Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress
Abstract
:1. Introduction
2. Results
2.1. Effects of NaCl Concentrations on Growth and Development of R. soongorica Seedling
2.2. De Novo Assembly and Annotation of the R. soongorica Transcriptome
2.3. Transcriptome Data Profiling of R. soongorica Leaves
2.4. Proteomic Data Profiling of R. soongorica Leaves
2.5. Transcriptomic and Proteomic Association Analysis
3. Materials and Methods
3.1. Experimental Materials and Treatment
3.2. Determination of Morphological and Physiological Indicators
3.3. RNA Sample Preparation and Transcriptome Analyses
3.4. Protein Sample Preparation and Proteomic Analysis
3.5. Statistical and Bioinformatic Analysis
3.6. Integrative Transcriptome-Proteome Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Growth Index | NaCl Concentration (mM·L−1) | Treatment Time/h | |||
---|---|---|---|---|---|
24 | 72 | 144 | 216 | ||
Plant height (cm) | 0 | 9.42 ± 0.231 a | 10.33 ± 0.207 bc | 10.86 ± 0.210 c | 12.87 ± 0.378 c |
100 | 9.77 ± 0.061 a | 10.79 ± 0.096 b | 11.12 ± 0.253 bc | 13.45 ± 0.258 b | |
200 | 9.97 ± 0.558 a | 11.37 ± 0.252 a | 11.78 ± 0.491 a | 14.40 ± 0.150 a | |
300 | 9.70 ± 0.387 a | 10.07 ± 0.113 c | 11.50 ± 0.452 ab | 12.46 ± 0.314 c | |
400 | 9.55 ± 0.444 a | 10.12 ± 0.150 c | 10.73 ± 0.111 c | 11.23 ± 0.469 d | |
500 | 9.35 ± 0.229 a | 9.54 ± 0.611 d | 10.10 ± 0.155 d | 10.59 ± 0.213 e | |
Root length (cm) | 0 | 8.60 ± 0.200 bc | 9.53 ± 0.368 ab | 10.42 ± 0.187 a | 11.27 ± 0.436 a |
100 | 8.85 ± 0.141 ab | 9.82 ± 0.104 a | 10.17 ± 0.262 ab | 10.98 ± 0.366 ab | |
200 | 9.20 ± 0.586 a | 9.92 ± 0.295 a | 10.06 ± 0.213 abc | 10.53 ± 0.530 bc | |
300 | 9.40 ± 0.305 a | 9.65 ± 0.202 ab | 9.82 ± 0.369 bc | 9.97 ± 0.337 cd | |
400 | 8.42 ± 0.092 bc | 9.2 ± 0.162 bc | 9.51 ± 0.413 cd | 9.74 ± 0.114 d | |
500 | 8.15 ± 0.218 c | 8.78 ± 0.144 c | 9.04 ± 0.291 d | 9.36 ± 0.240 d |
Accession Number | Gene Name | Gene Log2 Value | Up/ Down | Protein Fold Change | Up/ Down | Protein Description |
---|---|---|---|---|---|---|
D3THI6 | UGT71A15 | −1.75 | down | 0.51 | down | UDP-glycosyltransferase 71A15 |
Q9ZSA7 | DLO2 | −1.93 | down | 0.53 | down | Protein DMR6-LIKE OXYGENASE 2 |
O24370 | LOX2.1 | −2.15 | down | 0.53 | down | Linoleate 13S-lipoxygenase 2-1, chloroplastic |
Q7X999 | RCA2 | −1.58 | down | 0.57 | down | Ribulose bisphosphate carboxylase/oxygenase activase 2, chloroplastic |
Q8L5A7 | SOT15 | −2.36 | down | 0.58 | down | Cytosolic sulfotransferase 15 |
O49675 | CCD4 | −3.34 | down | 0.58 | down | Probable carotenoid cleavage dioxygenase 4, chloroplastic |
P49107 | PSAN | −1.86 | down | 0.59 | down | Photosystem I reaction center subunit N, chloroplastic |
P27522 | CAB8 | −1.17 | down | 0.59 | down | Chlorophyll a-b binding protein 8, chloroplastic |
P20152 | Vim | −2.17 | down | 0.60 | down | Vimentin |
K4BW79 | EO | −3.53 | down | 0.61 | down | 2-methylene-furan-3-one reductase |
Q9LR64 | PSB27-1 | −1.11 | down | 0.61 | down | Photosystem II repair protein PSB27-H1, chloroplastic |
Q9SQT8 | EMB3004 | −2.39 | down | 0.64 | down | Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic |
Q9SSK9 | MLP28 | −4.00 | down | 0.65 | down | MLP-like protein 28 |
Q9ZQI8 | LTPG12 | −2.27 | down | 0.66 | down | Non-specific lipid-transfer protein-like protein At2g13820 |
P11432 | ELIP | 2.88 | up | 1.51 | up | PEA early light-induced protein, chloroplastic |
O49432 | QRT3 | 1.51 | up | 1.52 | up | Polygalacturonase QRT3 |
Q9XJ57 | CHS2 | 1.20 | up | 1.53 | up | Chalcone synthase 2 |
Q9SF29 | SYP71 | 1.03 | up | 1.56 | up | Syntaxin-71 |
Q9SR86 | At3g08860 | 2.16 | up | 1.60 | up | Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial |
Q8L856 | CYB561A | 1.01 | up | 1.63 | up | Transmembrane ascorbate ferrireductase 1 |
Q08507 | ACO3 | 1.09 | up | 1.64 | up | 1-aminocyclopropane-1-carboxylate oxidase 3 |
Q6Z1G7 | Os08g42410 | 1.20 | up | 1.65 | up | Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial |
Q94JX5 | WLIM1 | 1.10 | up | 1.73 | up | LIM domain-containing protein WLIM1 |
Q9SXA6 | ENDO1 | 1.79 | up | 1.78 | up | Endonuclease 1 |
P53800 | FDFT | 1.02 | up | 1.84 | up | Squalene synthase |
A6QP05 | DHRS12 | 1.28 | up | 1.90 | up | Dehydrogenase/reductase SDR family member 12 |
Q04980 | LTI65 | 1.61 | up | 2.12 | up | Low-temperature-induced 65 kDa protein |
P22242 | PCC13-62 | 3.90 | up | 2.26 | up | Desiccation-related protein PCC13-62 |
Q8LPS2 | ACD6 | 6.09 | up | 2.51 | up | Protein ACCELERATED CELL DEATH 6 |
Q94BZ1 | ZIFL1 | 2.80 | up | 2.79 | up | Protein ZINC-INDUCED FACILITATOR-LIKE 1 |
Q55874 | sll0103 | 10.12 | up | 3.03 | up | Uncharacterized protein sll0103 |
O80433 | CS | 1.01 | up | 3.89 | up | Citrate synthase, mitochondrial |
No | Gene Name | Protein Description | KEGG Pathway | Pathway ID |
---|---|---|---|---|
1 | LOX2.1 | Linoleate 13S-lipoxygenase 2-1, chloroplastic | Linoleic acid metabolism | ko00591 |
2 | LOX2.1 | Linoleate 13S-lipoxygenase 2-1, chloroplastic | alpha-Linolenic acid metabolism | ko00592 |
3 | CCD4 | Probable carotenoid cleavage dioxygenase 4, chloroplastic | Carotenoid biosynthesis | ko00906 |
4 | PSAN | Photosystem I reaction center subunit N, chloroplastic | Photosynthesis | ko00195 |
5 | CAB8 | Chlorophyll a-b binding protein 8, chloroplastic | Photosynthesis—antenna proteins | ko00196 |
6 | PSB27-1 | Photosystem II repair protein PSB27-H1, chloroplastic | Photosynthesis | ko00195 |
7 | EMB3004 | Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic | Phenylalanine, tyrosine, and tryptophan biosynthesis | ko00400 |
8 | CHS2 | Chalcone synthase 2 | Flavonoid biosynthesis | ko00941 |
9 | CHS2 | Chalcone synthase 2 | Tropane, piperidine, and pyridine alkaloid biosynthesis | ko00960 |
10 | SYP71 | Syntaxin-71 | SNARE interactions in vesicular transport | ko04130 |
11 | At3g08860 | Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial | Alanine, aspartate and glutamate metabolism | ko00250 |
12 | At3g08860 | Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial | Glycine, serine and threonine metabolism | ko00260 |
13 | At3g08860 | Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial | Cysteine and methionine metabolism | ko00270 |
14 | At3g08860 | Alanine--glyoxylate aminotransferase 2 homolog 3, mitochondrial | Valine, leucine and isoleucine degradation | ko00280 |
15 | ACO3 | 1-aminocyclopropane-1-carboxylate oxidase 3 | Cysteine and methionine metabolism | ko00270 |
16 | Os08g42410 | Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial | Glycolysis / Gluconeogenesis | ko00010 |
17 | Os08g42410 | Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial | Citrate cycle (TCA cycle) | ko00020 |
18 | Os08g42410 | Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial | Pyruvate metabolism | ko00620 |
19 | FDFT | Squalene synthase | Steroid biosynthesis | ko00100 |
20 | CS | Citrate synthase, mitochondrial | Citrate cycle (TCA cycle) | ko00020 |
21 | CS | Citrate synthase, mitochondrial | Glyoxylate and dicarboxylate metabolism | ko00630 |
22 | LOX2.1 | Linoleate 13S-lipoxygenase 2-1, chloroplastic | Linoleic acid metabolism | ko00591 |
Gene Name | Gene Up/ Down | Protein Up/ Down | Protein Description | Role |
---|---|---|---|---|
PSAN | down | down | Photosystem I reaction center subunit N, chloroplastic | PSAN is a PSI-related gene, and salt stress significantly reduces the photochemical activity of PSI and decreases photosynthetic efficiency. This results in the down-regulation of the PSAN gene and protein expression. |
CHS2 | up | up | Chalcone synthase 2 | Up-regulates CHS2 gene and protein expression and increases secondary metabolites to reduce salt damage. |
SYP71 | up | up | Syntaxin-71 | Under salt stress, to ensure the smooth closure of ion channels and transporters on the plasma membrane and the separation of harmful ions during vesicular transport. By up-regulating the expression of the SYP71 gene and protein, which is involved in the vesicular transport pathway in leaf cells, the effect of Na+ and related ions on the growth of R. soongorica was mitigated. |
PCC13-62 | up | up | Desiccation-related protein PCC13-62 | The high osmotic effect of salt stress induces physiological drought in the plant root system, and the effect of salt stress on the growth of R. soongorica is mitigated by the up-regulation of the PCC13-62 gene and protein expression. |
ZIFL1 | up | up | Protein ZINC-INDUCED FACILITATOR-LIKE 1 | Enhanced growth hormone distribution and signaling to regulate R. soongorica’s response to salt stress by up-regulating the ZIFL1 gene and protein expression. |
CS | up | up | Citrate synthase, mitochondrial | CS is a core enzyme of the mitochondrial tricarboxylic acid cycle, which is an organic acid that regulates the tricarboxylic acid cycle and directly controls cellular functions. By up-regulating the expression of the CS gene and protein, the adaptation of plant cells to salt stress was improved with various metabolic processes. |
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Liu, H.; Chong, P.; Yan, S.; Liu, Z.; Bao, X.; Tan, B. Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress. Plants 2023, 12, 3542. https://doi.org/10.3390/plants12203542
Liu H, Chong P, Yan S, Liu Z, Bao X, Tan B. Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress. Plants. 2023; 12(20):3542. https://doi.org/10.3390/plants12203542
Chicago/Turabian StyleLiu, Hanghang, Peifang Chong, Shipeng Yan, Zehua Liu, Xinguang Bao, and Bingbing Tan. 2023. "Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress" Plants 12, no. 20: 3542. https://doi.org/10.3390/plants12203542