Identification and 3D gene expression patterns of WUSCEHEL-related homeobox (WOX) genes from Panax ginseng

Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.

The Genome-Level Survey of the WOX Gene Family in Melastoma dodecandrum Lour

Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Melastoma dodecandrum Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the WOX family genes in M. dodecandrum is imperative for elucidating its growth and development mechanisms. However, the WOX genes in M. dodecandrum have not yet been characterized. In this study, by identification 22 WOX genes in M. dodecandrum based on current genome data, we classified family genes into three clades and nine types with homeodomains. We highlighted gene duplications of MedWOX4, which offered evidences of whole-genome duplication events. Promoter analysis illustrated that cis-regulatory elements related to light and stress responses and plant growth were enriched. Expression pattern and RT-qPCR results demonstrated that the majority of WOX genes exhibited expression in the stem. MedWOX13s displayed highest expression across various tissues. MedWOX4s displayed a specific expression in the stem. Collectively, our study provided foundations for elucidating WOX gene functions and further molecular design breeding in M. dodecandrum.

WOX11: the founder of plant organ regeneration

De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.

Global Analysis of the WOX Transcription Factor Gene Family in Populus × xiaohei T. S. Hwang et Liang Reveals Their Stress−Responsive Patterns

The WUSCHEL−related homeobox (WOX) family is a group of plant−specific transcription factors that play important regulatory roles in embryo formation, stem cell stability, and organogenesis. To date, there are few studies on the molecular mechanisms involved in this family of genes in response to stress. Thus, in this study, eight WOX genes were obtained from an endemic Chinese resilient tree species, Populus × xiaohei T. S. Hwang et Liang. Bioinformatic analysis showed that the WOX genes all contained a conserved structural domain consisting of 60 amino acids, with some differences in physicochemical properties. Phylogenetic analysis revealed that WOX members were divided into three evolutionary clades, with four, one, and three members in the ancient, intermediate, and modern evolutionary clades, respectively. The conserved structural domain species as well as the organization and gene structure of WOX genes within the same subfamily were highly uniform. Chromosomal distribution and genome synteny analyses revealed seven segmental−duplicated gene pairs among the PsnWOX gene family that were mainly under purifying selection conditions. Semi−quantitative interpretation (SQ−PCR) analysis showed that the WOX gene was differentially expressed in different tissues, and it was hypothesized that the functions performed by different members were diverse. The family members were strongly and differentially expressed under CdCl2, NaCl, NaHCO3, and PEG treatments, suggesting that WOX genes function in various aspects of abiotic stress defense responses. These results provide a theoretical basis for investigating the morphogenetic effects and abiotic stress responses of this gene family in woody plants.

Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery

Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.

Ginsenosides regulate adventitious root formation in Panax ginseng via a CLE45-WOX11 regulatory module

Adventitious root branching is vital to plant growth and regeneration, but the regulation of this process remains unclear. We therefore investigated how ginsenosides regulate adventitious root branching in Panax ginseng. Cell proliferation and adventitious root branching were decreased in the presence of ginsenoside Rb1 and a high concentration of ginsenoside Re, but increased when treating with a low concentration of Re. Moreover, the exogenous application of a synthetic dodeca-amino acid peptide that has a CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) motif corresponding to PgCLE45 retarded root growth in both ginseng and Arabidopsis. The root Re levels and the expression of the DDS, CYP716A47, and CYP716A53 genes that encode enzymes involved in ginsenoside synthesis were decreased in the presence of PgCLE45. The expression profiles of PgWOX and PgCLE genes were determined to further investigate the CLE-WOX signaling pathway. The levels of PgWOX11 transcripts showed an inverse pattern to PgCLE45 transcripts. Using yeast one-hybrid assay, EMSA, and ChIP assay, we showed that PgWOX11 bound to the PgCLE45 promoter, which contained the HD motif. Transient expression assay showed that PgWOX11 induced the expression of PgCLE45 in adventitious roots, while PgCLE45 suppressed the expression of PgWOX11. These results suggest that there is a negative feedback regulation between PgCLE45 and PgWOX11. Taken together, these data show that ginsenosides regulate adventitious root branching via a novel PgCLE45-PgWOX11 regulatory loop, providing a potential mechanism for the regulation of adventitious root branching.