The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin
Abstract
:1. Introduction
2. Results
2.1. Molecular Characterization of the RLCK VI_A2 T-DNA Insertion Mutant and the Transgenic Plants Used in the Study
2.2. The RLCK VI_A2 Kinase Controls Seedling and Plant Growth
2.3. The RLCK VI_A2 Kinase Controls Cell Size
2.4. Gibberellic Acid Treatment Rectifies the rlck vi_a2 Mutant Phenotypes
2.5. The Effect of the rlck vi_a2 Mutation on Gibberellic Acid Level, Synthesis, and Signalling in Seedlings
2.6. Transcriptome Analysis Indicated a Gibberellin-Independent Role for the RLCK VI_A2 Kinase in Skotomorphogenesis
2.7. Transcriptome Analysis Revealed the Role of the RLCK VI_A2 Kinase in Cellular Transport and Cell Wall Organisation
3. Discussion
3.1. The RLCK VI_A Kinases Are Required for Cell Elongation and Organ Growth in Addition to Their Role in Stress Responses
3.2. How the RLCK VI_A2 Kinase May Affect Cell Expansion?
3.3. Gibberellin might Indirectly Complement for the Missing Kinase Function
4. Materials and Methods
4.1. Plant Material and Growth Conditions
4.2. Analysis of Hypocotyl Length and Rosette Size Measurement
4.3. Cell Size and Shape Analysis
4.4. Gibberellin Content Measurement by Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry
4.5. Hormone Treatments
4.6. Characterization of Mutant/Transgenic Plants by RT-PCR
4.7. RNA-Seq and Data Analysis
4.8. Real-Time Quantitative PCR (qRT PCR)
4.9. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ABCB | ATP-binding cassette B protein |
ARF | auxin response factor |
AtHB | Arabidopsis thaliana homeobox-leucine zipper protein |
AtRBK | Arabidopsis thaliana ROP-binding kinase |
BZR | brassinazole-resistant |
DEG | differentially expressed gene |
DELLA | protein domain of the key negative regulators of GA action (DELLA proteins) |
EIR | ethylene insensitivity of the root |
FDR | false discovery rate |
GA | gibberellin |
ga1 | gibberellic acid 1-gibberellin synthesis mutant |
GAI | gibberellic acid-insensitive protein |
GAPC-2 | glyceraldehyde 3-phosphate dehydrogenase C-2 |
GO | gene ontology |
GRAS | GA INSENSITIVE (GAI), REPRESSOR of ga1-3 (RGA), and SCARECROW (SCR) protein domain |
GTP | guanosine-5’-triphosphate |
HvRBK | Hordeum vulgare ROP-binding kinase |
LAX | Like auxin1 |
MtRRK1 | Medicago truncatula ROP-activated Receptor-like Kinase 1 |
NPF | NRT1/PTR family |
NRT | nitrate transporter |
PCR | polymerase chain reaction |
PIF | phytochrome interacting factor |
PIN | PINNOID protein |
PTR | peptide transporter |
RLCK | receptor-like cytoplasmic kinase |
RLK | receptor-like kinase |
ROP | Rho-of-plants |
SD | short day |
T-DNA | transfer-DNA |
TF | transcription factor |
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GO Term | Ontology | Description | p-Value | FDR |
---|---|---|---|---|
GO:0050896 | P | response to stimulus | 8.6 × 10−66 | 2.7 × 10−63 |
GO:0006950 | P | response to stress | 1.4 × 10−47 | 2.2 × 10−45 |
GO:0009605 | P | response to external stimulus | 1.8 × 10−36 | 2.00 × 10−34 |
GO:0009607 | P | response to biotic stimulus | 1.9 × 10−29 | 1.6 × 10−27 |
GO:0009628 | P | response to abiotic stimulus | 1.2 × 10−27 | 7.4 × 10−26 |
GO:0051704 | P | multi-organism process | 2.2 × 10−24 | 1.2 × 10−22 |
GO:0009719 | P | response to endogenous stimulus | 8.1 × 10−24 | 3.7 × 10−22 |
GO:0019748 | P | secondary metabolic process | 2.6 × 10−20 | 1.00 × 10−18 |
GO:0007154 | P | cell communication | 3.7 × 10−15 | 1.3 × 10−13 |
GO:0009056 | P | catabolic process | 6.3 × 10−12 | 2.00 × 10−10 |
GO:0007165 | P | signal transduction | 2.8 × 10−11 | 8.3 × 10−10 |
GO:0009987 | P | cellular process | 2.7 × 10−10 | 7.2 × 10−9 |
GO:0008152 | P | metabolic process | 2.2 × 10−9 | 5.4 × 10−8 |
GO:0051179 | P | localization | 3.3 × 10−9 | 7.6 × 10−8 |
GO:0009991 | P | response to extracellular stimulus | 1.5 × 10−8 | 3.1 × 10−7 |
GO:0006629 | P | lipid metabolic process | 2.1 × 10−8 | 4.1 × 10−7 |
GO:0006810 | P | transport | 3.2 × 10−8 | 6.1 × 10−7 |
GO:0051234 | P | establishment of localization | 4.7 × 10−8 | 8.4 × 10−7 |
GO:0005975 | P | carbohydrate metabolic process | 2.2 × 10−7 | 3.7 × 10−6 |
GO:0008219 | P | cell death | 7.9 × 10−6 | 0.00013 |
GO:0065008 | P | regulation of biological quality | 2.00 × 10−5 | 0.00031 |
GO:0065007 | P | biological regulation | 2.7 × 10−5 | 0.00039 |
GO:0042592 | P | homeostatic process | 5.6 × 10−5 | 0.00078 |
GO:0040007 | P | growth | 0.0009 | 0.012 |
GO:0009606 | P | tropism | 0.0011 | 0.014 |
GO:0032502 | P | developmental process | 0.0017 | 0.021 |
GO:0050789 | P | regulation of biological process | 0.002 | 0.024 |
GO:0050794 | P | regulation of cellular process | 0.0025 | 0.029 |
GO:0048856 | P | anatomical structure development | 0.0038 | 0.042 |
GO:0003824 | F | catalytic activity | 1.3 × 10−25 | 1.3 × 10−23 |
GO:0005215 | F | transporter activity | 4.2 × 10−9 | 2.1 × 10−7 |
GO:0016740 | F | transferase activity | 1.9 × 10−8 | 6.4 × 10−7 |
GO:0008289 | F | lipid binding | 1.2 × 10−7 | 3.00 × 10−6 |
GO:0030246 | F | carbohydrate binding | 5.7 × 10−6 | 0.00012 |
GO:0016787 | F | hydrolase activity | 1.2 × 10−5 | 0.0002 |
GO:0019825 | F | oxygen binding | 1.9 × 10−5 | 0.00027 |
GO:0016301 | F | kinase activity | 2.5 × 10−5 | 0.00032 |
GO:0000166 | F | nucleotide binding | 0.00014 | 0.0016 |
GO:0005488 | F | binding | 0.00021 | 0.0021 |
GO:0060089 | F | molecular transducer activity | 0.00041 | 0.0034 |
GO:0004872 | F | receptor activity | 0.00041 | 0.0034 |
GO:0016772 | F | transferase activity, transferring phosphorus-containing groups | 0.0012 | 0.009 |
GO:0005576 | C | extracellular region | 8.6 × 10−37 | 1.6 × 10−34 |
GO:0030312 | C | external encapsulating structure | 6.7 × 10−34 | 4.2 × 10−32 |
GO:0005618 | C | cell wall | 6.7 × 10−34 | 4.2 × 10−32 |
GO:0005886 | C | plasma membrane | 7.5 × 10−32 | 3.5 × 10−30 |
GO:0016020 | C | membrane | 1.3 × 10−25 | 4.9 × 10−24 |
GO:0005773 | C | vacuole | 4.1 × 10−5 | 0.0013 |
GO:0005783 | C | endoplasmic reticulum | 8.8 × 10−5 | 0.0023 |
GO:0012505 | C | endomembrane system | 0.0018 | 0.043 |
Gene_ID | Annotation | Fold Change | q_Value | Significant |
---|---|---|---|---|
DEGs Implicated in GA Metabolism/Response * | ||||
AT1G26960 | AtHB23 homeobox protein 23 | 2.25 | 0.026242 | yes |
AT1G74670 | GASA6 Gibberellin-regulated family protein | 2.07 | 0.001941 | yes |
AT2G37640 | EXP3 Barwin-like endoglucanases superfamily protein | 1.95 | 0.001941 | yes |
AT5G15230 | GASA4 GAST1 protein homolog 4 | 1.88 | 0.001941 | yes |
AT2G14900 | AT2G14900 Gibberellin-regulated family protein | 1.70 | 0.001941 | yes |
AT1G14920 | GAI GRAS family transcription factor family protein | 1.46 | 0.00859 | yes |
AT3G11280 | AT3G11280 Duplicated homeodomain-like superfamily protein | 0.69 | 0.00859 | yes |
AT4G19700 | RING SBP (S-ribonuclease binding protein) family protein | 0.68 | 0.038936 | yes |
AT1G75750 | GASA1 GAST1 protein homolog 1 | 0.56 | 0.003506 | yes |
AT5G44610 | MAP18 microtubule-associated protein 18 | 0.55 | 0.001941 | yes |
AT1G02400 | GA2OX6 gibberellin 2-oxidase 6 | 0.58 | 0.044627 | yes |
DEGs of NPF (NRT1/PTR FAMILY) Gibberellin Transporters ** | ||||
AT1G52190 | AT1G52190 Major facilitator superfamily protein, NPF1.2 a,b | 1.60 | 0.001941 | yes |
AT3G16180 | AT3G16180 Major facilitator superfamily protein, NPF 1.1 a | 1.79 | 0.001941 | yes |
AT5G46050 | PTR3 peptide transporter 3, NPF 5.2 a | 0.55 | 0.001941 | yes |
AT5G62680 | GTR2 Major facilitator superfamily protein, NPF 2.11 c | 0.65 | 0.031474 | yes |
DEGs of DELLA Transcription Regulators *** | ||||
AT1G14920 | GAI GRAS family transcription factor family protein | 1.46 | 0.00859 | yes |
AT2G01570 | RGL1 RGA-like 1 | 1.25 | 0.483175 | no |
AT1G66350 | RGA1 GRAS family transcription factor family protein | 1.11 | 0.773976 | no |
AT3G03450 | RGL2 RGA-like 2 | 1.58 | 0.496428 | no |
AT5G17490 | RGL3 RGA-like protein 3 | 1.21 | 0.819669 | no |
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Valkai, I.; Kénesi, E.; Domonkos, I.; Ayaydin, F.; Tarkowská, D.; Strnad, M.; Faragó, A.; Bodai, L.; Fehér, A. The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin. Int. J. Mol. Sci. 2020, 21, 7266. https://doi.org/10.3390/ijms21197266
Valkai I, Kénesi E, Domonkos I, Ayaydin F, Tarkowská D, Strnad M, Faragó A, Bodai L, Fehér A. The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin. International Journal of Molecular Sciences. 2020; 21(19):7266. https://doi.org/10.3390/ijms21197266
Chicago/Turabian StyleValkai, Ildikó, Erzsébet Kénesi, Ildikó Domonkos, Ferhan Ayaydin, Danuše Tarkowská, Miroslav Strnad, Anikó Faragó, László Bodai, and Attila Fehér. 2020. "The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin" International Journal of Molecular Sciences 21, no. 19: 7266. https://doi.org/10.3390/ijms21197266