Abstract
Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean. Our results showed that GsPP2C clade D (GsAPD) genes exhibit more gene duplications than AtPP2C clade D genes. Plant hormone and abiotic stress-responsive elements were identified in the promoter regions of most PP2C genes. Moreover, we investigated their expression patterns in roots, stems, and leaves. Quantitative real-time PCR analyses revealed that the expression levels of representative GsPP2C and AtPP2C clade D genes were significantly influenced by alkali and salt stresses, suggesting that these genes might be associated with or directly involved in the relevant stress signaling pathways. Our results established a foundation for further functional characterization of PP2C clade D genes in the future.
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Acknowledgements
This work was supported by the Heilongjiang Provincial Higher School Science and Technology Innovation Team Building Program (2011TD005), National Natural Science Foundation of China (31501331), and Advanced Talents Foundation of QAU (6631115032).
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Chao Chen, Yang Yu, Huizi Duanmu, and Lei Cao performed the experiment, analyzed data; Chao Chen, Yu Yang, and Dan Zhu wrote the manuscript; Beidong Liu, Xiaoli Sun, and Zaib-un-Nisa edited the manuscript; and Qiang Li, Yanming Zhu, and Xiaodong Ding provided ideas, designed the research; all authors read and approved the final manuscript.
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Supplemental Table 1
Gene-specific primers used for quantitative RT-PCR assays (DOCX 16 kb)
Supplemental Table 2
DNA sequence of cis-acting regulatory elements (DOCX 14 kb)
Supplemental Table 3
Distribution of cis-acting elements on the promoters of PP2C clade D genes in soybean (DOCX 14 kb)
Supplemental Fig. 1
Sequence analysis of GmPP2C and GsPP2C clade D proteins. Multiple sequence alignments of the full-length amino acid sequences of GmPP2C and GsPP2C clade D. Sequences were aligned using clustalx1.83. (JPEG 3492 kb)
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Supplemental Fig. 2
Phylogenetic relationships and exon-intron structure analysis of PP2C clade D genes in cultivated and wild soybean. The phylogenetic tree was produced using MEGA 5.0 by N-J method. Bootstrap values based on 1000 replications for each branch. Gene structure analysis of PP2C clade D was performed by using GSDS online tools. (JPEG 142 kb)
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Supplemental Fig. 3
Correlation with PP2C clade D genes in wild soybean (a) and Arabidopsis (b). The correlation of the gene expression patterns measured from root, stems and leaves in wild soybean and Arabidopsis plants. The relative expression levels were detected by qRT-PCR. r ≥ 8: two variables are highly correlation. (JPEG 225 kb)
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Supplemental Fig. 4
Expression analysis of four PP2C clade D genes in soybean under alkaline and salt treatments. Total RNA samples were extracted from 15-day-old soybean seedlings under 50 mM NaHCO3 and 200 mM NaCl treatments. The relative expression levels were detected using qRT-PCR. GAPDH was used as an internal control. Statistical analyses were performed by one-way ANOVA with Bonferroni post-test. *P < 0.05, **P < 0.01, as compared with the control before treatment (0 h). (JPEG 120 kb)
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Chen, C., Yu, Y., Ding, X. et al. Genome-wide analysis and expression profiling of PP2C clade D under saline and alkali stresses in wild soybean and Arabidopsis . Protoplasma 255, 643–654 (2018). https://doi.org/10.1007/s00709-017-1172-2
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DOI: https://doi.org/10.1007/s00709-017-1172-2