Transcription factors WOX11 and LBD16 function with histone demethylase JMJ706 to control crown root development in rice

Transcription factor WUSCHEL-related homeobox (WOX) underground revelations: Insights into plant root development

Plant roots are essential for nutrient and water uptake and play a crucial role in plant growth and development. The development of roots is a complex process regulated by numerous factors, among which transcription factors (TFs) like WUSCHEL-related homeobox (WOX) have an essential function. The importance of WOXs in root development cannot be overstated. They act as key regulators in maintaining the balance between cell proliferation and differentiation and ensure the proper formation and function of root tissues. This review comprehensively presents the roles of WOXs in various root development aspects across multiple plant species, including primary, lateral, adventitious, and crown root development, as well as root hair, rhizoid formation, de novo root regeneration, and root apical meristem maintenance. We also discuss how WOXs regulate root development through various mechanisms in different plant species. Overall, this review provides comprehensive insights into the complex regulatory networks governing plant root growth and the importance of WOXs therein. Understanding WOXs in root development can help improve crop root architecture and stress tolerance and provide insights into the regulatory networks of plant root growth, contributing to plant breeding and agricultural productivity.

The Overexpression of ORR3 Negatively Regulates the Growth of Young Rice Roots by Reducing the Cell Size and the Number in the Root Meristematic Zone

The growth of young roots is crucial for the development and yield of rice. However, the molecular mechanisms underlying young rice root development remain unclear. Our research indicates that the rice B-type cytokinin response regulator factor ORR3 negatively regulates the development of young rice roots. ORR3 is highly expressed in the root meristematic zone of young rice roots. In transgenic lines overexpressing ORR3, the lengths of primary roots and adventitious roots, as well as the corresponding root meristematic zone lengths, are significantly reduced. This is due to a decrease in both the number and size of longitudinal cells in the root meristematic zone. On the one hand, ORR3 can inhibit root apical cell division and reduce the number of longitudinal cells in the root meristematic zone by affecting the auxin synthesis and transport pathways. On the other hand, ORR3 may directly activate the transcription of cell wall metabolism-related genes, thereby restricting the size of cells in the root meristematic zone. In summary, ORR3 negatively regulates rice young root growth by responding to cytokinin signals to influence auxin signal transduction and cell wall metabolism pathways, thereby negatively regulating the number and size of cells in the root meristematic zone.

The uORF-HsfA1a-WOX11 module controls crown root development in rice

OsWOX11 is a key essential determinant of crown root development in rice. However, either overexpression or downregulation of OsWOX11 results in pleiotropic developmental defects, including dwarfism and reduced yield. Therefore, it is necessary to ensure an optimal level of OsWOX11 expression for balancing the subterranean root system and aerial organ development. OsHsfA1a activates OsWOX11 expression by directly binding to heat stress element-like elements within its promoter. Genetic evidence demonstrated that OsHsfA1a overexpressing or knockout transgenic plants phenocopied the crown root growth in OsWOX11 transgenic plants. Additionally, increased expression of OsWOX11 in OsHsfA1a RNAi background could partially complement the defective crown root phenotypes. A uORF (uORFHsfA1a) was identified within the 5'-untranslated region of OsHsfA1a. Transient expression assays coupled with ribosome profiling revealed that uORFHsfA1a attenuated the translation efficiency of OsHsfA1a mRNA. Furthermore, HsfA1aP:uORFHsfA1a-HsfA1a-GFP plants exhibited wild-type crown root phenotypes, whereas uORFHsfA1a knockout transgenic plants displayed similar crown root phenotypes to OsWOX11 overexpressing plants. These findings suggest that uORFHsfA1a fine-tunes the crown root development by repressing OsHsfA1a translation, thereby indirectly modulating OsWOX11 transcript levels. Our study demonstrated a novel uORFHsfA1a-HsfA1a-WOX11 regulatory module that coordinated transcriptional and translational control to maintain optimal OsWOX11 expression. This mechanism ensures the trade-off between root and shoot development. Importantly, targeting uORFHsfA1a regulatory elements provided a new strategy for engineering robust root system architecture without compromising agronomic traits, thereby addressing a critical challenge in cereal crop improvement.

Comprehensive Characterization and Functional Analysis of the Lateral Organ Boundaries Domain Gene Family in Rice: Evolution, Expression, and Stress Response

In this study, the LBD (Lateral Organ Boundaries Domain) gene family, a group of plant-specific transcription factors critical for plant growth and development as well as metabolic regulation, was comprehensively characterized in rice. We identified 36 LBD genes using multi-source genomic data and systematically classified them into Class I (31 genes) and Class II (5 genes). Analysis of their physicochemical properties revealed significant variations in amino acid length, molecular weight, isoelectric points, and hydropathicity. Motif analysis identified conserved LOB domains and other motifs potentially linked to functional diversity. Cis-acting element analysis indicated the involvement of these genes in various biological processes, including light response, hormone signaling, and stress response. Expression profiling demonstrated tissue-specific expression patterns, with several genes, such as XM_015770711.2, XM_015776632.2, and XM_015792766.2, showing relatively high expression in rice roots, implying their important role in root development. Transcriptome data further supported the involvement of specific genes in responses to phytohormones such as jasmonic acid (JA) and abscisic acid (ABA), as well as environmental stresses like cold and drought. Notably, XM_015770711.2, XM_015776632.2, and XM_015772758.2 may contribute to the regulation of rice environmental adaptability by mediating ABA and JA signaling pathways, respectively. In conclusion, this study identified members of the LBD gene family through the screening of two rice gene databases, and performed a comprehensive analysis of their physicochemical properties, evolutionary relationships, and expression profiles under various conditions. These findings provided valuable insights for further functional studies of LBD genes. Moreover, this study provides a foundation for targeting LBD genes to enhance stress resilience (e.g., drought/cold tolerance) and root architecture optimization. The LBD gene family possesses dual values in both stress resistance regulation and developmental optimization. The construction of its multidimensional functional map lays the theoretical and resource foundation for the precise design of high-yield and stress-resistant varieties.

4-Allylanisole Promotes the Root Growth of Arabidopsis thaliana by Inhibiting AtHDA9 Activity

This study elucidates the epigenetic mechanism through which 4-allylanisole, a key monoterpene in Foeniculum vulgare essential oils, regulates plant growth. Integrated RNA-Seq and ChIP-Seq analyses revealed 4-allylanisole enhances histone H3K9 acetylation (H3K9ac) at promoters of growth-related genes in Arabidopsis thaliana, concomitant with improved root development and biomass accumulation. Biochemical assays identified AtHDA9 histone deacetylase as the molecular target, showing 4-allylanisole directly inhibits its enzymatic activity through stable interactions with catalytic residues (Asp95, Phe202, Leu268, His174) confirmed by molecular docking and dynamics simulations. The suppressed deacetylation elevated endogenous indole-3-acetic acid (IAA) levels and amplified auxin signaling transduction. These findings establish a dual mechanism whereby 4-allylanisole epigenetically activates growth-related gene expression through H3K9ac accumulation while coordinately enhancing IAA biosynthesis and signaling. This work provides the first evidence of plant-derived volatile compounds regulating growth through histone modification-auxin crosstalk, proposing novel strategies for developing eco-friendly plant growth regulators.

Epigenetic regulation of ISPL10 enhances regional adaptability of rice varieties

Suppressing the heading date of rice under short-day (SD) conditions while promoting it under long-day (LD) conditions can significantly enhance the regional adaptability of rice varieties. However, rice germplasm resources with these traits are scarce. In this study, we report the Jumonji C (jmjC) protein-encoding gene ISPL10. The ispl10 mutant exhibited heading 7 days later under SD and 14 days earlier under LD compared with the wild type (WT). ISPL10 decreased H3 lysine 9 dimethylation (H3K9me2) levels at the OsMADS51 locus and activated the expression of OsMADS51, which then enhanced the expression of Ehd1 and up-regulated Hd3a under SD conditions. By contrast, ISPL10 is directly bound to the promoter of OsVIL2 to suppress its expression, thereby inhibiting Ehd1 expression and reducing RFT1 expression under LD conditions. Additionally, ISPL10 interacted with Se14, another jmjC protein that controlled H3K4me3 states in the RFT1 chromatin. The field tests showed that the ispl10 mutant not only extended the growth period in low-latitude regions but also shortened the maturity duration in high-latitude regions, and thus significantly increased grain yield in both low- and high-latitude regions compared with WT. Therefore, the ISPL10 locus could be a crucial factor in improving the regional adaptability of rice varieties.

Effect of exogenous IBA on root morphology and endogenous hormone Metabolic pathways in castor seedlings under Pb/Zn stress

Ricinus communis, a plant of significant industrial value for its oil, is renowned for its robust root system and vigorous growth, qualities that render it an exemplary candidate for the ecological remediation of soils contaminated with heavy metals. The impact of heavy metal stress on root development is characterized by inhibition, a phenomenon whose underlying mechanisms are not fully elucidated. To shed light on this, a study was conducted wherein varying concentrations of the exogenous auxin, IBA, were applied to the roots of Ricinus communis to scrutinize its influence on the endogenous indole-3-acetic acid (IAA) metabolism in seedlings and to delineate the molecular underpinnings of its effects on root morphology. It was observed that IBA significantly amplified the total root surface area by a factor of 1.29 and increased the number of root tips by 40.11% under lead (Pb) stress, and by 32.29% and 91.19%, respectively, under zinc (Zn) stress. These findings underscore the efficacy of IBA in promoting the proliferation of lateral roots in seedlings subjected to stress induced by either Pb or Zn. Further analysis of auxin signaling pathways revealed that the presence of Pb or Zn impedes root growth and lateral root formation by perturbing auxin transporters and signaling molecules. Notably, IBA was found to foster the development of lateral roots by modulating the expression of specific transporters. Post-application of IBA, the endogenous levels of IAA in roots exhibited a 2.80-fold elevation under Pb stress, IBA stimulated the activity of key biosynthetic enzymes, such as RcNIT and RcTAR, culminating in elevated IAA levels. Conversely, under Zn stress, IBA was observed to diminish the levels of RcTAR, which in turn led to reduced IAA levels. These outcomes contribute to a deeper comprehension of the modulatory role of IBA in the context of heavy metal stress.

A WUSCHEL-related homeobox transcription factor, SlWOX4, negatively regulates drought tolerance in tomato

KEY MESSAGE

CRISPR/Cas9-mediated knockout of SlWOX4 gene in tomato enhances tolerance to drought stress. Drought stress is one of the major abiotic factors that seriously affects plant growth and crop yield. WUSCHEL-related homeobox (WOX) transcription factors are involved in plant growth, development and stress response. However, little is known about the role of WOX genes in drought tolerance in tomato. Here, SlWOX4, a member of the WOX family in tomato, was functionally characterized in mediating drought tolerance. SlWOX4 was homologous to Nicotiana tabacum NtWOX4 with a conserved HD domain, and was localized in the nucleus. SlWOX4 was significantly down-regulated by drought and abscisic acid (ABA) treatments. The loss-of-function mutations of SlWOX4 produced using the CRISPR-Cas9 system in tomato improved drought tolerance by reducing water loss rate and enhancing stomatal closure. In addition, the wox4 lines exhibited reduced accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), increased antioxidant enzyme activity, proline contents and ABA contents under drought stress. Moreover, gene editing of SlWOX4 in tomato enhanced drought tolerance by regulating the expression of genes encoding antioxidants and ABA signaling molecules. In summary, SlWOX4 gene might negatively regulate drought stress tolerance in tomato and has great potential as a drought-resistant crop-breeding target genes.

Epigenetic control during root development and symbiosis

The roots of plants play multiple functions that are essential for growth and development, including anchoring to the soil as well as water and nutrient acquisition. These underground organs exhibit the plasticity to modify their root system architecture in response to environmental cues, allowing adaptation to change in water and nutrient availability. In addition, roots enter in mutualistic interactions with soil microorganisms, for example, the root nodule symbiosis (RNS) established between a limited group of plants and nitrogen-fixing soil bacteria and the arbuscular mycorrhiza symbiosis involving most land plants and fungi of the Glomeromycetes phylum. In the past 20 years, genetic approaches allowed the identification and functional characterization of genes required for the specific programs of root development, root nodule, and arbuscular mycorrhiza symbioses. These genetic studies provided evidence that the program of the RNS recruited components of the arbuscular mycorrhiza symbiosis and the root developmental programs. The execution of these programs is strongly influenced by epigenetic changes-DNA methylation and histone post-translational modifications-that alter chromatin conformation modifying the expression of key genes. In this review, we summarize recent advances that highlight how DNA methylation and histone post-translational modifications, as well as chromatin remodeling factors and long noncoding RNAs, shape the root system architecture and allow the successful establishment of both root nodule and arbuscular mycorrhiza symbioses. We anticipate that the analysis of dynamic epigenetic changes and chromatin 3D structure in specific single cells or tissue types of root organs will illuminate our understanding of how root developmental and symbiotic programs are orchestrated, opening exciting questions and new perspectives to modulate agronomical and ecological traits linked to nutrient acquisition.

The auxin-responsive CsSPL9-CsGH3.4 module finely regulates auxin levels to suppress the development of adventitious roots in tea (Camellia sinensis)

The cutting technique is extensively used in tea breeding, with key emphasis on promoting the growth of adventitious roots (ARs). Despite its importance in tea cultivation, the mechanisms underlying AR development in tea remain unclear. In this study, we demonstrated the essential role of auxins in the initiation and progression of AR and established that the application of exogenous 1-naphthaleneacetic acid-enhanced AR formation in tissue-cultured seedlings and cuttings. Then, we found that the auxin-responsive transcription factor CsSPL9 acted as a negative regulator of AR development by reducing the levels of free indole-3-acetic acid (IAA) in tea plants. Furthermore, we identified CsGH3.4 as a downstream target of CsSPL9, which was activated by direct binding to its promoter. CsGH3.4 also inhibited AR development and maintained low levels of free IAA. Thus, these results revealed the inhibitory effect of the auxin-responsive CsSPL9-CsGH3.4 module on AR development by reducing free IAA levels in tea. These findings have significant theoretical and practical value for enhancing tea breeding practices.

Identification and Expression Analysis of the WOX Transcription Factor Family in Foxtail Millet (Setaria italica L.)

WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet WOX gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet WOX genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The SiWOX genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet WOX genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: SiWOX1 and SiWOX13, SiWOX4 and SiWOX5, and SiWOX11 and SiWOX12. Collinearity analysis demonstrated that WOX genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The SiWOX genes primarily harbor two categories of cis-acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of SiWOX expression patterns and hormone responses unveiled potential functional diversity among different SiWOX genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of SiWOX genes.