Self-transcriptional repression of the Arabidopsis NAC transcription factor ATAF2 and its genetic interaction with phytochrome A in modulating seedling photomorphogenesis

Recombinant SpTransformer proteins bind to specific sites on sea urchin phagocytes and modulate SpTransformer gene expression and immune responsiveness

Introduction

The California purple sea urchin, Strongylocentrotus purpuratus, relies exclusively on an innate immune system to survive in its pathogen rich marine environment. Central to this defense is the SpTransformer (SpTrf) gene family that is unique to the euechinoid group of echinoderms. These genes were initially identified based on their striking upregulation in response to immune challenge. The SpTrf gene family encodes structurally similar proteins with a wide range of sequence diversity within and among individual sea urchins. A recombinant (r)SpTrf protein interacts specifically with a variety of non-self targets. Other rSpTrf proteins cross-linked to inert beads show distinct functions for cell binding and augmenting phagocytosis . However, whether the rSpTrf proteins bind to sea urchin phagocytes, and the cellular consequences of binding are largely unexplored.

Methods

rSpTrf protein binding to, and responses by phagocytes was investigated by cytology, flow cytometry, binding competitions using In-cell ELISA, and gene expression analyses.

Results

Soluble rSpTrf proteins bind specifically and exclusively to both live and fixed polygonal and small phagocytes. The different rSpTrf proteins appear to bind shared receptor(s) or other form of cell surface binding site. The phagocyte response to bound rSpTrf proteins culminates in modulated expression of the SpTrf gene family as well as other immune-related genes.

Conclusions

These findings underscore the multifaceted and dynamic functions of SpTrf proteins within the innate immune system of the purple sea urchin. Their varied functions enable a robust immune response while also providing a unique modulatory mechanism by which response levels are controlled and adjusted to the level of the foreign threat.

Identification of NAC Transcription Factors in Suaeda glauca and Their Responses to Salt Stress

NAC (NAM/ATAF1/2/CUC2) transcription factors regulate plant growth and development and stress responses. Because NAC transcription factors are known to play important roles in the regulation of salt tolerance in many plants, we aimed to explore their roles in the halophyte Suaeda glauca. Based on transcriptome sequencing data, we identified 25 NAC transcription factor gene family members. In a phylogenetic tree analysis with Arabidopsis thaliana NAC transcription factors, the SgNACs were divided into 10 groups. The physicochemical properties and conserved domains of the putative proteins, as well as the transcript profiles of their encoding genes, were determined for the 25 SgNAC genes using bioinformatic methods. Most of the S. glauca NAC genes were upregulated to some extent after 24 h of salt stress, suggesting that they play an important role in regulating the salt tolerance of S. glauca. These findings lay the foundation for further research on the functions and mechanisms of the NAC gene family in S. glauca.

NAC transcription factor ATAF1 negatively modulates the PIF-regulated hypocotyl elongation under a short-day photoperiod

Day length modulates hypocotyl elongation in seedlings to optimize their overall fitness. Variations in cell growth-associated genes are regulated by several transcription factors. However, the specific transcription factors through which the plant clock increases plant fitness are still being elucidated. In this study, we identified the no apical meristem, Arabidopsis thaliana-activating factor (ATAF-1/2), and cup-shaped cotyledon (NAC) family transcription factor ATAF1 as a novel repressor of hypocotyl elongation under a short-day (SD) photoperiod. Variations in day length profoundly affected the transcriptional and protein levels of ATAF1. ATAF1-deficient mutant exhibited increased hypocotyl length and cell growth-promoting gene expression under SD conditions. Moreover, ATAF1 directly targeted and repressed the expression of the cycling Dof factor 1/5 (CDF1/5), two key transcription factors involved in hypocotyl elongation under SD conditions. Additionally, ATAF1 interacted with and negatively modulated the effects of phytochrome-interacting factor (PIF), thus inhibiting PIF-promoted gene expression and hypocotyl elongation. Taken together, our results revealed ATAF1-PIF as a crucial pair modulating the expression of key transcription factors to facilitate plant growth during day/night cycles under fluctuating light conditions.

Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth

The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control in both mitochondria and chloroplasts, although its function in plastids is still under discussion. Here, we show that the overexpression of RPOTmp in Arabidopsis, targeted either to mitochondria or chloroplasts, disturbs the dormant seed state, and it causes the following effects: earlier germination, decreased ABA sensitivity, faster seedling growth, and earlier flowering. The germination of RPOTmp overexpressors is less sensitive to NaCl, while rpotmp knockout is highly vulnerable to salt stress. We found that mitochondrial dysfunction in the rpotmp mutant induces an unknown retrograde response pathway that bypasses AOX and ANAC017. Here, we show that RPOTmp transcribes the accD, clpP, and rpoB genes in plastids and up to 22 genes in mitochondria.

Genome-wide analysis of NAC transcription factors and exploration of candidate genes regulating selenium metabolism in Broussonetia papyrifera

MAIN CONCLUSION

Genome-wide identification revealed 79 BpNAC genes belonging to 16 subfamilies, and their gene structures and evolutionary relationships were characterized. Expression analysis highlighted their importance in plant selenium stress responses. Paper mulberry (Broussonetia papyrifera), a deciduous arboreal plant of the Moraceae family, is distinguished by its leaves, which are abundant in proteins, polysaccharides, and flavonoids, positioning it as a novel feedstock. NAC transcription factors, exclusive to plant species, are crucial in regulating growth, development, and response to biotic and abiotic stress. However, extensive characterization of the NAC family within paper mulberry is lacking. In this study, 79 BpNAC genes were identified from the paper mulberry genome, with an uneven distribution across 13 chromosomes. A comprehensive, genome-wide analysis of BpNACs was performed, including investigating gene structures, promoter regions, and chromosomal locations. Phylogenetic tree analysis, alongside comparisons with Arabidopsis thaliana NACs, allowed for categorizing these genes into 16 subfamilies in alignment with gene structure and motif conservation. Collinearity analysis suggested a significant homologous relationship between the NAC genes of paper mulberry and those in Morus notabilis, Ficus hispida, Antiaris toxicaria, and Cannabis sativa. Integrating transcriptome data and Se content revealed that 12 BpNAC genes were associated with selenium biosynthesis. Subsequent RT-qPCR analysis corroborated the correlation between BpNAC59, BpNAC62 with sodium selenate, and BpNAC55 with sodium selenite. Subcellular localization experiments revealed the nuclear functions of BpNAC59 and BpNAC62. This study highlights the potential BpNAC transcription factors involved in selenium metabolism, providing a foundation for strategically breeding selenium-fortified paper mulberry.

Cooperative transcriptional regulation by ATAF1 and HY5 promotes light-induced cotyledon opening in Arabidopsis thaliana

The opening of the embryonic leaves (cotyledons) as seedlings emerge from the dark soil into the light is crucial to ensure the survival of the plant. Seedlings that sprout in the dark elongate rapidly to reach light but keep their cotyledons closed. During de-etiolation, the transition from dark to light growth, elongation slows and the cotyledons open. Here, we report that the transcription factor ACTIVATING FACTOR1 (ATAF1) participates in de-etiolation and facilitates light-induced cotyledon opening. The transition from dark to light rapidly induced ATAF1 expression and ATAF1 accumulation in cotyledons. Seedlings lacking or overexpressing ATAF1 exhibited reduced or enhanced cotyledon opening, respectively, and transcriptomic analysis indicated that ATAF1 repressed the expression of genes associated with growth and cotyledon closure. The activation of the photoreceptor phytochrome A (phyA) by far-red light induced its association with the ATAF1 promoter and stimulation of ATAF1 expression. The transcription factor ELONGATED HYPOCOTYL5 (HY5), which is also activated in response far-red light, cooperated with phyA to induce ATAF1 expression. ATAF1 and HY5 interacted with one another and cooperatively repressed the expression of growth-promoting and cotyledon closure genes. Together, our study reveals a mechanism through which far-red light promotes cotyledon opening.

Characteristics and Functions of MYB (v-Myb avivan myoblastsis virus oncogene homolog)-Related Genes in Arabidopsis thaliana

The MYB (v-Myb avivan myoblastsis virus oncogene homolog) transcription factor family is one of the largest families of plant transcription factors which plays a vital role in many aspects of plant growth and development. MYB-related is a subclass of the MYB family. Fifty-nine Arabidopsis thaliana MYB-related (AtMYB-related) genes have been identified. In order to understand the functions of these genes, in this review, the promoters of AtMYB-related genes were analyzed by means of bioinformatics, and the progress of research into the functions of these genes has been described. The main functions of these AtMYB-related genes are light response and circadian rhythm regulation, root hair and trichome development, telomere DNA binding, and hormone response. From an analysis of cis-acting elements, it was found that the promoters of these genes contained light-responsive elements and plant hormone response elements. Most genes contained elements related to drought, low temperature, and defense and stress responses. These analyses suggest that AtMYB-related genes may be involved in A. thaliana growth and development, and environmental adaptation through plant hormone pathways. However, the functions of many genes do not occur independently but instead interact with each other through different pathways. In the future, the study of the role of the gene in different pathways will be conducive to a comprehensive understanding of the function of the gene. Therefore, gene cloning and protein functional analyses can be subsequently used to understand the regulatory mechanisms of AtMYB-related genes in the interaction of multiple signal pathways. This review provides theoretical guidance for the follow-up study of plant MYB-related genes.

NAC domain transcription factors VNI2 and ATAF2 form protein complexes and regulate leaf senescence

The NAM, ATAF1/2, and CUC2 (NAC) domain transcription factor VND-INTERACTING2 (VNI2) negatively regulates xylem vessel formation by interacting with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel formation. Here, we screened interacting proteins with VNI2 using yeast two-hybrid assay and isolated two NAC domain transcription factors, Arabidopsis thaliana ACTIVATION FACTOR 2 (ATAF2) and NAC DOMAIN CONTAINING PROTEIN 102 (ANAC102). A transient gene expression assay showed that ATAF2 upregulates the expression of genes involved in leaf senescence, and VNI2 effectively inhibits the transcriptional activation activity of ATAF2. vni2 mutants accelerate leaf senescence, whereas ataf2 mutants delay leaf senescence. In addition, the accelerated leaf senescence phenotype of the vni2 mutant is recovered by simultaneous mutation of ATAF2. Our findings strongly suggest that VNI2 interacts with and inhibits ATAF2, resulting in negatively regulating leaf senescence.

The NAC transcription factor ATAF2 promotes ethylene biosynthesis and response in Arabidopsis thaliana seedlings

Arabidopsis thaliana ACTIVATING FACTOR 2 (ATAF2) plays extensive regulatory roles in pathogenesis, seedling development, and stress responses. Here, we performed transcriptome analysis on ATAF2 loss- and gain-of-function mutants to identify differentially expressed genes (DEGs). Gene ontology analyses on DEGs reveal that ATAF2 enhances seedling responses to multiple hormone and stress signals. In particular, our transcriptome analysis suggests that ATAF2 promotes ethylene biosynthesis and responses via activating relevant genes. This novel role of ATAF2 was further demonstrated by using multiple ATAF2 null and overexpression lines for reverse transcription quantitative PCR verification, ethylene production measurements, and assays of seedlings growth responses to the ethylene immediate biosynthetic precursor 1-aminocyclopropane-1-carboxylic acid (ACC). ACC suppresses ATAF2 expression to form a negative feedback regulation loop.

MusaATAF2 like protein, a stress-related transcription factor, induces leaf senescence by regulating chlorophyll catabolism and H2 O2 accumulation

NAC transcription factors are known for their diverse role in plants. In this study, we have demonstrated the role of MusaATAF2, a banana NAC transcription factor, in leaf senescence. Its expression gets strongly up-regulated during the early stress responses of drought and high salinity exposure and down-regulated under ABA application, which suggests MusaATAF2 is a stress-related NAC transcription factor. To study the role of MusaATAF2 in banana, we have transformed the banana embryogenic cells with MusaATAF2 coding region and generated transgenic banana plants. Overexpression of MusaATAF2 in banana plants caused yellow leaf phenotype under control condition, suggesting its role as a senescence-associated transcription factor. Transgenic banana leaves exhibited low chlorophyll content and high H₂ O₂ accumulation. Hormone analysis of the leaves demonstrated a higher accumulation of ABA in the transgenic plants than the controls. Transgenic plants overexpressing MusaATAF2 have a higher transcript abundance of two chlorophyll catabolic pathway genes (PAO and HCAR) and lower transcript abundance of ROS scavenging enzymes (TDP, THIO, CAT, APX, and PRXDN) than control. Together, all these analyses indicate that MusaATAF2 induces senescence by inducing chlorophyll degradation and H₂ O₂ accumulation in banana plants and controls its own expression using an ABA-dependent feedback loop.

Two ATAF transcription factors ANAC102 and ATAF1 contribute to the suppression of cytochrome P450-mediated brassinosteroid catabolism in Arabidopsis

PHYB ACTIVATION TAGGED SUPPRESSOR 1 (BAS1) and SUPPRESSOR OF PHYB-4 7 (SOB7) are two cytochrome P450 enzymes that inactivate brassinosteroids (BRs) in Arabidopsis. The NAC transcription factor (TF) ATAF2 (ANAC081) and the core circadian clock regulator CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) both suppress the expression of BAS1 and SOB7 via direct promoter binding. Additionally, BRs cause feedback suppression on ATAF2 expression. Here, we report that two ATAF-subgroup TFs, ANAC102 and ATAF1 (ANAC002), also contribute to the transcriptional suppression of BAS1 and SOB7. ANAC102 and ATAF1 gene-knockout mutants exhibit elevated expression of both BAS1 and SOB7, expanded tissue-level accumulation of their protein products and reduced hypocotyl growth in response to exogenous BR treatments. Similar to ATAF2, both ANAC102 and ATAF1 are transcriptionally suppressed by BRs and white light. Neither BAS1 nor SOB7 expression is further elevated in ATAF double or triple mutants, suggesting that the suppression effect of these three ATAFs is not additive. In addition, ATAF single, double, and triple mutants have similar levels of BR responsiveness with regard to hypocotyl elongation. ATAF2, ANAC102, ATAF1, and CCA1 physically interact with itself and each other, suggesting that they may coordinately suppress BAS1 and SOB7 expression via protein-protein interactions. Despite the absence of CCA1-binding elements in their promoters, ANAC102 and ATAF1 have similar transcript circadian oscillation patterns as that of CCA1, suggesting that these two ATAF genes may be indirectly regulated by the circadian clock.

Effects of selenate on Se, flavonoid, and glucosinolate in broccoli florets by combined transcriptome and metabolome analyses

Broccoli is a nutritious vegetable popular all over the world. This study investigated the effects of different concentrations of selenate (0, 0.1, 0.2, 0.4, 0.8, and 1.6 mmol/L) on the selenium (Se), glucosinolate, and flavonoid contents of broccoli florets. Results showed that the total Se, selenomethionine, and methyl selenocysteine contents increased following selenate dosage. Interestingly, selenate treatment of 0.4 mmol/L decreased the flavonoid but increased the glucosinolate content. Metabolome analysis revealed changes in the individual contents of glucosinolates and flavonoids. Conjoint analysis of transcriptome and metabolome showed that the glucosinolate and flavonoid compounds were potentially regulated by two sulfate transporter genes (Sultr3;1 and Sultr4;2) and several cytochrome P450 genes (e.g., CYP71B21, CYP72C1, and CYP81F1). These new findings indicated that Se treatment may influence glucosinolate and flavonoid accumulation by regulating the expression of these genes. The results of this study provide some novel insights into the effects of Se on glucosinolates and flavonoids in broccoli florets and deepen our understanding of the regulatory network between some specific genes and these compounds.