Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of PLATZ Gene Family Members in Solanum Lycopersicum L. under Multiple Abiotic Stresses

Abstract

PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, but their role in tomato has not been explored yet. In the present work, 20 non-redundant Solanum lycopersicum PLATZ (SlPLATZ) genes with three segmentally duplicated gene pairs and four tandemly duplicated gene pairs were identified on eight tomato chromosomes. The comparative modeling and gene ontology (GO) annotations of tomato PLATZ proteins indicated their probable roles in defense response, transcriptional regulation, and protein metabolic processes as well as their binding affinity for various ligands, including nucleic acids, peptides, and zinc. SlPLATZ10 and SlPLATZ17 were only expressed in 1 cm fruits and flowers, respectively, indicating their preferential involvement in the development of these organs. The expression of SlPLATZ1, SlPLATZ12, and SlPLATZ19 was up- or down-regulated following exposure to various abiotic stresses, whereas that of SlPLATZ11 was induced under temperature stresses (i.e., cold and heat stress), revealing their probable function in the abiotic stress tolerance of tomato. Weighted gene co-expression network analysis corroborated the aforementioned findings by spotlighting the co-expression of several stress-associated genes with SlPLATZ genes. Confocal fluorescence microscopy revealed the localization of SlPLATZ–GFP fusion proteins in the nucleus, hinting at their functions as transcription factors. These findings provide a foundation for a better understanding of the structure and function of PLATZ genes and should assist in the selection of potential candidate genes involved in the development and abiotic stress adaptation in tomato.

Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato

“…This number is comparable to cabbage and higher than the numbers for Arabidopsis [ 17 ] and Ginkgo [ 26 ]. Compared to Wai’s [ 27 ] findings, which discovered 20 SlPLATZ genes, this is different. We found that Wai used a tomato assembly version other than Sl5.0 L., which may be the main reason for the disparity in the number of PLATZ genes.…”

“…Phylogeny is the study of the origin and evolutionary history of biological groups, each of which has its own origins and developmental history, regardless of its size. Along with the organisms we included together, I left out Amborella ( Amborella trichopoda ), moss ( Physcomitrella patens ), and green algae ( Chlamydomonas reinhardtii ) concerning Wai’s [ 27 ], but with Pennellii included. The PLATZ genes differed significantly depending on where the plant was in its evolutionary history.…”

“…Duplicate genes in a phylogenetic tree belong to the same group, which provides the building blocks for the evolution of mechanistic novelty and makes it easier for new functions to evolve. While we discovered three gene pairs in cultivated tomatoes and four duplicated pairs in pennellii, Wai [ 27 ] discovered a total of seven duplicated gene pairs in the tomato PLATZ gene family. A ratio of non-synonymous substitutions (Ka) to synonymous substitutions (Ks) greater than 1 is widely thought to signal positive selection for faster evolution, and Ka/Ks < 1 shows that gene duplication suffers from purifying selection [ 32 ].…”

“…However, further studies are needed to determine the mechanisms of NAA, BR, and MT induction of SlPLATZ21 and SlPLATZ23 and their roles in NAA, BR, and MT. Wai [ 27 ] investigated the effects of drought, salt stress, low temperatures, heat stress, and ABA on tomato Ailsa Craig. Our study, however, investigated the gene expression profiles of “M82” under various salt treatments and the expression patterns of cherry tomatoes “Jingfan Pink Star No.…”

Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)

“…The drought-responsive element MBS motif was detected in the promoters of SlE2F/DP 6, SlE2F/DP 7 and SlE2F/DP 8 suggested their role in abiotic stress. These MBS elements were reported in HVA22 gene and PLATZ transcription factor against abiotic stress [ 39 , 40 ]. The ABRE cis-elements and the Meja responsive motif is abundant in SlE2F/DP genes.…”