A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses
Abstract
1. Introduction
2. Results
2.1. Identification of RLCK-IV/CRCK Subfamily Members in P. deltoides
2.2. Phylogenetic Analysis of RLCK-IV/CRCKs
2.3. Gene Structure and Conserved Motifs of PdeCRCKs
2.4. Chromosome Distribution and Collinearity Analysis of PdeCRCKs
2.5. Cis-Acting Regulatory Element Identification in Promoter of PdeCRCKs
2.6. Expression Profiles of PdeCRCKs Under Polyethylene Glycol (PEG), Mannitol, and ABA Stresses
2.7. Subcellular Localization and Potential Functions of PdeCRCK3/5/6
2.8. Proteins That Interact with PdeCRCK6
3. Discussion
4. Materials and Methods
4.1. Identification of RLCK-IV Genes in P. deltoides
4.2. Physicochemical Property Characterization of PdeCRCKs
4.3. Sequence Alignment and Phylogenetic Tree Construction
4.4. Gene Structure, Motif Identification, and Chromosomal Location
4.5. Cis-Acting Regulatory Elements’ Identification in Putative Promoter Sequences
4.6. Synteny Relationships of RLCK-IV/CRCK Subfamily Members
4.7. Plant Materials, Drought Stress, RNA Extraction, and qRT–PCR Analysis
4.8. Subcellular Localization and Transient Expression Analysis of PdeCRCKs in Tobacco
4.9. Quantitative qRT–PCR Analysis
4.10. Immunoprecipitation–Mass Spectrometry (IP–MS)
4.11. Yeast Two-Hybird Assays
4.12. Quantification and Statistical Analysis
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene Locations | CDS (bp) | Protein Length (aa) | MW (kDa) | PI | Instability Index | Aliphatic Index | Sub Location |
---|---|---|---|---|---|---|---|---|
PdeCRCK1 | Podel.02G178500.1.v2.1 | 1171 | 389 | 43,623 | 8.78 | 45.49 | 83.5 | Nucleus |
PdeCRCK2 | Podel.02G180200.1.v2.1 | 1324 | 440 | 49,046 | 8.59 | 50.25 | 76.7 | Nucleus |
PdeCRCK3 | Podel.06G069100.1.v2.1 | 1527 | 508 | 56,946 | 7.94 | 39.78 | 90.93 | Cell membrane and nucleus |
PdeCRCK4 | Podel.09G041200.1.v2.1 | 1356 | 451 | 49,881 | 9.49 | 41.82 | 78.69 | Nucleus |
PdeCRCK5 | Podel.14G089100.1.v2.1 | 1320 | 439 | 48,644 | 9.24 | 49.59 | 81.12 | Nucleus |
PdeCRCK6 | Podel.18G126600.1.v2.1 | 1542 | 513 | 57,581 | 7.99 | 38.31 | 93.1 | Cell membrane |
ID | Gene Id | Pfam | GO | Best-Hit-Arabi | Arabi-Defline |
---|---|---|---|---|---|
1 | Podel.02G006800.1 | PF02672, PF00044, and PF02800 | GO:0055114 and GO:0016620 | AT1G42970.1 | Glyceraldehyde-3-phosphate dehydrogenase B subunit |
2 | Podel.04G229700.1 | ||||
3 | Podel.05G065100.1 | PF05496 | GO:0009378, GO:0006310, and GO:0006281 | AT5G64580.1 | AAA-type ATPase family proteins |
4 | Podel.10G049300.1 | PF00044 and PF02800 | GO:0055114 and GO:0016620 | AT3G04120.1 | Glyceraldehyde-3-phosphate dehydrogenase C subunit 1 |
5 | Podel.12G142900.1 | PF05199 and PF00732 | GO:0055114, GO:0016614, and GO:0050660 | AT5G51950.1 | Glucose–methanol–choline (GMC) oxidoreductase family proteins |
6 | Podel.14G119200.1 | PF00240 and PF01599 | GO:0005515 and GO:0006412, GO:0005840, and GO:0003735 | AT2G47110.2 | Ubiquitin 6 |
7 | Podel.T155200.1 | PF00657 | GO:0016788 | AT1G29670.1 | GDSL-like Lipase/Acylhydrolase superfamily proteins |
Gene ID | Primer Sequence F (5′-3′) | Primer Sequence R (5′-3′) |
---|---|---|
PdeRG5-RT | CCCAGAGCCGCACCAACT | TGGGTTTCTTGATGCCATTTTG |
Podel.06G209700.1-RT | AAGCCTCCGGAGCAAATGAA | CCTGCACTTGGTGTCCTCTT |
Podel.02G016400.1-RT | ATGCATCGGCACAGACTTGA | TCATGCTCGCAAACTCCTCA |
Podel.16G071000.1-RT | TGGGTCCTTGACTAAAGTGC | GAGGCTTGTTTGGTCTTGCG |
Podel.01G118600.1-RT | GGGCATGATGGGAAGTGGAA | GGTCTTGCCTTTCATGGGGA |
Podel.05G261000.1-RT | ACCAACCAACACCACCTATACC | TTCCCGACGCCTTCTCTGTA |
PdeCRCK1-RT | TTTTGTCTTTTGCCCACGCT | GCCTCGATTTGAACCTTGCC |
PdeCRCK2-RT | TTCTGGGAGCAGTGAAAGAAGG | CACCTTGTCCAATCTTGAATGTG |
PdeCRCK3-RT | ACCCCCATGAGTGACGTGTA | ACCTCCGTGTCCACCTTTTC |
PdeCRCK4-RT | TGCGAGATTGACCACCGAAT | TCAATCGGGTGTCTTCCTGT |
PdeCRCK5-RT | GTAGGCGCCCTATTGAAGCA | GCCAAGTTATTTGCTGCGGT |
PdeCRCK6-RT | GCGCCCTGTGGAGATGAAG | TACACCTTTCAGGTAGTCTGCT |
NtUBQ-RT | TCCAGGACAAGGAGGGTAT | CATCAACAACAGGCAACCTAG |
NtSOD-RT | AGCTACATGACGCCATTTCC | CCCTGTAAAGCAGCACCTTC |
NtPOD-RT | AAATGGTGGCGCTAGCCGGTG | GCATTGAAGACGTGCCGCTGG |
NtSAMDC-RT | CATTCACATTACCCCGGAAG | AGCAACATCAGCATGCAAAG |
NtNCED1-RT | AAGAATGGCTCCGCAAGTTA | GCCTAGCAATTCCAGAGTGG |
PdeCRCK3-GFP | gtgttacttctgcaggagctcATGGCCACGGCTGCATT | catggatccggtaccgagctcCCCTTTCTTTACACCTTTCAG |
PdeCRCK5-GFP | gtgttacttctgcaggagctcATGAAGAGCCCATATTC | catggatccggtaccgagctcTTCTTCTGTTATTACTGAAAT |
PdeCRCK6-GFP | gtgttacttctgcaggagctcATGGCCACGGCTGCATT | catggatccggtaccgagctcCCCTTTCTTTACACCTTTCAG |
PdeCRCK6-2300 | cggggatcctctagagtcgacATGGCTATGAATGCATT | tccggtaccgagctcgtcgacCCCTTTCTTTACACC |
PdeCRCK6-BD | tggccatggaggccgaattcATGGCTATGAATGCATT | cgctgcaggtcgacggatccTTACCCTTTCTTTACACC |
Podel.02G006800.1-AD | gccatggaggccagtgaattcATGGCCACCCACGCAG | atgcccacccgggtggaattcCTAAGCTTCATAGACTTTGC |
Podel.04G229700.1-AD | gccatggaggccagtgaattcATGAACATTGATAGAC | atgcccacccgggtggaattcTCAAGGACGTACGATAGCA |
Podel.05G065100.1-AD | gccatggaggccagtgaattcATGAAATCCCTCGTTTC | atgcccacccgggtggaattcTCAAAGGAAATGGCTGGCC |
Podel.10G049300.1-AD | gccatggaggccagtgaattcATGGCATGTGATAAGA | atgcccacccgggtggaattcTCAAGCTTGAGTCTTGGCC |
Podel.14G119200.1-AD | gccatggaggccagtgaattcATGGCTAAATCCGTACT | atgcccacccgggtggaattcTTAATCACCACCAGCCGTC |
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Pan, H.; He, Z.; Liu, L.; Cai, R.; Huang, H.; Xie, X.; Cao, X.; Li, Y.; Qiu, W.; Lu, Z.; et al. A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses. Plants 2024, 13, 3371. https://doi.org/10.3390/plants13233371
Pan H, He Z, Liu L, Cai R, Huang H, Xie X, Cao X, Li Y, Qiu W, Lu Z, et al. A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses. Plants. 2024; 13(23):3371. https://doi.org/10.3390/plants13233371
Chicago/Turabian StylePan, Huanhuan, Zhengquan He, Linxiu Liu, Renyue Cai, Hu Huang, Xinru Xie, Xun Cao, Yanan Li, Wenmin Qiu, Zhuchou Lu, and et al. 2024. "A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses" Plants 13, no. 23: 3371. https://doi.org/10.3390/plants13233371
APA StylePan, H., He, Z., Liu, L., Cai, R., Huang, H., Xie, X., Cao, X., Li, Y., Qiu, W., Lu, Z., Han, X., Qiao, G., Zhuo, R., Hu, J., & Xu, J. (2024). A Genome-Wide Characterization of Receptor-like Cytoplasmic Kinase IV Subfamily Members in Populus deltoides Identifies the Potential Role of PdeCRCK6 in Plant Osmotic Stress Responses. Plants, 13(23), 3371. https://doi.org/10.3390/plants13233371