Genome-wide survey of the GATA gene family in camptothecin-producing plant Ophiorrhiza pumila

Abstract

Background: Ophiorrhiza pumila (Rubiaceae) is capable of producing camptothecin (CPT), one monoterpene indole alkaloid extensively employed in the treatment of multiple cancers. Transcription factors (TFs) GATA are a group of transcription regulators involved in plant development and metabolism, and show the feature of binding to the GATA motif within the promoters of target genes. However, GATA TFs have not been characterized in O. pumila.

Result: In this study, a total of 18 GATA genes classified into four subfamilies were identified, which randomly distributed on 11 chromosomes of O. pumila. Synteny analysis of GATA genes between O. pumila and other plant species such as Arabidopsis thaliana, Oryza sativa, Glycine max, Solanum lycopersicum, Vitis vinifera, and Catharanthus roseus genomes were analyzed. Tissue expression pattern revealed that OpGATA1 and OpGATA18 were found to be correlated with ASA, MK, CPR and GPPS, which were highly expressed in leaves. OpGATA7, showed high expression in roots as most of the CPT biosynthetic pathway genes did, suggesting that these OpGATAs may be potential candidates regulating CPT biosynthesis in O. pumila.

Conclusions: In this study, we systematically analyzed the OpGATA TFs, and provided insights into the involvement of OpGATA TFs from O. pumila in CPT biosynthesis.

Keywords: Camptothecin; Expression pattern; GATA; Genome-wide; Ophiorrhiza pumila.

Fig. 1

Neighbor-joining tree representing the relationship among GATA proteins of O. pumila, O. sativa and A. thaliana. Constructed with MEGA v7 using full-length amino acid sequences and the bootstrap test replicate was set as 1000 times

Fig. 2

Schematic representation of phylogenetic relationships, conserved motifs and gene structures of the GATA genes in O. pumila. a A phylogenetic tree of 18 OpGATA proteins. b The motif composition of OpGATA proteins. The motifs are displayed in different colored boxes. c Exon/intron structures of OpGATA genes

Fig. 3

Alignments of GATA domain sequences of the GATA family members in O. pumila

Fig. 4

The chromosomal distribution and synteny analysis of OpGATA genes in O. pumila. The locations of all the OpGATA genes are depicted in the chromosomes. Red-colored genes belong to subfamily I, blue-colored genes belong to subfamily II, green-colored genes belong to subfamily III, purple-colored genes belong to subfamily IV. Background gray lines indicate all O. pumila genome synteny blocks, and the Colored lines highlight the duplicated OpGATA gene pairs. ID of the chromosomes is indicated at the bottom

Fig. 5

Synteny analysis of GATA genes between O. pumila and five representative plant species (A. thaliana, O. sativa, G. max, S. lycopersicum, V. vinifera and C. roseus). Gray lines in the background indicate the collinear blocks within O. pumila and other plant genomes, while red lines highlight syntenic GATA gene pairs

Fig. 6

The expression patterns of key enzyme genes and OpGATAs in leaves, roots, stems, cell suspension cultures and hairy roots examined by QRT-PCR. The color scale represents relative expression levels from high (red color) to low (blue color)

Fig. 7

The correlation between the gene expression patterns of OpGATA and key enzyme genes. Red: positively correlated; blue: negatively correlated. Significant difference was calculated, *P < 0.05, **P < 0.01, ***P < 0.001