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. 2024 Mar 27;25(1):315.
doi: 10.1186/s12864-024-10227-z.

A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L

Ritu Devi  1   2   3 , Pooja Goyal  1   2   4 , Bhawna Verma  1   2   3 , Shahnawaz Hussain  1   2   3 , Fariha Chowdhary  1   2   3 , Palak Arora  1   2 , Suphla Gupta  5   6   7
Affiliations

A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L

Ritu Devi et al. BMC Genomics. .

Abstract

Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein-Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.

Keywords: Glycyrrhiza glabra; ATP-binding cassette transporter; Gene expression; N-1-naphthylphthalamic acid; Nucleotide binding domain; Phytohormones; Transmembrane binding domain.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Motif visualization and classification of GgABC family proteins. Sub-families (ABCA, ABCB, ABCC, ABCF, ABCG and ABCI) were phylogenetically classified with the architecture of conserved NBD (left side). The conserved motifs (13) are represented in different color (right side). The tree was constructed using NJ method with 100 bootstrap values; conserved motifs were predicted by MEME program
Fig. 2
Fig. 2
Phylogenetic tree of GgABC family. a ABCA subfamily comprising of ABCAs from Glycyrrhiza glabra (11), Arabidopsis thaliana (12) and Glycyrrhiza uralensis (5); (b) ABCB subfamily ABCBs of Glycyrrhiza glabra (45), Arabidopsis thaliana (29) and Glycyrrhiza uralensis (26); (c) ABCC subfamily. ABCCs of Glycyrrhiza glabra (54), Arabidopsis thaliana (15) and Glycyrrhiza uralensis (17); (d) ABCF subfamily. ABCFs of Glycyrrhiza glabra (13), Arabidopsis thaliana (5) and Glycyrrhiza uralensis (5); (e) ABCG subfamily. ABCGs of Glycyrrhiza glabra (50), Arabidopsis thaliana (41) and Glycyrrhiza uralensis (53); (f) ABCI subfamily. ABCIs of Glycyrrhiza glabra (8), Arabidopsis thaliana (9) and Glycyrrhiza uralensis (3). All the trees were subjected to phylogenetic analysis with 1000 bootstrap value. The tree was constructed using MEGA7 and represented by iTOL
Fig. 3
Fig. 3
Protein–Protein interaction network of ABCB gene subfamily. Specific interactions between ABCBs and associated proteins based on Arabidopsis orthologs engaged in auxin transportation as predicted by STRING search tool. It predicted nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) with their corresponding five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21)
Fig. 4
Fig. 4
Real- time expression profiling of selected genes from ABCB subfamily of Glycyrrhiza glabra. The selected GgABC genes (a) under three different conditions (in-vitro, growth chamber and field) in tissues (shoot, root and leaf); (b) under six abiotic stresses; carbon starvation, senescence, cold, dark, UV-C and drought in shoot tissues. The Y-axis indicates relative expression level and X-axis indicates tissues under different conditions/stress. Three biological replicates were used to calculate error bars using standard deviation. Asterisks indicate that the corresponding gene was significantly up- or down regulated in a given treatment (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001)
Fig. 5
Fig. 5
Expression analysis of selected GgABCB subfamily genes in shoot and root tissues under phytohormonal (a to d) and N-1-Naphthylphthalamic acid treatment (e). GgABCB genes are present in rows and treatment time duration in columns of the matrix. Heat map showing-Cluster analysis of GgABCB genes according to their expression profiles in Naphthaleneacetic acid (NAA) treated (a) shoots, (b) roots; and Methyl jasmonate (MeJA) treated (c) shoots, (d) roots for 0, 4, 8, 16, 32, 64 and 128 h time interval; (e) qRT-PCR expression (fold) represented in the form of bar graph of the PIN1, PIN3/4/7, TWD1 (TWISTED DWARF1) and selected ABCB genes under the influence of NPA (N-1-naphthylphthalamic acid) post 15 days of treatment. Actin was used as an internal reference. Three biological replicates were used to calculate error bars using standard deviation. The Y-axis indicates relative expression level and X-axis indicates shoot/root tissues. Statistical significance was determined using One-way ANOVA in Graphpad prism 8.0 software. When compared with the control, single asterisk shows a significant difference with a P-value < 0.05. Double asterisks show a significant difference with a P-value < 0.01, three asterisks show a significant difference with a P-value < 0.001 and four asterisks shows a significant difference with a P-value < 0.0001
Fig. 6
Fig. 6
Schematic representation of IAA transportation under the influence of NPA. IAA transportation is mediated by ABCBs. A positive regulator, TWD1, PGP1-mediated auxin transporter, acts as a chaperone in association with ABCB subfamily for transportation from Endoplasmic reticulum to Plasma membrane. N-1-naphthylphthalamic acid (NPA), a polar auxin transport inhibitor, binds with high affinity to ABCBs and TWD1 complex of plant membranes [76, 77]. NPA (10 µM) disrupts TWD1-ABCB interaction resulting in inhibition of auxin transportation. Blue arrows indicate auxin biosynthesis pathways. Brown dotted arrows indicates trafficking of ABCB transporter by TWD1 from Endoplasmic reticulum to Plasma membrane, when no NPA is present. In the presence of NPA (10 µM), its binds to the ABCB –TWDI Complex and blocks the transportation
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