Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants

Identification, growth characteristics, and genomic potential analysis of indole-3-acetic acid producing strain D1 in the rhizosphere of ancient tea forests

Chryseobacterium is one of the important beneficial microorganisms groups for protecting plant health. It has the functions of promoting host plant growth, stress resistance, inducing systemic resistance, and resisting pathogens, playing an important role in reducing soil biological barriers, and has broad application prospects. Therefore, screening for IAA producing Chryseobacterium and quickly understanding its genomic potential is of great significance in agricultural production. The unique ecological environment of wild ancient tea forests nurtures rhizosphere microbial resources with unique properties. This study identified the high-yielding indole-3-acetic acid (IAA) producing strain D1 from the rhizosphere of ancient tea forests as a new species of the Chryseobacterium genus, which is closely related to Chryseobacterium aureum and is recommended to be named Chryseobacterium tea sp. nov. Strain D1 exhibits excellent fermentation performance in producing IAA, achieving a maximum IAA yield of 149.24 mg/L after 60 h of fermentation in tryptophan medium. The optimal growth temperature for strain D1 is 25 °C, the optimal growth pH is 6, and the tolerance concentration to sodium chloride is 30 g/L. The genome of strain D1 contains abundant genetic resources for carbohydrate active enzymes, heavy metal resistance, secondary metabolite synthesis gene clusters, and plant pathogen resistance. This study enhances our understanding of the cultivation and genomic function of Chryseobacterium tea sp. nov, as well as the understanding of rhizosphere microorganisms in wild ancient tea forests. It also provides a theoretical basis for the development of Chryseobacterium tea sp. nov as functional fertilizers for crops.

Transcriptome analyses for revealing leaf abscission of Cyclocarya paliurus stem segments in vitro

Leaf abscission of Cyclocarya paliurus stem segments in vitro is very serious, and more than 90% of the leaves gradually fall off with prolonged culture time, which hinders breeding. This study investigated the molecular mechanism of leaf abscission. The emerged leaves of C. paliurus stem segments were cultured for 22 days (T0) in vitro; leaves at 27 days (T1) and leaves that had fallen after ≥ 32 days (T2) were used as materials for analysis of the physiological characteristics and transcriptome data. During the leaf abscission process of C. paliurus, the Indole-3-acetic acid (IAA) content gradually decreased, whereas the carotenoid, 1-aminocyclopropane-1-carboxylic acid (ACC) and lignin contents and pectinase and cellulase activities significantly increased; 1807 and 10,908 DEGs were obtained in T0 vs T1 and T1 vs T2, respectively. The plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway and flavonoid biosynthesis pathway were significantly enriched in the KEGG metabolic pathway analysis. The differential expression of related genes affected AUX and Ethylene (ETH) biosynthesis and signal transduction, lignin synthesis, ROS metabolism, leaf color changes. Weighted gene coexpression network analysis (WGCNA) identified 10 hub genes (U-box protein, ERF5, ERF109, ERF4, SAUR36, CML19, MYC2-like,SPHK1, TOE3, POD55) that interact to activate abscission signaling, which subsequently influences the genes expression involved in the biosynthesis and signal transduction of auxin and ethylene; this resulted in an imbalance of endogenous hormone levels in the leaves, leading to the upregulation of pectinase, cellulase, and lignin biosynthesis genes and acceleration of the rupture of the abscission zone (AZ) cell and vascular cell wall, which ultimately led to leaf abscission. The present study illustrates a regulatory mechanism of leaf abscission of C. paliurus stem segments in vitro, which provides potential application value for guiding the inhibition of leaf abscission in vitro.

Integrated Metabolome and Transcriptome Analyses Provides Insights into Ovule Abortion in Camellia oleifera

Camellia oleifera is a unique woody edible oil tree species in China, and the ovule development affects the yield of seeds. This study selected three different types of C. oleifera clones and used LC-MS, RNA-seq, and other techniques to compare the endogenous hormone contents, gene expression levels, and metabolite changes between normal and aborted ovules. The results showed that high levels of ABA, JA, and SA may lead to the phenotype of ovule abortion. A total of 270 differential metabolites were identified in the metabolome, with L-methionine, citrulline, L-tryptophan, L-phenylalanine, and indolepyruvate being downregulated to varying degrees in the aborted ovules. Genes involved in plant hormone synthesis and response, such as GH3.1, IAA14, PIN1, AUX22, ARF1_2, BZR1_2, GA2ox, ERFC3, ABF2, and PYL8, responded to ovule development. This study elucidates the physiological, metabolic, and transcriptional responses to ovule abortion, providing a theoretical basis for understanding ovule development and yield regulation in C. oleifera.

Auxin signaling related to H+-ATPase synthesis and antioxidant enzyme activities regulates fluoranthene uptake by ryegrass roots

Previous research has shown that fluoranthene (Flu) exhibits dual uptake behavior in ryegrass. At low concentrations (1-10 mg/L), Flu uptake is higher, whereas at higher concentrations (20-40 mg/L), uptake appears to decrease. Furthermore, indole-3-acetic acid (IAA) content and antioxidant enzyme activity play distinct roles in this process. However, the molecular mechanisms underlying these behaviors remain unclear. To address this, we exposed ryegrass to different Flu concentrations (0, 5, and 20 mg/L) and conducted a combined transcriptomic and physiological analysis of the root system to elucidate the specific mechanisms of Flu uptake. Our results revealed that under 5 mg/L Flu treatment, ryegrass has a higher bioconcentration factor (BCF). The genes involved in IAA synthesis (TAA1, ALDH, and AAO1/2) were upregulated, which led to an increase in IAA content. Elevated IAA levels, in turn, promoted the expression of genes encoding H+-ATPase (ATP5A1, ATP5B, ATP5H, and ATP6E) and the ABC transporter protein (ABCB1), resulting in enhanced H+-ATPase activity, and facilitated the active transport of Flu. In contrast, the 20 mg/L Flu treatment resulted in a lower BCF. The downregulation of IAA synthesis genes (amiE and YUCCA) decreased IAA content. The downregulation of the H+-ATPase gene (ATP6C) and the ABC transporter protein gene (ABCG2), resulting in decreased H+-ATPase activity and inhibited Flu transport. Moreover, the promoted expression of redox-related genes (POD1, SOD1 and SOD2) further reduced Flu uptake. Elucidating the molecular mechanisms underlying Flu uptake in ryegrass may provide a theoretical foundation for developing strategies to regulate Flu accumulation in plants.

An Overview of the Mechanisms through Which Plants Regulate ROS Homeostasis under Cadmium Stress

Cadmium (Cd2+) is a non-essential and highly toxic element to all organic life forms, including plants and humans. In response to Cd stress, plants have evolved multiple protective mechanisms, such as Cd2+ chelation, vesicle sequestration, the regulation of Cd2+ uptake, and enhanced antioxidant defenses. When Cd2+ accumulates in plants to a certain level, it triggers a burst of reactive oxygen species (ROS), leading to chlorosis, growth retardation, and potentially death. To counteract this, plants utilize a complex network of enzymatic and non-enzymatic antioxidant systems to manage ROS and protect cells from oxidative damage. This review systematically summarizes how various elements, including nitrogen, phosphorus, calcium, iron, and zinc, as well as phytohormones such as abscisic acid, auxin, brassinosteroids, and ethylene, and signaling molecules like nitric oxide, hydrogen peroxide, and hydrogen sulfide, regulate the antioxidant system under Cd stress. Furthermore, it explores the mechanisms by which exogenous regulators can enhance the antioxidant capacity and mitigate Cd toxicity.

Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa)

BACKGROUND

The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle.

RESULTS

Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups.

CONCLUSIONS

These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

IbNF-YA1 is a key factor in the storage root development of sweet potato

As a major worldwide root crop, the mechanism underlying storage root yield formation has always been a hot topic in sweet potato [Ipomoea batatas (L.) Lam.]. Previously, we conducted the transcriptome database of differentially expressed genes between the cultivated sweet potato cultivar "Xushu18," its diploid wild relative Ipomoea triloba without storage root, and their interspecific somatic hybrid XT1 with medium-sized storage root. We selected one of these candidate genes, IbNF-YA1, for subsequent analysis. IbNF-YA1 encodes a nuclear transcription factor Y subunit alpha (NF-YA) gene, which is significantly induced by the natural auxin indole-3-acetic acid (IAA). The storage root yield of the IbNF-YA1 overexpression (OE) plant decreased by 29.15-40.22% compared with the wild type, while that of the RNAi plant increased by 10.16-21.58%. Additionally, IAA content increased significantly in OE plants. Conversely, the content of IAA decreased significantly in RNAi plants. Furthermore, real-time quantitative reverse transcription-PCR (qRT-PCR) analysis demonstrated that the expressions of the key genes IbYUCCA2, IbYUCCA4, and IbYUCCA8 in the IAA biosynthetic pathway were significantly changed in transgenic plants. The results indicated that IbNF-YA1 could directly target IbYUCCA4 and activate IbYUCCA4 transcription. The IAA content of IbYUCCA4 OE plants increased by 71.77-98.31%. Correspondingly, the storage root yield of the IbYUCCA4 OE plant decreased by 77.91-80.52%. These findings indicate that downregulating the IbNF-YA1 gene could improve the storage root yield in sweet potato.

Auxin regulates bulbil initiation by mediating sucrose metabolism in Lilium lancifolium

Lily bulbils, which serve as advantageous axillary organs for vegetative propagation, have not been extensively studied in terms of the mechanism of bulbil initiation. The functions of auxin and sucrose metabolism have been implicated in axillary organ development, but their relationship in regulating bulbil initiation remains unclear. In this study, exogenous indole-3-acetic acid (IAA) treatment increased the endogenous auxin levels at leaf axils and significantly decreased bulbil number, whereas treatment with the auxin polar transport inhibitor N-1-naphthylphthalamic acid (NPA), which resulted in a low auxin concentration at leaf axils, stimulated bulbil initiation and increased bulbil number. A low level of auxin caused by NPA spraying or silencing of auxin biosynthesis genes YUCCA FLAVIN MONOOXYGENASE-LIKE 6 (LlYUC6) and TRYPTOPHAN AMINOTRANSFERASERELATED 1 (LlTAR1) facilitated sucrose metabolism by activating the expression of SUCROSE SYNTHASES 1 (LlSusy1) and CELL WALL INVERTASE 2 (LlCWIN2), resulting in enhanced bulbil initiation. Silencing LlSusy1 or LlCWIN2 hindered bulbil initiation. Moreover, the transcription factor BASIC HELIX-LOOP-HELIX 35 (LlbHLH35) directly bound the promoter of LlSusy1, but not the promoter of LlCWIN2, and activated its transcription in response to the auxin content, bridging the gap between auxin and sucrose metabolism. In conclusion, our results reveal that an LlbHLH35-LlSusy1 module mediates auxin-regulated sucrose metabolism during bulbil initiation.

CLV3-CLV1 signaling governs flower primordia outgrowth across environmental temperatures

The initiation and outgrowth of floral primordia are critical for flower formation and reproductive success; however, the underlying mechanisms are still unclear. Two reports (Jones et al.; John et al.) shed light on how CLV3-CLV1 signaling promoted flower primordia formation and outgrowth by regulating auxin biosynthesis under distinct environmental temperatures.

Plant Growth Regulation in Cell and Tissue Culture In Vitro

Precise knowledge of all aspects controlling plant tissue culture and in vitro plant regeneration is crucial for plant biotechnologists and their correlated industry, as there is increasing demand for this scientific knowledge, resulting in more productive and resilient plants in the field. However, the development and application of cell and tissue culture techniques are usually based on empirical studies, although some data-driven models are available. Overall, the success of plant tissue culture is dependent on several factors such as available nutrients, endogenous auxin synthesis, organic compounds, and environment conditions. In this review, the most important aspects are described one by one, with some practical recommendations based on basic research in plant physiology and sharing our practical experience from over 20 years of research in this field. The main aim is to help new plant biotechnologists and increase the impact of the plant tissue culture industry worldwide.

The Roles of GRETCHEN HAGEN3 (GH3)-Dependent Auxin Conjugation in the Regulation of Plant Development and Stress Adaptation

The precise control of free auxin (indole-3-acetic acid, IAA) gradient, which is orchestrated by biosynthesis, conjugation, degradation, hydrolyzation, and transport, is critical for all aspects of plant growth and development. Of these, the GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetase family, pivotal in conjugating IAA with amino acids, has garnered significant interest. Recent advances in understanding GH3-dependent IAA conjugation have positioned GH3 functional elucidation as a hot topic of research. This review aims to consolidate and discuss recent findings on (i) the enzymatic mechanisms driving GH3 activity, (ii) the influence of chemical inhibitor on GH3 function, and (iii) the transcriptional regulation of GH3 and its impact on plant development and stress response. Additionally, we explore the distinct biological functions attributed to IAA-amino acid conjugates.

Identification and evolution analysis of YUCCA genes of Medicago sativa and Medicago truncatula and their expression profiles under abiotic stress

The YUCCAs (YUC) are functionally identified flavin-containing monooxidases (FMOs) in plants that act as an important rate-limiting enzyme functioning in the auxin synthesis IPA (indole-3-pyruvic acid) pathway. In this study, 12 MsYUCs and 15 MtYUCs containing characteristic conserved motifs were identified in M. sativa (Medicago sativa L.) and M. truncatula (Medicago truncatula Gaertn.), respectively. Phylogenetic analysis revealed that YUC proteins underwent an evolutionary divergence. Both tandem and segmental duplication events were presented in MsYUC and MtYUC genes. Comparative syntenic maps of M. sativa with M. truncatula, Arabidopsis (Arabidopsis thaliana), or rice (Oryza sativa L.) were constructed to illustrate the evolution relationship of the YUC gene family. A large number of cis-acting elements related to stress response and hormone regulation were revealed in the promoter sequences of MsYUCs. Expression analysis showed that MsYUCs had a tissue-specific, genotype-differential expression and a differential abiotic stress response pattern based on transcriptome data analysis of M. sativa online. In addition, RT-qPCR confirmed that salt stress significantly induced the expression of MsYUC1/MsYUC10 but significantly inhibited MsYUC2/MsYUC3 expression and the expression of MsYUC10/MsYUC11/MsYUC12 was significantly induced by cold treatment. These results could provide valuable information for functional analysis of YUC genes via gene engineering of the auxin synthetic IPA pathway in Medicago.

Biosynthetic Pathways of Hormones in Plants

Phytohormones exhibit a wide range of chemical structures, though they primarily originate from three key metabolic precursors: amino acids, isoprenoids, and lipids. Specific amino acids, such as tryptophan, methionine, phenylalanine, and arginine, contribute to the production of various phytohormones, including auxins, melatonin, ethylene, salicylic acid, and polyamines. Isoprenoids are the foundation of five phytohormone categories: cytokinins, brassinosteroids, gibberellins, abscisic acid, and strigolactones. Furthermore, lipids, i.e., α-linolenic acid, function as a precursor for jasmonic acid. The biosynthesis routes of these different plant hormones are intricately complex. Understanding of these processes can greatly enhance our knowledge of how these hormones regulate plant growth, development, and physiology. This review focuses on detailing the biosynthetic pathways of phytohormones.