Auxin Response Factor Research Articles

Silencing of the MP Gene via dsRNA Affects Root Development and Growth in the Invasive Weed Mikania micrantha

Mikania micrantha (“mile-a-minute” weed) is a global invasive alien weed that can cause severe damage to agroforestry ecosystems and significant agricultural losses worldwide. Although chemical, manual, or mechanical control methods are widely used to control M. micrantha, RNA interference (RNAi)-based biocontrol methods have rarely been reported for this species. The MONOPTEROS (MP) gene, encoding an auxin response factor, plays an essential role in embryonic root initiation in Arabidopsis thaliana. In this study, we identified the MP gene from M. micrantha via orthologous gene analysis. A total of 37 MP orthologous genes was identified in 4 plants, including 9 MP candidate genes in M. micrantha, 13 in Helianthus annuus, 6 in Chrysanthemum nankingense, and 9 in Lactuca sativa. Phylogenetic analysis revealed that an MP candidate gene in M. micrantha (Mm01G000655, named MmMP) was clustered into one clade with the MP gene in A. thaliana (AtMP). In addition, both MmMP and AtMP contain a B3-DNA binding domain that is shared by transcription factors that regulate plant embryogenesis. To study gene function, dsRNA against MmMP (dsMmMP) was applied to the roots of M. micrantha. Compared with those of the controls, the expression of MmMP was reduced by 43.3%, 22.1%, and 26.2% on the first, third, and fifth days after dsMmMP treatment, respectively. The dsMmMP-treated plants presented several morphological defects, mostly in the roots. Compared with water-treated plants, the dsMmMP-treated plants presented reduced developmental parameters, including root length, number of adventitious roots, root fresh and dry weights, plant height, and aboveground biomass. Additionally, safety assessment suggested that this dsMmMP treatment did not silence MP genes from non-target plants, including rice and tomato; nor did it inhibit root growth in those species. Collectively, these results suggest that MmMP plays an important role in root development in M. micrantha and provides a potential target for the development of species-specific RNAi-based herbicides.

Deciphering the Genetic and Biochemical Drivers of Fruit Cracking in Akebia trifoliata.

This study investigates the molecular mechanisms underlying fruit cracking in Akebia trifoliata, a phenomenon that significantly impacts fruit quality and marketability. Through comprehensive physiological, biochemical, and transcriptomic analyses, we identified key changes in cell wall components and enzymatic activities during fruit ripening. Our results revealed that ventral suture tissues exhibit significantly elevated activities of polygalacturonase (PG) and β-galactosidase compared to dorsoventral line tissues, indicating their crucial roles in cell wall degradation and structural weakening. The cellulose content in VS tissues peaked early and declined during ripening, while DL tissues maintained relatively stable cellulose levels, highlighting the importance of cellulose dynamics in fruit cracking susceptibility. Transcriptomic analysis revealed differentially expressed genes (DEGs) associated with pectin biosynthesis and catabolism, cell wall organization, and oxidoreductase activities, indicating significant transcriptional regulation. Key genes like AKT032945 (pectinesterase) and AKT045678 (polygalacturonase) were identified as crucial for cell wall loosening and pericarp dehiscence. Additionally, expansin-related genes AKT017642, AKT017643, and AKT021517 were expressed during critical stages, promoting cell wall loosening. Genes involved in auxin-activated signaling and oxidoreductase activities, such as AKT022903 (auxin response factor) and AKT054321 (peroxidase), were also differentially expressed, suggesting roles in regulating cell wall rigidity. Moreover, weighted gene co-expression network analysis (WGCNA) identified key gene modules correlated with traits like pectin lyase activity and soluble pectin content, pinpointing potential targets for genetic manipulation. Our findings offer valuable insights into the molecular basis of fruit cracking in A. trifoliata, laying a foundation for breeding programs aimed at developing crack-resistant varieties to enhance fruit quality and commercial viability.

VvFHY3 links auxin and endoplasmic reticulum stress to regulate grape anthocyanin biosynthesis at high temperatures.

Anthocyanins affect quality in fruits such as grape (Vitis vinifera). High temperatures reduce anthocyanin levels by suppressing the expression of anthocyanin biosynthesis genes and decreasing the biosynthetic rate. However, the regulatory mechanisms that coordinate these two processes remain largely unknown. In this study, we demonstrate that high-temperature-mediated inhibition of anthocyanin biosynthesis in grape berries depends on the auxin and endoplasmic reticulum (ER) stress pathways. Inactivation of these pathways restores anthocyanin accumulation under high temperatures. We identified and characterized FAR-RED ELONGATED HYPOCOTYL3 (FHY3), a high-temperature-modulated transcription factor that activates multiple anthocyanin biosynthesis genes by binding to their promoters. The auxin response factor VvARF3 interacts with VvFHY3 and represses its transactivation activity, antagonizing VvFHY3-induced anthocyanin biosynthesis. Additionally, we found that the ER stress sensor VvbZIP17 represses anthocyanin biosynthesis. VvFHY3 suppresses VvbZIP17 activity by directly binding to the VvbZIP17 promoter to repress its transcription and by physically interacting with VvbZIP17 to block its DNA binding ability. Furthermore, AUXIN RESPONSE FACTOR 3 (ARF3) interferes with the VvFHY3-VvbZIP17 interaction, releasing VvbZIP17 to activate the unfolded protein response and further suppress anthocyanin production. Our results unravel the VvARF3-VvFHY3-VvbZIP17 regulatory module, which links the auxin and ER stress pathways to coordinately repress anthocyanin structural gene expression and biosynthesis under high-temperature stress.

Exploring Genomic Regions Associated with Fruit Traits in Pepper: Insights from Multiple GWAS Models.

This study utilized 303 pepper accessions from diverse Capsicum species to explore fruit traits, including length, width, wall thickness, and weight. Descriptive statistics revealed a mean fruit length of 66.19 mm, width of 23.48 mm, wall thickness of 1.89 mm, and weight of 15.29 g, with significant variability, particularly in fruit weight. Correlation analysis demonstrated strong positive relationships between fruit width, weight, and fruit wall thickness (r = 0.89 and r = 0.86, respectively), while fruit length showed weaker correlations with these traits. Analysis of fruit positions revealed that the majority of accessions had a pendent fruit position (156), followed by erect (85) and intermediate (8). In terms of fruit shape, triangular and narrow triangular shapes were the most common, observed in 102 and 98 accessions, respectively. Genome-wide association studies (GWAS) identified significant single nucleotide polymorphisms (SNPs) associated with fruit traits across four models (Blink, FarmCPU, MLM, MLMM). The number of significantly associated SNPs were as follows: fruit length (89), fruit width (55), fruit weight (63), fruit wall thickness (48), fruit shape (151), and fruit position (51). Several genes were also identified where the SNPs are located or adjacent to, providing candidate genes for further exploration of the genetic basis of fruit morphology. Notably, genes such as E3 ubiquitin-protein ligase RGLG1 (associated with fruit width), Homeobox-leucine zipper protein HDG11 (involved in fruit width), Auxin response factor 23 (linked to fruit shape), and ATP-dependent zinc metalloprotease FtsH (related to fruit weight) were identified. These findings enhance our understanding of the genetic basis of fruit morphology in Capsicum, offering valuable insights for breeding and agricultural practices.

Fast and simple fluorometric measurement of phloem loading exposes auxin-dependent regulation of Arabidopsis sucrose transporter AtSUC2.

The rate of sucrose export from leaves is a major factor in balancing whole-plant carbon and energy partitioning. A comprehensive study of its dynamics and relationship to photosynthesis, sink demand, and other relevant processes is hampered by the shortcomings of current methods for measuring sucrose phloem loading. We utilize the ability of sucrose transporter proteins, known as SUCs or SUTs, to specifically transport the fluorescent molecule esculin in a novel assay to measure phloem loading rates. Esculin was administered to source leaves and its fluorescence in the leaf extract was measured after 1 or 2 h. Dicot plants with an active phloem loading strategy showed an export-dependent reduction of esculin fluorescence. Relative leaf esculin export rates correlated with leaf export rates of isotopic carbon and phloem exudate sucrose levels. We used esculin experiments to examine the effects of phytohormones on phloem loading in Arabidopsis, showing, for example, that auxin induces phloem loading while cytokinin reduces it. Transcriptional regulation of AtSUC2 by AUXIN RESPONSE FACTOR1 (ARF1) corroborated the link between auxin signaling and phloem loading. Unlike established methods, the esculin assay is rapid and does not require specialized equipment. Potential applications and limitations of the esculin assay are discussed.

A mobile miR160-triggered transcriptional axis controls root stem cell niche maintenance and regeneration in Arabidopsis.

In multicellular organisms, communication between cells is vital for their fate determination. In plants, the quiescent center (QC) signals to adjacent stem cells to maintain them undifferentiated. However, how surrounding stem cells instruct the QC remains poorly understood. Here, we show that in the Arabidopsis root, microRNA160 (miR160) moves from stele stem cells (SSCs) to the QC, where it degrades the mRNAs of two auxin response factors, ARF10 and ARF17. This degradation relieves BRAVO from direct transcriptional repression, maintaining QC quiescence. We further identify that blocking miR160 movement due to DNA damage-induced SSC death and restricted symplastic transport reduces BRAVO and WOX5 expression, leading to QC division to replenish damaged stem cells during root regeneration. Together, our results demonstrate that a transcriptional axis initiated by mobile miR160 regulates the QC and stem cell behavior, advancing our understanding of the communication between stem cells and their surrounding cellular environment.

The OsMAPK5-OsWRKY72 module negatively regulates grain length and grain weight in rice.

Grain size and grain weight are important determinants for grain yield. In this study, we identify a novel OsMAPK5-OsWRKY72 module that negatively regulates grain length and grain weight in rice. We found that loss-of-function of OsMAPK5 leads to larger cell size of the rice spikelet hulls and a significant increase in both grain length and grain weight in an indica variety Minghui 86 (MH86). OsMAPK5 interacts with OsMAPKK3/4/5 and OsWRKY72 and phosphorylates OsWRKY72 at T86 and S88. Similar to the osmapk5 MH86 mutants, the oswrky72 knockout MH86 mutants exhibited larger size of spikelet hull cells and increased grain length and grain weight, whereas the OsWRKY72-overexpression MH86 plants showed opposite phenotypes. OsWRKY72 targets the W-box motifs in the promoter of OsARF6, an auxin response factor involved in auxin signaling. Dual-luciferase reporter assays demonstrated that OsWRKY72 activates OsARF6 expression. The activation effect of the phosphorylation-mimicking OsWRKY72T86D/S88D on OsARF6 expression was significantly enhanced, whereas the effects of the OsWRKY72 phosphorylation-null mutants were significantly reduced. In addition, auxin levels in young panicles of the osmapk5 and oswrky72 mutants were significantly higher than that in the wild-type MH86. Collectively, our study uncovered novel connections of the OsMAPKK3/4/5-OsMAPK5-mediated MAPK signaling, OsWRKY72-mediated transcription regulation, and OsARF6-mediated auxin signaling pathways in regulating grain length and grain weight in an indica-type rice, providing promising targets for molecular breeding of rice varieties with high yield and quality.

Plant hormone signaling is involved in regulating flower bud size of daylily

To explore the role and metabolic differences of plant hormones in regulating the flower bud size of daylily, we collected the flower buds from two daylily varieties 'Datong Huanghua' and 'Dongbei Huanghua' at the young bud, green, yellowing, and yellow stages for transcriptome sequencing. The differentially expressed genes (DEGs) were screened, and the exogenous plant hormone spraying experiments were conducted. A total of 199 DEGs related to the biosynthesis and metabolism of plant hormones was screened out at different flower development stages of 'Datong Huanghua' and 'Dongbei Huanghua'. These genes regulated the biosynthesis and metabolism of six plant hormones: abscisic acid, gibberellin, auxin, jasmonate, cytokinin, and ethylene. The DEGs associated with auxin were the most, which suggested that auxin played a role in regulating flower bud development. The auxin response factor (ARF) presented up-regulated expression at all the four stages of flower bud development, indicating that ARF played a positive regulatory role throughout the flower bud development of daylily. The experiments with exogenous spraying of six hormones further verified that indole-3-acetic acid (IAA) significantly promoted the growth and increased the nutrient content in the flower buds of 'Datong Huanghua', suggesting that IAA played a role in regulating flower bud development. Our results laid a theoretical foundation for probing into the regulatory mechanism of flower bud development of 'Datong Huanghua' and 'Dongbei Huanghua'.

Tomato SlARF5 participate in the flower organ initiation process and control plant height

Plant height is a critical agronomic trait closely linked to yield, primarily regulated by Gibberellins (GA) and auxins, which interact in complex ways. However, the mechanism underlying their interactions remain incompletely understood. In this study, we identified a tomato mutant exhibiting significantly reduced plant height. Through gene cloning and bulked segregant analysis (BSA) sequencing, we found that the mutant gene corresponds to the tomato auxin response factor gene SlARF5/MP. Here, we show that overexpression of SlARF5/MP significantly enhances plant height. Additionally, treatment with GA3 restored the plant height of the mutant to wild-type (WT) levels, indicating that GA content is a key factor influencing plant height. We also observed significant upregulation of GA-biosynthesis genes, including GA2-oxidases GA20ox3 and GA20ox4, as well as the GA3 biosynthesis gene GA3ox1, in SlARF5-overexpressing plants. Furthermore, we demonstrated that SlARF5 directly binds to SlGA2ox3, which mediates the conversion of GA3 to inactive GA, therebyregulating its expression. Our findings suggest that SlARF5 modulates GA3 metabolism by regulating GA synthesis genes, ultimately leading to alterations in plant height.

GhGRF4/GhARF2-GhGASA24 module regulates fiber cell wall thickness by modulating cellulose biosynthesis in upland cotton (Gossypium hirsutum).

Fiber elongation rate is an essential characteristic of cotton fiber in the textile industry, yet it has been largely overlooked in genetic studies. Gibberellins (GAs) and auxin (IAA) are recognized for their role in directing numerous developmental processes in plants by influencing cell differentiation and elongation. However, the degree to which GA-IAA interaction governs cellular elongation in cotton fiber cells remains to be fully understood. In this study, we identified a causal gene, Gibberellic Acid-Stimulated in Arabidopsis 24 (GhGASA24), that appears to be responsible for fiber elongation rate via regulating fiber cell wall thickness. Subsequent experiments revealed that GhGASA24 influences cell wall formation by promoting the expression of GhCesA8 and GhCesA10. Our findings suggest that Auxin Response Factor 2 (GhARF2) regulates fiber elongation rate by directly binding to the AuxRE elements in GhGASA24 promoter. In addition, we identified Growth Regulation Factor 4 (GhGRF4) as a transcription factor that interacts with GhARF2 to form a heterodimer complex, which also transcriptionally activates GhGASA24. Intriguingly, GhGRF4 regulates GhARF2 expression by directly binding to its promoter, thereby acting as a cascade regulator to enhance the transcriptional levels of GhGASA24. We propose that the GhGRF4/GhARF2-GhGASA24-GhCesAs module may contribute to fiber cell wall thickness by modulating cellulose biosynthesis, and provide a theoretical basis for improvement of fiber quality.

Pseudomonas chlororaphis subsp. aurantiaca Stimulates Lateral Root Development by Integrating Auxin and Reactive Oxygen Species Signaling in Arabidopsis.

Plant growth-promoting rhizobacteria (PGPR) can promote lateral root formation, while the underlying mechanisms are not fully understood. Here, we found that Pseudomonas chlororaphis subsp. aurantiaca inoculation enhanced auxin accumulation in lateral root primordia (LRP). Upon reaching LRPs, auxin activated the AUXIN RESPONSE FACTOR 7 and 19 (ARF7/19) and promoted lateral root formation in Arabidopsis. Moreover, we found that reactive oxygen species (ROS) is required for auxin-dependent lateral root emergence, and P. chlororaphis upregulated the expression of RESPIRATORY BURST OXIDASE D and F (RBOHD/F), leading to the accumulation of ROS in LRP. Although scavenging ROS or rbohd/f mutants exhibited decreased lateral roots after P. chlororaphis inoculation, the bacteria-triggered auxin signals were not altered. Conversely, the application of auxin or mutants defective in auxin signaling disturbed P. chlororaphis-derived ROS accumulation in lateral roots. Collectively, these results suggest that ARF7/19-dependent auxin signaling activates RBOHD/F to produce ROS, coordinately facilitating lateral root development after P. chlororaphis treatment.

AUXIN RESPONSE FACTOR 2 mediates repression of strawberry receptacle ripening via auxin-ABA interplay.

Cultivated strawberry (Fragaria × ananassa) is a popular, economically important fruit. The ripening of the receptacle (pseudocarp), the main edible part, depends on endogenously produced abscisic acid (ABA) and is suppressed by the high level of auxin produced from achenes (true fruit) during early development. However, the mechanism whereby auxin regulates receptacle ripening through inhibiting ABA biosynthesis remains unclear. Here, we identified AUXIN RESPONSE FACTOR 2 (FaARF2), which showed decreased expression with reduced auxin content in the receptacle, leading to increased ABA levels and accelerated ripening. Dual-luciferase, yeast one-hybrid, and electrophoretic mobility shift assays demonstrated that FaARF2 could bind to the AuxRE element in the promoter of 9-CIS-EPOXYCAROT-ENOID DIOXYGENASE 1 (FaNCED1), a key ABA biosynthetic gene, to suppress its transcriptional activity. Transiently overexpressing FaARF2 in the receptacles decreased FaNCED1 expression and ABA levels, resulting in inhibition of receptacle ripening and of development of quality attributes, such as pigmentation, aroma, and sweetness. This inhibition caused by overexpressing FaARF2 was partially recovered by the injection of exogenous ABA; conversely, transient silencing of FaARF2 using RNA interference produced the opposite results. The negative targeting of FaNCED1 by FaARF2 is a key link between auxin-ABA interactions and regulation of strawberry ripening.

Auxin response factor 10 insensitive to miR160regulation induces apospory-like phenotypes in Arabidopsis

The Arabidopsis megaspore mother cell (MMC) arises from somatic cells in the ovule primordium and enters meiosis to generate four megaspores. Only the most chalazal (functional megaspore, FM) survives, undergoing a series of mitoses to form the female gametophyte. We show that this commitment to the sexual germline requires spatial regulation of A UXIN R ESPONSE F ACTOR 10 (ARF10). GFP-fusion lines reveal ARF10 expression to be restricted to cells surrounding the MMC in wild type, but ectopically disseminated throughout the ovule in transgenic mARF10 lines insensitive to miR160, an ARF10 downregulator. Significantly, mARF10 ovules develop multiple FMs with differing ploidies, forming putative supernumerary gametophytes with altered polarity and cell identities- features of aposporous apomixis. Furthermore, we confirm the complexity of ovular ARF10 expression, being mediated by SEEDSTICK, ARGONAUTE1, and miR160. This work adds to our understanding of molecular switches possibly regulating aposporous apomixis, and may contribute the development of innovative plant breeding strategies.

Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance.

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

Exploring Novel Genomic Loci and Candidate Genes Associated with Plant Height in Bulgarian Bread Wheat via Multi-Model GWAS.

In the context of crop breeding, plant height (PH) plays a pivotal role in determining straw and grain yield. Although extensive research has explored the genetic control of PH in wheat, there remains an opportunity for further advancements by integrating genomics with growth-related phenomics. Our study utilizes the latest genome-wide association scan (GWAS) techniques to unravel the genetic basis of temporal variation in PH across 179 Bulgarian bread wheat accessions, including landraces, tall historical, and semi-dwarf modern varieties. A GWAS was performed with phenotypic data from three growing seasons, the calculated best linear unbiased estimators, and the leveraging genotypic information from the 25K Infinium iSelect array, using three statistical methods (MLM, FarmCPU, and BLINK). Twenty-five quantitative trait loci (QTL) associated with PH were identified across fourteen chromosomes, encompassing 21 environmentally stable quantitative trait nucleotides (QTNs), and four haplotype blocks. Certain loci (17) on chromosomes 1A, 1B, 1D, 2A, 2D, 3A, 3B, 4A, 5B, 5D, and 6A remain unlinked to any known Rht (Reduced height) genes, QTL, or GWAS loci associated with PH, and represent novel regions of potential breeding significance. Notably, these loci exhibit varying effects on PH, contribute significantly to natural variance, and are expressed during seedling to reproductive stages. The haplotype block on chromosome 6A contains five QTN loci associated with reduced height and two loci promoting height. This configuration suggests a substantial impact on natural variation and holds promise for accurate marker-assisted selection. The potentially novel genomic regions harbor putative candidate gene coding for glutamine synthetase, gibberellin 2-oxidase, auxin response factor, ethylene-responsive transcription factor, and nitric oxide synthase; cell cycle-related genes, encoding cyclin, regulator of chromosome condensation (RCC1) protein, katanin p60 ATPase-containing subunit, and expansins; genes implicated in stem mechanical strength and defense mechanisms, as well as gene regulators such as transcription factors and protein kinases. These findings enrich the pool of semi-dwarfing gene resources, providing the potential to further optimize PH, improve lodging resistance, and achieve higher grain yields in bread wheat.

Identification of potential auxin response candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis.

Throughout domestication, crop plants have gone through strong genetic bottlenecks, dramatically reducing the genetic diversity in today's available germplasm. This has also reduced the diversity in traits necessary for breeders to develop improved varieties. Many strategies have been developed to improve both genetic and trait diversity in crops, from backcrossing with wild relatives, to chemical/radiation mutagenesis, to genetic engineering. However, even with recent advances in genetic engineering we still face the rate limiting step of identifying which genes and mutations we should target to generate diversity in specific traits. Here, we apply a comparative evolutionary approach, pairing phylogenetic and expression analyses to identify potential candidate genes for diversifying soybean (Glycine max) canopy cover development via the nuclear auxin signaling gene families, while minimizing pleiotropic effects in other tissues. In soybean, rapid canopy cover development is correlated with yield and also suppresses weeds in organic cultivation. We identified genes most specifically expressed during early canopy development from the TIR1/AFB auxin receptor, Aux/IAA auxin co-receptor, and ARF auxin response factor gene families in soybean, using principal component analysis. We defined Arabidopsis thaliana and model legume species orthologs for each soybean gene in these families allowing us to speculate potential soybean phenotypes based on well-characterized mutants in these model species. In future work, we aim to connect genetic and functional diversity in these candidate genes with phenotypic diversity in planta allowing for improvements in soybean rapid canopy cover, yield, and weed suppression. Further development of this and similar algorithms for defining and quantifying tissue- and phenotype-specificity in gene expression may allow expansion of diversity in valuable phenotypes in important crops.

MCTP controls nucleocytoplasmic partitioning of AUXIN RESPONSE FACTORs during lateral root development.

The plant hormone auxin orchestrates almost all aspects of plant growth and development. AUXIN RESPONSE FACTORs (ARFs) control the transcription of auxin-responsive genes, forming cytoplasmic condensates to modulate auxin sensitivity and diversify auxin response regulation. However, the dynamic control of ARF distribution across different subcellular compartments remains largely obscure. Here, we show that three MULTIPLE C2 DOMAIN AND TRANSMEMBRANE REGION PROTEINs (MCTPs), MCTP3, MCTP4, and MCTP6, control ARF nucleocytoplasmic partitioning and determine lateral root development. MCTP3/4/6 are highly expressed in lateral roots and specifically interact with ARF7 and ARF19 to dissolve their cytoplasmic condensates. This promotes ARF nuclear localization in lateral root primordia and enhances auxin signaling during lateral root formation. Our findings confer MCTP as a key switch to modulate auxin responses and outline an MCTP-ARF signaling cascade that is crucial for the establishment of the plant root system.

Genome-Wide Identification of the Auxin Response Factor Gene Family in Maple (Acer truncatum) and Transcriptional Expression Analysis at Different Coloration Stages of Leaves

Auxin response factors (ARFs) are involved in the mechanism of plant leaf color regulation, inhibiting chlorophyll synthesis while promoting anthocyanin production. However, it is not clear whether the ARF gene family is involved in autumn leaf color changes in maple. The differentially expressed genes for autumn leaf discoloration were obtained by transcriptome sequencing, and the AtARF family was constructed by homologous gene search. The results show that the AtARFs consist of 21 members distributed on 11 chromosomes and can be divided into three subfamilies, which are mainly distributed in the nucleus. The promoter regions of the AtARFs contain light-responsive elements, abiotic stress-responsive elements, and hormone-responsive elements. The analyses presented in this paper provide comprehensive information on ARFs and help to elucidate their functional roles in leaf color change in Acer truncatum.

Genome-wide characterization, identification, and isolation of auxin response factor (ARF) gene family in maize

Auxin response factors (ARFs) are key regulators of numerous aspects of plant growth and development through mediating auxin signaling. In this study, we conducted a comprehensive genome-wide analysis of ZmARFs to identify and validate all auxin response factor genes in maize. These ZmARF genes were categorized into four distinct groups (I-IV) based on phylogenetic analysis, revealing seven sister pairs. We presented detailed information on gene sequences, structures, chromosome locations, and conserved motifs of ZmARFs. Through transient expression assays, we identified transcriptional activators or repressors among ZmARFs. Notably, our study demonstrated, for the first time, that ZmARF3 acts as a positive regulator of adventitious roots development in maize. This study not only provides basic insights into the maize ARF gene family but also sheds light on the specific functions of ZmARF3, paving the way for a more precise understanding of ZmARFs' roles in plant growth and development in maize.

Transcription Factor and Protein Regulatory Network of PmACRE1 in Pinus massoniana Response to Pine Wilt Nematode Infection

Pine wilt disease, caused by Bursaphelenchus xylophilus, is a highly destructive and contagious forest affliction. Often termed the “cancer” of pine trees, it severely impacts the growth of Masson pine (Pinus massoniana). Previous studies have demonstrated that ectopic expression of the PmACRE1 gene from P. massoniana in Arabidopsis thaliana notably enhances resistance to pine wilt nematode infection. To further elucidate the transcriptional regulation and protein interactions of the PmACRE1 in P. massoniana in response to pine wilt nematode infection, we cloned a 1984 bp promoter fragment of the PmACRE1 gene, a transient expression vector was constructed by fusing this promoter with the reporter GFP gene, which successfully activated the GFP expression. DNA pull-down assays identified PmMYB8 as a trans-acting factor regulating PmACRE1 gene expression. Subsequently, we found that the PmACRE1 protein interacts with several proteins, including the ATP synthase CF1 α subunit, ATP synthase CF1 β subunit, extracellular calcium-sensing receptor (PmCAS), caffeoyl-CoA 3-O-methyltransferase (PmCCoAOMT), glutathione peroxidase, NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase 1, cinnamyl alcohol dehydrogenase, auxin response factor 16, and dehydrin 1 protein. Bimolecular fluorescence complementation (BiFC) assays confirmed the interactions between PmACRE1 and PmCCoAOMT, as well as PmCAS proteins in vitro. These findings provide preliminary insights into the regulatory role of PmACRE1 in P. massoniana’s defense against pine wilt nematode infection.