Research Article: Genome-wide identification and gene expression pattern of ABC transporter gene family in Capsicum spp.

Date Published: April 30, 2019

Publisher: Public Library of Science

Author(s): Carlos Lopez-Ortiz, Sudip Kumar Dutta, Purushothaman Natarajan, Yadira Peña-Garcia, Venkata Abburi, Thangasamy Saminathan, Padma Nimmakayala, Umesh K. Reddy, Rajesh Mehrotra.

http://doi.org/10.1371/journal.pone.0215901

Abstract

ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three Capsicum species, i.e., Capsicum annuum, Capsicum baccatum and Capsicum chinense. Capsicum is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in C. annuum, C. baccatum and C. chinense genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location, Cis elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the Capsicum ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common cis-elements involved in the transcriptional regulation were also identified in the promoter regions of all Capsicum ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different Capsicum species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.

Partial Text

Pepper (Capsicum spp.) is a member of the Solanaceae family and is closely related to potato, tomato, eggplant, tobacco and petunia. Pepper represents an important horticultural crop worldwide not only because of its economic importance, but also due to its medicinal value. Moreover, pepper fruits have been widely used as a coloring agent, food flavoring, cosmetic and pharmaceutical ingredient, and as an ornamental product. It also has nutrimental value by containing vitamins A, B, C, and E, as well as phytochemicals such as phenolic compounds, carotenoids, and capsaicin. In addition to dietary and culinary importance, capsaicinoid compounds (capsaicin and dihydrocapsaicin) of pepper have a beneficial effect for humans, including antioxidant, anticarcinogenic, antimutagenic, antiaging, and antibacterial properties [1–4].

Although the ABC transporter gene superfamily has been widely studied among extant organisms including plants, the present study is the first to report the presence of 572 putative ABC transporter proteins in the entire pepper genome sequences of three different Capsicum species. Our results provide fundamental and exhaustive information about the pepper ABC transporters by performing a comprehensive genome-wide identification and expression patterns of these proteins family. Based on their evolutionary origin, phylogenetic analysis classified the ABC proteins into 8 main subfamilies (designated A to G, and I). Chromosomal mapping revealed that members of ABCG, ABCB and ABCC subfamilies were the most abundant genes, whereas the ABCD and ABCE subfamilies were manifested in a lesser abundance. Our results suggest that the ABC transporters, specifically the ABCC and ABCG subfamilies, interfere in capsaicin and dihydrocapsaicin content in pepper. Indirectly, these two subfamilies may be involved in the transportation of secondary metabolites such as capsaicinoids to the placenta vacuoles for their storage. Moreover, we suggest that the ABBC and ABCG subfamilies play a role in the H2O2 detoxification process to reduce capsaicin degradation, specifically in the C. chinense fruits. Our study will provide clues for further research on the evolution of the ABC transporter gene family and their influence in specific biological functions of Capsicum fruits including plant growth, development and capsaicinoid content in pepper.

 

Source:

http://doi.org/10.1371/journal.pone.0215901

 

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