More Like this

1. Transcriptional Tuning: How Auxin Strikes Unique Chords in Gene Regulation

   https://doi.org/10.1111/ppl.70229  

   Taylor, Joseph S; Bargmann, Bastiaan_O R (May 2025, Physiologia Plantarum)

   Abstract Auxin is a central regulator of plant growth, development, and responses to environmental cues. How a single phytohormone mediates such a diverse array of developmental responses has remained a longstanding question in plant biology. Somehow, perception of the same auxin signal can lead to divergent responses in different organs, tissues, and cell types. These responses are primarily mediated by the nuclear auxin signaling pathway, composed of ARF transcription factors, Aux/IAA repressors, and TIR1/AFB auxin receptors, which act together to regulate auxin‐dependent transcriptional changes. Transcriptional specificity likely arises through the functional diversity within these signaling components, forming many coordinated regulatory layers to generate unique transcriptional outputs. These layers include differential binding affinities forcis‐regulatory elements, protein–protein interaction‐specificity, subcellular localization, co‐expression patterns, and protein turnover. In this review, we explore the experimental evidence of functional diversity within auxin signaling machinery and discuss how these differences could contribute to transcriptional output specificity. 

   more » « less
2. Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root

   https://doi.org/10.1126/science.adf4721  

   Nolan, Trevor M.; Vukašinović, Nemanja; Hsu, Che-Wei; Zhang, Jingyuan; Vanhoutte, Isabelle; Shahan, Rachel; Taylor, Isaiah W.; Greenstreet, Laura; Heitz, Matthieu; Afanassiev, Anton; et al (March 2023, Science)

   Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive gene expression specific to different cell types and developmental stages of theArabidopsisroot, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall–related genes. Our analysis revealedHOMEOBOX FROM ARABIDOPSIS THALIANA 7(HAT7) andGT-2-LIKE 1(GTL1) as brassinosteroid-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as a site of brassinosteroid-mediated growth and unveil a brassinosteroid signaling network regulating the transition from proliferation to elongation, which illuminates aspects of spatiotemporal hormone responses. 

   more » « less
3. Patch Track Software for Measuring Kinematic Phenotypes of Arabidopsis Roots Demonstrated on Auxin Transport Mutants

   https://doi.org/10.3390/ijms242216475  

   Henry, Ashley R.; Miller, Nathan D.; Spalding, Edgar P. (November 2023, International Journal of Molecular Sciences)

   Plant roots elongate when cells produced in the apical meristem enter a transient period of rapid expansion. To measure the dynamic process of root cell expansion in the elongation zone, we captured digital images of growing Arabidopsis roots with horizontal microscopes and analyzed them with a custom image analysis program (PatchTrack) designed to track the growth-driven displacement of many closely spaced image patches. Fitting a flexible logistics equation to patch velocities plotted versus position along the root axis produced the length of the elongation zone (mm), peak relative elemental growth rate (% h−1), the axial position of the peak (mm from the tip), and average root elongation rate (mm h−1). For a wild-type root, the average values of these kinematic traits were 0.52 mm, 23.7% h−1, 0.35 mm, and 0.1 mm h−1, respectively. We used the platform to determine the kinematic phenotypes of auxin transport mutants. The results support a model in which the PIN2 auxin transporter creates an area of expansion-suppressing, supraoptimal auxin concentration that ends 0.1 mm from the quiescent center (QC), and that ABCB4 and ABCB19 auxin transporters maintain expansion-limiting suboptimal auxin levels beginning approximately 0.5 mm from the QC. This study shows that PatchTrack can quantify dynamic root phenotypes in kinematic terms. 

   more » « less
4. Strigolactone promotes cotton fiber cell elongation by de-repressing DWARF53 on linolenic acid biosynthesis

   https://doi.org/10.1016/j.devcel.2024.12.009  

   Wang, Huiqin; Zhu, Liping; Fan, Mengyuan; Weng, Shuangshuang; Zhou, Xin; Zhao, Hanxuan; Shen, Yongcui; Chai, Jiaquan; Hou, Liyong; Hao, Miaomiao; et al (December 2024, Developmental Cell)

   Strigolactone (SL) is a plant hormone required for plant development. DWARF53 (D53) functions as a transcription repressor in SL signaling. However, the role of D53 in cotton (Gossypium hirsutum, Gh) fiber development remains unclear. Here, we identify that GhD53 suppresses fiber elongation by repressing transcription of GhFAD3 genes, which control linolenic acid (C18:3) biosynthesis. Mechanistically, GhD53 interacts with SL-related transcriptional activate factor (GhSLRF) to prevent its binding on Omega-3 fatty acid desaturase gene (GhFAD3) promoters, thereby inhibiting GhFAD3 transcription. Upon SL exposure, GhD53 is degraded and leads to GhSLRF activation. This activation further promotes GhFAD3 transcription, C18:3 biosynthesis, and fiber elongation. Our findings identify the molecular mechanism of how SL controls cell elongation via D53 and offer potential strategies to improve cotton quality through SL application. 

   more » « less
5. Integrating Single-Cell and Spatial Multi-Omics to Decode Plant–Microbe Interactions at Cellular Resolution

   https://doi.org/10.3390/microorganisms14020380  

   Li, Yaohua; Vigil, Jared; Pradhan, Rajashree; Zhu, Jie; Libault, Marc (February 2026, Microorganisms)

   Understanding the intimate interactions between plants and their microbiota at the cellular level is essential for unlocking the full potential of plant holobionts in agricultural systems. Traditional bulk and microbial community-level sequencing approaches reveal broad community patterns but fail to resolve how distinct plant cell types interact with or regulate microbial colonization, as well as the diverse antagonistic and synergistic interactions and responses existing between various microbial populations. Recent advances in single-cell and spatial multi-omics have transformed our understanding of plant cell identities as well as gene regulatory programs and their dynamic regulation in response to environmental stresses and plant development. In this review, we highlight the single-cell discoveries that uncover the plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation, particularly in roots, nodules, and leaves. We further discuss how integrating transcriptomic, epigenomic, and spatial data can reconstruct multilayered interaction networks that connect plant cell-type-specific regulatory states with microbial spatial niches and inter-kingdom signaling (e.g., ligand–receptor and metabolite exchange), providing a foundation for developing new strategies to engineer crop–microbiome interactions to support sustainable agriculture. We conclude by outlining key methodological challenges and future research priorities that point toward building a fully integrated cellular interactome of the plant holobiont. 

   more » « less