Exploring the role of ATP-binding cassette transporters in tomato (Solanum lycopersicum) under cadmium stress through genome-wide and transcriptomic analysis

Abstract

ATP-binding cassette (ABC) transporters are integral membrane proteins involved in the active transport of various substrates, including heavy metals, across cellular membrane. In this study, we performed a genome-wide analysis and explored the expression profiles of ABC transporter genes in Solanum lycopersicum to identify their role in cadmium (Cd) stress tolerance. Several techniques were employed to determine the regulatory role of ABC transporters. A total of 154 ABC transporter genes were identified in the genome of S. lycopersicum, located on all 12 chromosomes. Comparative phylogenetic analysis between S. lycopersicum and Arabidopsis thaliana revealed several orthologous gene pairs, which were duly supported by the structural analysis of the genes by studying the exon-intron pattern and motif analysis. Collinearity analysis revealed multiple gene duplication events owing to intra-chromosomal and inter-chromosomal mutations. The cis-regulatory analysis identified several hormone-responsive elements suggesting that ABCs are actively involved in transporting hormones like ABA, SA, MeJA, auxin, and gibberellin. These hormones are known to combat a number of stress conditions, hence validating the role of ABCs in Cd stress. Under Cd stress, expression profiling demonstrated that several SlABCs exhibit significant transcriptional changes, indicating their involvement in Cd transport, sequestration, and detoxification mechanisms. Specific genes, including Groups 3 and 5 members, were upregulated under Cd exposure, suggesting their functional roles in mitigating Cd toxicity. The study revealed differential expressions of various SlABC genes encoding ATP binding cassette transporters, including the upregulation of several genes like Solyc08g067620.2, Solyc08g067610.3, Solyc12g019640.2, Solyc06g036240.2, and Solyc05g053610.2 in response to different concentrations of Cd. This study comprehensively explains the ABC transporter gene family in S. lycopersicum, emphasizing their critical roles in Cd stress tolerance. This study could prove useful in combating Cd stress not only in S. lycopersicum but also in other fleshy fruit plants; however, further advanced studies on specific pathways that lead to differential expression of the ABC genes are required to understand the mechanism behind tolerance to heavy metals fully.

Keywords: ABC transporters; Solanum lycopersicum; gene expression; heavy metals; phylogenetic analysis.

Figure 1

The phylogenetic tree of 154 SlABCs constructed using Maximum Likelihood (ML) method with the help of MEGA-11 software with 1000 bootstrap replicates. The major 15 phylogenetic groups are designated as 1-15, respectively.

Figure 2

A joint phylogenetic tree was constructed by aligning 154 SlABCs and 130 A. thaliana ABCs using the Maximum Likelihood (ML) method with the help of MEGA-11 software with 1000 bootstrap replicates. The resulting thirteen groups, labeled A-M respectively, are shown in different colors.

Figure 3

(A) Chromosomal positions and inter-chromosomal groups of duplicated SlABCs pairs were mapped on chromosomes (Chr1–Chr12) of S. lycopersicum. The lines represent the network zone of duplication among SlABCs, (B) Synteny analysis for identification of locus relationship among S. lycopersicum and A. thaliana genes.

Figure 4

Schematic distribution of 20 conserved motifs in SlABCs using MEME Analysis. The motif consensus along with motif symbol is provided in the legend.

Figure 5

Exon–intron pattern analysis of SlABCs. The blue box represents upstream/downstream, the yellow box indicates exons, whereas the lines represent introns.

Figure 6

Identified Cis-regulatory modules in SlABCs. The legend in the middle shows the designated color for each regulatory module whereas the legend at the bottom displays the number of regulatory elements in individual SlABCs.

Figure 7

(A) Network of Protein-protein interaction among SlABCs based on their available information. The prediction of interacting network was carried out using STRING analysis. Different line colors represent the types of evidence for the associations (B) Gene ontology (GO) enrichment of SlABCs representing biological process (C) Gene ontology (GO) enrichment of SlABCs representing molecular functions (D) Gene ontology (GO) enrichment of SlABCs representing cellular components. The sizes of the circles indicate the number of genes in each category, while the x-axis bars indicate fold enrichment.

Figure 8

(A) Hierarchical clustering indicate the substantial difference in SlABCs genes induced by 1 mM and 2 mM Cd stress (B) Venn Diagram showing the number of SlABCs that were upregulated in response to Cd1 (1mM Cd) and Cd2 (2mM Cd) (C) Venn diagram showing the number of differentially expressed SlABC gene in plants exposed to Cd1 (1mM Cd) and Cd2 (2mM Cd) (D) Heatmap demonstrating the differentially expressed gene pattern. Expression changes in the genes are represented by the color scheme displayed in the legend.

Figure 9

qRT-PCR based quantification of selected SlABCs for the validation of RT-PCR results. The x-axis displays the type of treatment, whereas the y-axis displays the gene expression level. The data is expressed in terms of Mean ± SE. Different letters over bar indicates significant difference in treatment according to Duncan's multiple range test DMRT p≤ 0.05).