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Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.).
Gene. 2018 Dec 15; 678:143-154.GENE

Abstract

FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated. The genes are clustered on ten tomato chromosomes and are categorised into two sub-classes; single and multiple domains protein gene. One of the main features of tomato FKBPs is their large fractions localized in chloroplast (in silico analysis) and clustered together phylogenetically. Tissue-specific expression analysis using available RNA-seq data revealed the spatiotemporal expression of the FKBPs, but few genes were observed with relatively high expressions in certain developmental stages. However, the quantitative expression profile of all genes under hormone stress provided a supporting evidence for their potential role in hormone signal pathways. Our prediction not only providing the foundation for better understanding the complex physiological regulation of FKBP gene family in tomato but also providing the potential aids to accelerate tolerance and survival in tomato under stressful condition.

Authors+Show Affiliations

School of Life Sciences, Chongqing University, Chongqing, China.Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan.School of Life Sciences, Chongqing University, Chongqing, China.School of Life Sciences, Chongqing University, Chongqing, China. Electronic address: gyq@cqu.edu.cn.School of Life Sciences, Chongqing University, Chongqing, China. Electronic address: zhengguoli@cqu.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30096455

Citation

Waseem, Muhammad, et al. "Genome-wide Identification of FK506-binding Domain Protein Gene Family, Its Characterization, and Expression Analysis in Tomato (Solanum Lycopersicum L.)." Gene, vol. 678, 2018, pp. 143-154.
Waseem M, Ahmad F, Habib S, et al. Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.). Gene. 2018;678:143-154.
Waseem, M., Ahmad, F., Habib, S., Gao, Y., & Li, Z. (2018). Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.). Gene, 678, 143-154. https://doi.org/10.1016/j.gene.2018.08.021
Waseem M, et al. Genome-wide Identification of FK506-binding Domain Protein Gene Family, Its Characterization, and Expression Analysis in Tomato (Solanum Lycopersicum L.). Gene. 2018 Dec 15;678:143-154. PubMed PMID: 30096455.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.). AU - Waseem,Muhammad, AU - Ahmad,Fiaz, AU - Habib,Sidra, AU - Gao,Yanqiang, AU - Li,Zhengguo, Y1 - 2018/08/07/ PY - 2018/04/22/received PY - 2018/07/16/revised PY - 2018/08/04/accepted PY - 2018/8/11/pubmed PY - 2018/10/23/medline PY - 2018/8/11/entrez KW - Abiotic stress KW - FKBPs KW - Isoform KW - PPlase KW - Tomato SP - 143 EP - 154 JF - Gene JO - Gene VL - 678 N2 - FK506-protein also called FKBP protein belongs to PPIase (peptidylprolylcis-trans isomerase) super family of immune suppressive drugs that act as molecular protein chaperones. In plants, FKBPs are ubiquitous and involved in various biological and physiological processes like plant germination, development, stress response and hormonal signaling. Here, we identified 24 FKBP family genes in tomato by using different tools and bioinformatic approaches. The specific structure, domain organisation, cis-regulatory elements, phylogenetic analysis, multiple sequence alignment, tissue-specific expression patterns and expression under abiotic and phytohormone stresses of all genes were investigated. The genes are clustered on ten tomato chromosomes and are categorised into two sub-classes; single and multiple domains protein gene. One of the main features of tomato FKBPs is their large fractions localized in chloroplast (in silico analysis) and clustered together phylogenetically. Tissue-specific expression analysis using available RNA-seq data revealed the spatiotemporal expression of the FKBPs, but few genes were observed with relatively high expressions in certain developmental stages. However, the quantitative expression profile of all genes under hormone stress provided a supporting evidence for their potential role in hormone signal pathways. Our prediction not only providing the foundation for better understanding the complex physiological regulation of FKBP gene family in tomato but also providing the potential aids to accelerate tolerance and survival in tomato under stressful condition. SN - 1879-0038 UR - https://www.unboundmedicine.com/medline/citation/30096455/Genome_wide_identification_of_FK506_binding_domain_protein_gene_family_its_characterization_and_expression_analysis_in_tomato__Solanum_lycopersicum_L___ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0378-1119(18)30870-9 DB - PRIME DP - Unbound Medicine ER -