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. 2024 Feb 12;25(1):169.
doi: 10.1186/s12864-024-10063-1.

Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri)

Xiaobing Kou #  1 , Zhen Zhao #  2 , Xinqi Xu  3 , Chang Li  3 , Juyou Wu  2 , Shaoling Zhang  4
Affiliations

Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri)

Xiaobing Kou et al. BMC Genomics. .

Abstract

Background: ATP-binding cassette (ABC) transporter proteins constitute a plant gene superfamily crucial for growth, development, and responses to environmental stresses. Despite their identification in various plants like maize, rice, and Arabidopsis, little is known about the information on ABC transporters in pear. To investigate the functions of ABC transporters in pear development and abiotic stress response, we conducted an extensive analysis of ABC gene family in the pear genome.

Results: In this study, 177 ABC transporter genes were successfully identified in the pear genome, classified into seven subfamilies: 8 ABCAs, 40 ABCBs, 24 ABCCs, 8 ABCDs, 9 ABCEs, 8 ABCFs, and 80 ABCGs. Ten motifs were common among all ABC transporter proteins, while distinct motif structures were observed for each subfamily. Distribution analysis revealed 85 PbrABC transporter genes across 17 chromosomes, driven primarily by WGD and dispersed duplication. Cis-regulatory element analysis of PbrABC promoters indicated associations with phytohormones and stress responses. Tissue-specific expression profiles demonstrated varied expression levels across tissues, suggesting diverse functions in development. Furthermore, several PbrABC genes responded to abiotic stresses, with 82 genes sensitive to salt stress, including 40 upregulated and 23 downregulated genes. Additionally, 91 genes were responsive to drought stress, with 22 upregulated and 36 downregulated genes. These findings highlight the pivotal role of PbrABC genes in abiotic stress responses.

Conclusion: This study provides evolutionary insights into PbrABC transporter genes, establishing a foundation for future research on their functions in pear. The identified motifs, distribution patterns, and stress-responsive expressions contribute to understanding the regulatory mechanisms of ABC transporters in pear. The observed tissue-specific expression profiles suggest diverse roles in developmental processes. Notably, the significant responses to salt and drought stress emphasize the importance of PbrABC genes in mediating adaptive responses. Overall, our study advances the understanding of PbrABC transporter genes in pear, opening avenues for further investigations in plant molecular biology and stress physiology.

Keywords: ABC transporter; Drought stress; Expression file; Pyrus bretchneideri; Salt stress.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Phylogenetic relationships of ABC transporters in Arabidopsis and pear. Full-length ABC transporters sequences were aligned using the Clustal X software, and the neighbor-joining (NJ) phylogenetic tree was constructed using MEGA 7.0 with 1000 bootstrap replicates. Different subfamilies are highlighted in different colors
Fig. 2
Fig. 2
Distributions of conserved motifs in ABC transporters from Arabidopsis and pear. The motif of ABC transporters was analyzed by MEME tool. Ten motifs (1–10) were identified and are indicated by different colors
Fig. 3
Fig. 3
Chromosomal localization and syntenic relationships of ABC transporters in pear. PbrABC transporter genes are mapped on different chromosomes and syntenic gene pairs are linked by colored lines
Fig. 4
Fig. 4
Cis-regulatory element analysis of PbrABC transporter genes. The cis-acting elements were predicted in the promoter sequences of the PbrABC transporter genes. Rectangular boxes of distinct colored boxes represent the different types of cis-acting elements
Fig. 5
Fig. 5
Expression file of PbrABC transporter genes in pear different tissues. Relative expression of PbrABC transporter genes in stem, leaf, bud, sepal, petal, overy, pollen and fruit were determined by RNA-Seq data from pear. Blue indicates low expression, and red indicates high expression. The heatmap was generated with TBtools
Fig. 6
Fig. 6
Expression levels of PbrABC transporter genes under salt stress. RNA-seq data were used to measure the expression level of PbrABC transporter genes under salt treatment. Blue indicates a low expression level and red indicates a high expression level. The heatmap was generated using TBtools
Fig. 7
Fig. 7
Expression levels of PbrABC transporter genes under drought stress. RNA-seq data were used to measure the expression level of PbrABC transporter genes under drought treatment. Blue indicates a low expression level and red indicates a high expression level. The heatmap was generated using TBtools
Fig. 8
Fig. 8
qRT–PCR analysis of 12 PbrABC transporter genes under salt and drought stress. A. Expression pattern of 12 PbrABC transporter genes under salt treatment for 0 h, 4 h, 6 h, 12 h, 24 h and 48 h, respectively. B. Expression pattern of 12 PbrABC transporter genes under drought treatment (10% PEG6000) for 0 h, 1 h, 3 h, 6 h and rehydration for 24 h, respectively. All experiments were performed independently at least three times
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References

    1. Higgins CF. ABC transporters. physiology, structure and mechanism--an overview. Res Microbiol. 2001;152(3-4):205–210. doi: 10.1016/S0923-2508(01)01193-7. - DOI - PubMed
    1. Locher KP. Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nat Struct Mol Biol. 2016;23(6):487–493. doi: 10.1038/nsmb.3216. - DOI - PubMed
    1. Rees DC, Johnson E, Lewinson O. ABC transporters: the power to change. Nat Rev Mol Cell Bio. 2009;10(3):218–227. doi: 10.1038/nrm2646. - DOI - PMC - PubMed
    1. Srikant S, Gaudet R. Mechanics and pharmacology of substrate selection and transport by eukaryotic ABC exporters. Nat Struct Mol Biol. 2019;26(9):792–801. doi: 10.1038/s41594-019-0280-4. - DOI - PMC - PubMed
    1. Xie T, Zhang Z, Fang Q, Du B, Gong X. Structural basis of substrate recognition and translocation by human ABCA4. Nat Commun. 2021;12(1):3853. doi: 10.1038/s41467-021-24194-6. - DOI - PMC - PubMed

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