1α cds was cloned into the PGBKT7 vector, and the cds
 of PpSnRK1β3 was cloned into the PGADT7 vector (Primers: Table S2). These
 two vectors were transformed together into Y2H gold yeast strain and
 cultured on SD/−T-L (−Leu/−Trp) and SD/−T-L-H-A (−Leu/−Trp/-His/−Ade)
 selective medium and incubated at 28°C for two days. The strong
 interaction genes PGBKT7-53 and PGADT7-T were transformed as positive
 controls, and PGBKT7-α and PGADT7 empty vectors, PGADT7-β3 and PGBKT7
 empty vectors and two empty vectors were used as negative controls [4].
 The yeast spots on the two-defect medium were diluted with ddH2O by 10−1,
 10−2, 10−3 fold to the four-defect medium to observe the growth of the
 yeast.  
 <em>Bimolecular fluorescence complementation (BiFC)
 assay</em>   The cds
 of PpSnRK1α was cloned into the YC vector and PpSnRK1β3 was cloned into
 the YN vector (Primers: Table S2). The two vectors were mixed, transferred
 to Agrobacterium GV3101, and injected into the leaves of *Nicotiana
 benthamiana*. The PpSnRK1α-YC with YN empty vectors and PpSnRK1β3-YN with
 YC empty vectors were used as negative controls [5]. Fluorescence within
 the tobacco cells was observed using laser confocal microscopy (LSM880,
 Zeiss, Germany) after two days of dark treatment. DAPI indicated the
 location of the nucleus, and the mixed field was composed of bright field,
 YFP fluorescence field, and DAPI field.
   <em>Dual luciferase
 assay</em>   The
 coding sequences of PpSnRK1α and PpSnRK1β3 were cloned into the pGreenII
 0800-nLUC vector and the pGreenII 0800-cLUC vector (Primers: Table S2).
 Negative controls included the PpSnRK1β3-CLUC and NLUC empty vectors, as
 well as the PpSnRK1α-NLUC and CLUC empty vectors, along with the empty
 NLUC and CLUC vectors. These vectors were introduced into Agrobacterium
 GV3101 and delivered into the leaves of Nicotiana benthamiana. Following a
 3-day incubation period, fluorescence was visualized using a fluorescence
 microscope (AXIO, Zeiss, Germany) [4].
   <em>Acquisition and experimental
 treatment of overexpressed tomato material</em>
   The cds of PpSnRK1β3 was cloned into
 the Pri101 vector and transformed into *Agrobacterium* GV3101. Based on
 the method of *Goel D et al. *[6], the stem segments of tomato were
 infected with *Agrobacterium*, and the transgenic T0 generation plants
 were obtained in symbiotic medium, differentiation medium and rooting
 medium . After two generations of screening and typing, the T2 generation
 of overexpressing PpSnRK1β3-1, PpSnRK1β3-2 and PpSnRK1β3-3 strains was
 obtained.   In 2024, the
 experiments were conducted at Shandong Agricultural University's
 experimental base in Tai’an City, Shandong Province, China (36◦170 745900
 N,117◦160 771200 E). Each T2 generation tomato was planted in a plastic
 black square 8.5 cm× 6 cm × 8 cm pot, mixed with substrate at a peat
 soil:vermiculite =ratio of 1:1, and cultivated in the tissue culture
 laboratory under light:darkness = 16 h:8 h conditions.
   Transgenic and wild-type tomatoes with
 consistent growth at the seedling stage were selected for transcriptome
 sequencing and the determination of physiological indicators. Transgenic
 and wild-type tomatoes were treated with 4% PEG-6000 to simulate a drought
 environment for 14 days, and the tomatoes without drought treatment were
 used as the control [7]. Physiological indicators of the tomatoes under
 stress in each group were measured.  
 <em>Determination of chlorophyll
 content</em>   Samples
 of fresh, clean peach leaves (0.2 g) were extracted for 24 h in a 95%
 ethanol solution. The extract was analyzed using a Pharma-Spec UC-2450
 ultraviolet spectrophotometer from Shimadzu (Kyoto, Japan) at OD665,
 OD649, and OD470. These measurements were used to calculate the
 chlorophyll content of the leaves [8].
   <em>Determination of
 photosynthetic parameters</em>  
 The net photosynthetic rate (Pn) was recorded using a CIRAS-3
 portable photosynthetic system (PP Systems, Massachusetts, USA) under
 light conditions [69]. A SPAD chlorophyll instrument (spad-502,
 Hanshatech, China) was used to determine the leaf SPAD value [9]. The
 leaves were darkened for 30 min and then the Fv/Fm ratio was determined
 using a hand-held leaf fluorometer (Handy PEA, Hanshatech, China)
 [10].  
 <em>Measurement of MDA, H2O2, O2− ,relative electrolyte
 leakage</em>   The
 malondialdehyde (MDA) content of the tomatoes was measured using the
 thiobarbituric acid (TBA) method [11]. The relative electrolyte leakage of
 the tomatoes was assessed using a DDS-12 conductometer (Hangzhou Wanda
 Instrument Factory, Hangzhou, China) [12].In addition, the hydrogen
 peroxide content in the tomato leaves was determined by the
 trichloroacetic acid (TCA) method, the superoxide anion content of the
 tomato leaves was measured using the sulfonamide colorimetric method
 [13].  
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description: # Genetic analysis of SnRK13 subunit of peach and the functional
 identification of overexpression transformed tomato
 [https://doi.org/10.5061/dryad.6djh9w19t](https://doi.org/10.5061/dryad.6djh9w19t) ## Description of the data and file structure The files uploaded for this assay include sequencing files (*b3-bifc.ab1*, *a-bifc-2.ab1*, *a-nluc-1.ab1*, *b3-cluc.ab1*, *a-nluc-2.ab1*, *a-bifc-1.ab1*, *a-BD-1.ab1*, *a-BD-2.ab1*, *b3-AD.ab1*,*b3-GFP.ab1*), sequence files (*CDS-α-DNA.fa*, *CDS-β3-DNA.fa*, *Evolutionary tree proteins.fa*) and phenotypic raw data file (*Physiological data.txt*). **b3-bifc.ab1, a-bifc-2.ab1,a-bifc-1.ab1** Sequencing results of PpSnRK1α and PpSnRKβ3 interaction construction vectors identified by Bifc assay (sequence + peak plots). **a-nluc-1.ab1,a-nluc-2.ab1,b3-cluc.ab1** Sequencing results of PpSnRK1α and PpSnRKβ3 interaction construction vectors identified by Dual luciferase assay (sequence + peak plots). **a-BD-1.ab1, a-BD-2.ab1,b3-AD.ab1** Sequencing results of PpSnRK1α and PpSnRKβ3 interaction construction vectors identified by Yeast two-hybrid assay (sequence + peak plots). **b3-GFP.ab1** Sequencing results of the overexpression vector PpSnRKβ3-GFP (sequence + peak plots). **CDS-α-DNA.fa**  PpSnRK1α(Prupe.3G262900) cds from the NCBI database ([https://www.ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov/gene/18773156)). **CDS-β3-DNA.fa** PpSnRK1β3 (Prupe.6G107300) cds from the NCBI database ([https://www.ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov/gene/18773156)). **Evolutionary tree proteins.fa** For phylogenetic tree construction, we selected PpSnRK1β3 along with several other plant-encoded proteins:AtSnRK1β3(NP_001323590.1),PtSnRK1β3(XP_006384933.1),PpSnRK1β3(XP_006384933.1),VvSnRK1β3(XP_019076263.1),MdSnRK1β3(XP_008359553.1),PaSnRK1β3(XP_021812278.1),AcSnRK1β3(XP_020085356.1),NaSnRK1β3(XP_019255734.1),CiSnRK1β3(XP_042955180.1),MiSnRK1β3(XP_044506124.1),DzSnRK1β3(XP_022732265.1),PbSnRK1β3(XP_048444836.1),TaSnRK1β3(XP_044447578.1),GhSnRK1β3(XP_016748682.2) from the NCBI database ([https://www.ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov/gene/18773156)). **Physiological data.txt** The role of PpSnRK1β3 in tomato plants was explored by introducing the coding sequences seqences that encode protein into stem segments infected with the Pri-101 vector. We compared the phenotypic differences of overexpressing PpSnRK1β3 (OEPpSnRK1β3) with WT tomatoes. Comparison of plant height, stem diameter, leaf area, number of days in the growth period for three strains of OEPpSnRK1β3 and WT tomatoes. Comparison of maximum net photosynthetic efficiency, chlorophyll content, stomatal conductance , intercellular carbon dioxide concentration for three strains of OEPpSnRK1β3 and WT tomatoes. The state of OEPpSnRK1β3 and WT tomatoes under normal and 14-day drought stress. Comparison of maximum photochemical efficiency , malondialdehyde content , hydrogen peroxide content, superoxide anion content , relative electrolyte leakage for three strains of OEPpSnRK1β3 and WT tomatoes under normal and 14-day drought stress conditions. ### Software Sequencing data in ab1 format can be downloaded for viewing on Snapgene Software ([https://www.snapgene.com/).Import](https://www.snapgene.com/\).Import) the target sequences queried on the NCBI database, and then select aligned sequences in the toolbar to import the sequencing data, and the two can be compared. ### Version changes **23-Se**p**-2024  **The phenotypic data H2O2 content and O2- content data were uploaded incorrectly，the data was re-uploaded. **10-Nov-2024 **Phenotypic data: Due to the phenotypic identification of some of the same indicators at the same time in our different transgenic materials, some data were uploaded incorrectly. Through identification, we updated the plant height, stem base width, and SPAD value data of overexpressed tomatoes.The chlorophyll content data uploaded in the previous version is actually chlorophyll a content, and the total chlorophyll content data has been updated. ## Access information Other publicly accessible locations of the data: * None Data was derived from the following sources: * Genetic analysis of SnRK13 subunit of peach and the functional identification of overexpression transformed tomato.