Genetic analysis of SnRK1β3 subunit of peach and the functional identification of overexpression transformed tomato

Zhao, Shilong1

Published Aug 30, 2024 on Dryad. https://doi.org/10.5061/dryad.6djh9w19t

Data files

Aug 30, 2024 version files 3.07 MB

a-BD-1.ab1

315.78 KB
a-BD-2.ab1

308.47 KB
a-bifc-1.ab1

304 KB
a-bifc-2.ab1

306.36 KB
a-nluc-1.ab1

304.92 KB
a-nluc-2.ab1

315.82 KB
b3-AD.ab1

307.41 KB
b3-bifc.ab1

294.46 KB
b3-cluc.ab1

292.82 KB
b3-GFP.ab1

307.41 KB
CDS-α-DNA.fa

1.61 KB
CDS-β3-DNA.fa

372 B
Evolutionary_tree_proteins.fa

1.83 KB
Physiological_data.txt

2.14 KB
README.md

3.72 KB

Abstract

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.

README: Genetic analysis of SnRK13 subunit of peach and the functional identification of overexpression transformed tomato

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).

CDS-β3-DNA.fa

PpSnRK1β3 (Prupe.6G107300) cds from the NCBI database (https://www.ncbi.nlm.nih.gov).

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).

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 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.

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.

Methods

Phylogenetic tree analysis

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].

Yeast two-hybrid (Y2H) assay

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.

Bimolecular fluorescence complementation (BiFC) assay

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.

Dual luciferase assay

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].

Acquisition and experimental treatment of overexpressed tomato material

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.

Determination of chlorophyll content

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].

Determination of photosynthetic parameters

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].

Measurement of MDA, H2O2, O2− ,relative electrolyte leakage

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].

References

1. Kumar S, Stecher G, Tamura K: **MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets.*** Molecular biology and evolution* 2016; **33**(7):1870-1874.

2. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL: **The Pfam protein families database.** *Nucleic acids research* 2004; **32**(suppl_1):D138-D141.

3. Liang J, Pan Y, Li Y, Fang F, Wu K, You J: **Genetic diversity assessment of Saccharum species and elite cultivars from China using SSR markers.** *Guihaia* 2010; **30**(5):594-600.

4. Yang Y, An X, Rui L, Liu G, Tian Y, You C, Wang X: **MdSnRK1. 1 interacts with MdGLK1 to regulate abscisic acid-mediated chlorophyll accumulation in apple. ***Horticulture Research* 2024; **11**(2):uhad288.

5. Kerppola TK: **Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells.** *Annu. Rev. Biophys.* 2008; **37**(1):465-487.

6. Goel D, Singh A K, Yadav V, Babbar SB, Bansal KC: **Overexpression of osmotin gene confers tolerance to salt and drought stresses in transgenic tomato (Solanum lycopersicum L.).** *Protoplasma* 2010; **245**:133-141.

7. Ahmad MA, Javed R, Adeel M, Rizwan M, Yang Y: **PEG 6000-stimulated drought stress improves the attributes of in vitro growth, steviol glycosides production, and antioxidant activities in Stevia rebaudiana Bertoni.***Plants* 2020;**9**(11):1552

8. Gao T, Zhang Z, Liu X, Wu Q, Chen Q, Liu Q, van Nocker S, Ma F, Li C: **Physiological and transcriptome analyses of the effects of exogenous dopamine on drought tolerance in apple. ***Plant Physiology and Biochemistry* 2020; **148**:260-272.

9. Uddling J, Gelang-Alfredsson J, Piikki K, Pleijel H: **Evaluating the relationship between leaf chlorophyll concentration and SPAD-502 chlorophyll meter readings.** *Photosynthesis research* 2007; **91**:37-46.

10. Ye L, Gao H, Zou Q: **Responses of the antioxidant systems and xanthophyll cycle in Phaseolus vulgaris to the combined stress of high irradiance and high temperature.** *Photosynthetica* 2000; **38**:205-210.

11. Ma Q, Sun M, Lu J, Liu Y, You C, Hao Y: **An apple CIPK protein kinase targets a novel residue of AREB transcription factor for ABA-dependent phosphorylation.** *Plant Cell Environment* 2017; **40**:2207–2219.

12. Hu W, Huang C, Deng X, Zhou S, Chen L, Li Y, Wang C, Ma Z, Yuan Q, Wang Y: **TaASR1, a transcription factor gene in wheat, confers drought stress tolerance in transgenic tobacco.** *Plant Cell Environment* 2013; **36**:1449–1464.

13. Xiao Y, Wu X, Sun M, Peng F: **Hydrogen sulfide alleviates waterlogging-induced damage in peach seedlings via enhancing antioxidative system and inhibiting ethylene synthesis.** *Frontiers in plant science* 2020; **11**:696.