CALMODULIN-LIKE-38 and PEP1 RECEPTOR 2 integrate nitrate and brassinosteroid signals to regulate root growth

Calmodulin-like protein MdCML15 interacts with MdBT2 to modulate iron homeostasis in apple

BTB and TAZ domain proteins (BTs) function as specialized adaptors facilitating substrate recognition of the CUL3-RING ubiquitin ligase (CRL3) complex that targets proteins for ubiquitination in reaction to diverse pressures. Nonetheless, knowledge of the molecular mechanisms by which the apple scaffold protein MdBT2 responds to external and internal signals is limited. Here we demonstrate that a putative Ca 2+ sensor, calmodulin-like 15 (MdCML15), acts as an upstream regulator of MdBT2 to negatively modulate its functions in plasma membrane H+-ATPase regulation and iron deficiency tolerance. MdCML15 was identified to be substantially linked to MdBT2, and to result in the ubiquitination and degradation of the MdBT2 target protein MdbHLH104. Consequently, MdCML15 repressed the MdbHLH104 target, MdAHA8's expression, reducing levels of a specific membrane H+-ATPase. Finally, the phenotype of transgenic apple plantlets and calli demonstrated that MdCML15 modulates membrane H+-ATPase-produced rhizosphere pH lowering alongside iron homeostasis through an MdCML15-MdBT2-MdbHLH104-MdAHA8 pathway. Our results provide new insights into the relationship between Ca2+ signaling and iron homeostasis.

Recent Advances in the Crosstalk between Brassinosteroids and Environmental Stimuli

Due to their sessile lifestyle, plants need to optimize their growth in order to adapt to ever-changing environments. Plants receive stimuli from the environment and convert them into cellular responses. Brassinosteroids (BRs), as growth-promoting steroid hormones, play a significant role in the tradeoff between growth and environmental responses. Here, we provide a comprehensive summary for understanding the crosstalk between BR and various environmental stresses, including water availability, temperature fluctuations, salinization, nutrient deficiencies and diseases. We also highlight the bottlenecks that need to be addressed in future studies. Ultimately, we suppose to improve plant environmental adaptability and crop yield by excavating natural BR mutants or modifying BR signaling and its targets.

A spatially concerted epidermal auxin signaling framework steers the root hair foraging response under low nitrogen

As a major determinant of the nutrient-acquiring root surface, root hairs (RHs) provide a low-input strategy to enhance nutrient uptake. Although primary and lateral roots exhibit elongation responses under mild nitrogen (N) deficiency, the foraging response of RHs and underlying regulatory mechanisms remain elusive. Employing transcriptomics and functional studies revealed a framework of molecular components composing a cascade of auxin synthesis, transport, and signaling that triggers RH elongation for N acquisition. Through upregulation of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8, low N increases auxin accumulation in the root apex. Auxin is then directed to the RH differentiation zone via the auxin transport machinery, AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon arrival to the RH zone, auxin activates the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6/8) to promote the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to steer RH elongation in response to low N. Our study uncovers a spatially defined regulatory signaling cascade for N foraging by RHs, expanding the mechanistic framework of hormone-regulated nutrient sensing in plant roots.

Finding Balance in Adversity: Nitrate Signaling as the Key to Plant Growth, Resilience, and Stress Response

To effectively adapt to changing environments, plants must maintain a delicate balance between growth and resistance or tolerance to various stresses. Nitrate, a significant inorganic nitrogen source in soils, not only acts as an essential nutrient but also functions as a critical signaling molecule that regulates multiple aspects of plant growth and development. In recent years, substantial advancements have been made in understanding nitrate sensing, calcium-dependent nitrate signal transmission, and nitrate-induced transcriptional cascades. Mounting evidence suggests that the primary response to nitrate is influenced by environmental conditions, while nitrate availability plays a pivotal role in stress tolerance responses. Therefore, this review aims to provide an overview of the transcriptional and post-transcriptional regulation of key components in the nitrate signaling pathway, namely, NRT1.1, NLP7, and CIPK23, under abiotic stresses. Additionally, we discuss the specificity of nitrate sensing and signaling as well as the involvement of epigenetic regulators. A comprehensive understanding of the integration between nitrate signaling transduction and abiotic stress responses is crucial for developing future crops with enhanced nitrogen-use efficiency and heightened resilience.

Zinc deficiency-induced defensin-like proteins are involved in the inhibition of root growth in Arabidopsis

The depletion of cellular zinc (Zn) adversely affects plant growth. Plants have adaptation mechanisms for Zn-deficient conditions, inhibiting growth through the action of transcription factors and metal transporters. We previously identified three defensin-like (DEFL) proteins (DEFL203, DEFL206 and DEFL208) that were induced in Arabidopsis thaliana roots under Zn-depleted conditions. DEFLs are small cysteine-rich peptides involved in defense responses, development and excess metal stress in plants. However, the functions of DEFLs in the Zn-deficiency response are largely unknown. Here, phylogenetic tree analysis revealed that seven DEFLs (DEFL202-DEFL208) were categorized into one subgroup. Among the seven DEFLs, the transcripts of five (not DEFL204 and DEFL205) were upregulated by Zn deficiency, consistent with the presence of cis-elements for basic-region leucine-zipper 19 (bZIP19) or bZIP23 in their promoter regions. Microscopic observation of GFP-tagged DEFL203 showed that DEFL203-sGFP was localized to the apoplast and plasma membrane. Whereas a single mutation of the DEFL202 or DEFL203 genes only slightly affected root growth, defl202 defl203 double mutants showed enhanced root growth under all growth conditions. We also showed that the size of the root meristem was increased in the double mutants compared with the wild type. Our results suggest that DEFL202 and DEFL203 are redundantly involved in the inhibition of root growth under Zn-deficient conditions through a reduction in root meristem length and cell number.

Growth or survival: What is the role of calmodulin-like proteins in plant?

Calcium signalling, including pulse, amplitude, and duration, is essential for plant development and response to various stimuli. However, the calcium signalling should be decoded and translated by calcium sensors. In plants, three classes of calcium-binding proteins have been identified as calcium sensors, including calcium-dependent protein kinase (CDPK), calcineurin B-like protein (CBL), and calmodulin (CaM). Calmodulin-like proteins (CMLs), which have several EF-hands, also serve as specific calcium sensors and can sense, bind, and interpret the calcium signal during the plant's growth and defense decision-making processes. In recent decades, the function of CMLs in plant development and response to various stimuli has been systematically reviewed, shedding light on the molecular mechanism of plant CML-mediated networks in calcium signal transduction. Here, by providing an overview of CML expression and biological function in plants, we demonstrate that growth-defense trade-offs occur during calcium sensing, an aspect that has not been well studied in recent years.

Crosstalk between brassinosteroid signaling and variable nutrient environments

Brassinosteroid (BR) represents a group of steroid hormones that regulate plant growth and development as well as environmental adaptation. The fluctuation of external nutrient elements is a situation that plants frequently face in the natural environment, in which nitrogen (N) and phosphorus (P) are two of the most critical nutrients restraint of the early growth of plants. As the macronutrients, N and P are highly required by plants, but their availability or solubility in the soil is relatively low. Since iron (Fe) and P always modulate each other's content and function in plants mutually antagonistically, the regulatory mechanisms of Fe and P are inextricably linked. Recently, BR has emerged as a critical regulator in nutrient acquisition and phenotypic plasticity in response to the variable nutrient levels in Arabidopsis and rice. Here, we review the current understanding of the crosstalk between BR and the three major nutrients (N, P, and Fe), highlighting how nutrient signaling regulates BR synthesis and signaling to accommodate plant growth and development in Arabidopsis and rice.

Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4, FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified.

Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling

Calcium (Ca²⁺) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca²⁺-signature, and are decoded by plethora of Ca²⁺ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca²⁺-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca²⁺ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca²⁺ sensor protein in plants. Their ability to bind Ca²⁺, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca²⁺ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca²⁺, the Ca²⁺ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca²⁺ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca²⁺ signaling.

Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth

Plant root architecture flexibly adapts to changing nitrate (NO₃^-) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO₃^--mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO₃^- in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO₃^- availability. Under low-NO₃^- availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.

More than growth: Phytohormone-regulated transcription factors controlling plant immunity, plant development and plant architecture

Activation of immunity by exogenous signals or mutations leading to autoimmunity has long been associated with decreased plant growth, known as the growth-defense tradeoff. Originally thought to be a redirection of metabolic resources towards defense and away from growth, recent studies have demonstrated that growth and defense can be uncoupled, indicating that metabolic regulation is not solely responsible for the growth-defense tradeoff. Immunity activation has effects on plant development beyond the reduction of plant biomass, including changes in plant architecture. Phytohormone signaling pathways, and crosstalk between these pathways, are responsible for regulating plant growth and development, and plant defense responses. Here we review the hormonal regulation of transcription factors that play roles in both defense and development, with a focus on their effects on plant architecture, and suggest the targeting of these transcription factors to increase plant immunity and change plant growth and form for enhancement of agronomical traits.

Regulation of pattern-triggered immunity and growth by phytocytokines

Endogenous signalling peptides play diverse roles during plant growth, development and stress responses. Research in recent years has unravelled peptides with previously known growth-regulatory function as immune-modulatory agents that fine-tune pattern-triggered immunity (PTI). Moreover, peptides that are long known as endogenous danger signals were recently implicated in growth and development. In analogy to metazoan systems these peptides are referred to as phytocytokines. In this review we will highlight recent progress made on our understanding of phytocytokines simultaneously regulating growth and PTI which shows the complex interplay of peptide signalling pathways regulating multiple aspects of a plant's life.

Characteristics of SlCML39, a Tomato Calmodulin-like Gene, and Its Negative Role in High Temperature Tolerance of Arabidopsis thaliana during Germination and Seedling Growth

Calmodulin-like (CML) proteins are primary calcium sensors and function in plant growth and response to stress stimuli. However, so far, the function of plant CML proteins, including tomato, is still unclear. Previously, it was found that a tomato (Solanum lycopersicum) CML, here named SlCML39, was significantly induced by high temperature (HT) at transcription level, but its biological function is scarce. In this study, the characteristics of SlCML39 and its role in HT tolerance were studied. SlCML39 encodes a protein of 201 amino acids containing four EF hand motifs. Many cis-acting elements related to plant stress and hormone response appear in the promoter regions of SlCML39. SlCML39 is mainly expressed in the root, stem, and leaf and can be regulated by HT, cold, drought, and salt stresses as well as ABA and H₂O₂. Furthermore, heterologous overexpression of SlCML39 reduces HT tolerance in Arabidopsis thaliana at the germination and seedling growth stages. To better understand the molecular mechanism of SlCML39, the downstream gene network regulated by SlCML39 under HT was analyzed by RNA-Seq. Interestingly, we found that many genes involved in stress responses as well as ABA signal pathway are down-regulated in the transgenic seedlings under HT stress, such as KIN1, RD29B, RD26, and MAP3K18. Collectively, these data indicate that SlCML39 acts as an important negative regulator in response to HT stress, which might be mediated by the ABA signal pathway.