The AT-hook motif-containing protein AHL22 regulates flowering initiation by modifying FLOWERING LOCUS T chromatin in Arabidopsis

The ZmAHL25-ZmPUB19-ZmMPK5 Module Positively Regulates Resistance to Rhizoctonia solani in Maize

Ubiquitin-mediated proteolysis is a crucial mechanism in plant defenses against pathogens. However, the role of E3 ubiquitin ligases in the maize (Zea mays) defense response against Rhizoctonia solani, a major soil-borne fungal pathogen that causes banded leaf and sheath blight, remains unclear. We previously identified the maize ZmPUB19 gene, which encodes a U-box E3 ubiquitin ligase and is upregulated upon R. solani infection, suggesting its potential involvement in maize defense responses. In this study, we established that ZmPUB19 positively influences the maize defense response to R. solani. In vitro and in vivo experiments revealed that ZmPUB19 interacts with and ubiquitinates the mitogen-activated protein kinase ZmMPK5, resulting in ZmMPK5 degradation in response to R. solani infection. The Zmmpk5 mutant demonstrated superior resistance to R. solani compared to the wild type. Additionally, we identified an AT-Hook Motif Nuclear Localized (AHL) transcription factor, ZmAHL25, which binds to the AT-rich cis-element in the ZmPUB19 promoter and activates its expression under R. solani attack. Notably, decreased expression of ZmAHL25 increased maize susceptibility to R. solani. Collectively, our findings show that the ZmAHL25-ZmPUB19-ZmMPK5 module plays a positive role in regulating maize defense responses to R. solani infection.

PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism

It is crucial to understand the transcription mechanisms of miRNAs, especially considering the presence of peptides encoded by miRNAs. Since promoters function as the switch for gene transcription, precisely identifying these regions is essential for fully annotating miRNA transcripts. Nonetheless, existing computational methods still have room for improvement in the characterization of promoter regions. Here, we present PmiProPred, an advanced tool designed for predicting plant miRNA promoters from a wide spectrum of genomes. It consists of two core components: multi-stream deep feature extraction (MsDFE) and multi-stream deep feature refinement (MsDFR). The MsDFE utilizes Transformer and CNN to gather multi-view features, while the MsDFR focuses on aligning and refining them using channel and spatial attention mechanisms. Ultimately, a multi-layer perceptron is employed to accomplish the miRNA promoter identification task. Across three independent testing datasets, PmiProPred achieves accuracies of 94.630%, 96.659%, and 92.480%, respectively, substantially surpassing the latest methods. Additionally, PmiProPred is employed to identify potential core promoters in the upstream 2-kb regions of intergenic miRNAs in five plant species. We further conduct cis-regulatory elements mining on the predicted promoters and perform an in-depth analysis of the identified motifs. Altogether, PmiProPred is a robust and effective tool for discovering plant miRNA promoters.

Salt stress activates the CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis

Salt stress has devastating effects on agriculture, yet the key regulators modulating the transcriptional dynamics of salt-responsive genes remain largely elusive in plants. Here, we discover that salt stress substantially induces the kinase activity of Mediator cyclin-dependent kinase 8 (CDK8), which is essential for its positive role in regulating salt tolerance. CDK8 is identified to phosphorylate AT-hook motif nuclear-localized protein 10 (AHL10) at serine 314, leading to its degradation under salt stress. Consistently, AHL10 is found to negatively regulate salt tolerance. Transcriptome analysis further indicates that CDK8 regulates over 20% of salt-responsive genes, half of which are co-regulated by AHL10. Moreover, AHL10 is revealed to recruit SU(VAR)3-9 homologs (SUVH2/9) to AT-rich DNA sequences in the nuclear matrix-attachment regions (MARs) of salt-responsive gene promoters, facilitating H3K9me2 deposition and repressing salt-responsive genes. Our study thereby has identified the CDK8-AHL10-SUVH2/9 module as a key molecular switch controlling transcriptional dynamics in response to salt stress.

Transcriptome Profiling Reveals Key Regulatory Networks for Age-Dependent Vernalization in Welsh Onion (Allium fistulosum L.)

Plants exhibit diverse pathways to regulate the timing of flowering. Some plant species require a vegetative phase before being able to perceive cold stimuli for the acceleration of flowering through vernalization. This research confirms the correlation between the vernalization process and seedling age in Welsh onions. Findings from two vernalization experiments conducted at different time intervals demonstrate that seedlings must reach a vegetative phase of at least 8 weeks to consistently respond to vernalization. Notably, 8-week-old seedlings subjected to 6 weeks of vernalization displayed the shortest time to bolting, with an average duration of 138.1 days. Transcriptome analysis led to the identification of genes homologous to those in Arabidopsis thaliana that regulate flowering. Specifically, AfisC7G05578 (CO), AfisC2G05881 (AP1), AfisC1G07745 (FT), AfisC1G06473 (RAP2.7), and AfisC2G01843 (VIM1) were identified and suggested to have potential significance in age-dependent vernalization in Welsh onions. This study not only presents a rapid vernalization method for Welsh onions but also provides a molecular foundation for understanding the interplay between seedling age and vernalization.

Comprehensive analysis of AHL genes in Malus domestica reveals the critical role of MdAHL6 in flowering induction

AT-hook motif nuclear localized (AHL) genes are crucial in various biological processes, yet the AHL gene family in apples has remained largely unexplored. In this study, we isolated 36 MdAHL genes from the apple genome and grouped them into two distinct clades. We characterized the gene structure, conserved motifs, protein biochemical properties, and promoter regions of the MdAHL genes. Transcriptional analysis revealed that MdAHL genes are preferentially and predominantly expressed in flowers and leaves. Notably, during the floral induction phase, the MdAHL6 gene exhibited remarkably high transcriptional activity. Overexpression of MdAHL6 resulted in shortened hypocotyls and delayed flowering by regulating hypocotyl- and floral-related genes. Y1H, EMSA, GUS activity, and molecular docking assays revealed that MdAHL6 directly binds to AT-rich regions, inhibiting the expression of FLOWERING LOCUS T (MdFT). Furthermore, Y2H, pull-down, and BiFC assays demonstrated a physical interaction between MdAHL6 and the class II knotted-like transcription factor MdKNOX19, which significantly enhances the inhibitory effect of MdAHL6 on MdFT expression. This comprehensive initial analysis unveils the critical role of the MdKNOX19-MdAHL6-MdFT module in flowering induction and lays a theoretical foundation for future functional exploration.

Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis

MAIN CONCLUSION

A novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches. The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein-protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein-protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches.

MutL homolog 1 participates in interference-sensitive meiotic crossover formation in soybean

MutL homolog 1 (MLH1), a member of the MutL homolog family, is required for normal recombination in most organisms. However, its role in soybean (Glycine max) remains unclear to date. Here, we characterized the Glycine max female and male sterility 1 (Gmfms1) mutation that reduces pollen grain viability and increases embryo sac abortion in soybean. Map-based cloning revealed that the causal gene of Gmfms1 is Glycine max MutL homolog 1 (GmMLH1), and CRISPR/Cas9 knockout approach further validated that disruption of GmMLH1 confers the female-male sterility phenotype in soybean. Loss of GmMLH1 function disrupted bivalent formation, leading to univalent mis-segregation during meiosis and ultimately to female-male sterility. The Gmmlh1 mutant showed about a 78.16% decrease in meiotic crossover frequency compared to the wild type. The residual chiasmata followed a Poisson distribution, suggesting that interference-sensitive crossover formation was affected in the Gmmlh1 mutant. Furthermore, GmMLH1 could interact with GmMLH3A and GmMLH3B both in vivo and in vitro. Overall, our work demonstrates that GmMLH1 participates in interference-sensitive crossover formation in soybean, and provides additional information about the conserved functions of MLH1 across plant species.

Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses

Plant galls generated by insects have highly organized structures, providing nutrients and shelter to the insects living within them. Most research on the physiological and molecular mechanisms of gall development has focused on single galls. To understand the diversity of gall development, we examined five galls with different morphologies generated by distinct species of Rhopalomyia (gall midge; Diptera: Cecidomyiidae) on a single host plant of Artemisia indica var. maximowiczii (Asteraceae). Vasculature developed de novo within the galls, indicating active transport of nutrients between galls and the host plant. Each gall had a different pattern of vasculature and lignification, probably due to differences in the site of gall generation and the gall midge species. Transcriptome analysis indicated that photosynthetic and cell wall-related genes were down-regulated in leaf and stem galls, respectively, compared with control leaf and stem tissues, whereas genes involved in floral organ development were up-regulated in all types of galls, indicating that transformation from source to sink organs occurs during gall development. Our results help to understand the diversity of galls on a single herbaceous host plant.

Genome-wide analysis of radish AHL gene family and functional verification of RsAHL14 in tomato

The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factors involved in plant growth, development, and stress responses. However, AHLs have not been systematically analyzed in radish (Raphanus sativus). Therefore, we performed genome-wide identification and expression pattern, gene structure, and function verifications of radish AHLs. We identified 52 radish AHLs (RsAHL1-RsAHL52), which were unevenly distributed across nine chromosomes. Phylogenetic analysis showed that the RsAHLs were divided into two clades (A and B) and subdivided into three types (I, II, and III). Collinearity analysis revealed that the 52 RsAHLs produced 49 repeat events. Tissue expression profiles revealed differential expression of RsAHLs across different tissues, with higher expression observed in flower organs, particularly petals and anthers. qRT-PCR results indicated that RsAHLs responded to abscisic acid, methyl jasmonate, and abiotic stress (low and high temperatures and drought). Additionally, RsAHL14 induced a dwarf phenotype in tomato plants, and RsAHL14-overexpression tomato plants presented significantly decreased expression levels of the gibberellin (GA) synthetic genes ent-Copalyl diphosphatase, GA3ox-3/-4/-5, and GA20ox-1/-2/-3, but significantly increased expression of the degradation gene GA2ox-1/-3. Thus, RsAHL14 might affect plant growth by regulating GA content. Collectively, our study comprehensively identified RsAHLs in radish and provided a reference for further research on these genes.

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits

The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.

The AT-hook protein AHL29 promotes Bacillus subtilis colonization by suppressing SWEET2-mediated sugar retrieval in Arabidopsis roots

Beneficial Bacillus subtilis (BS) symbiosis could combat root pathogenesis, but it relies on root-secreted sugars. Understanding the molecular control of sugar flux during colonization would benefit biocontrol applications. The SWEET (Sugar Will Eventually Be Exported Transporter) uniporter regulates microbe-induced sugar secretion from roots; thus, its homologs may modulate sugar distribution upon BS colonization. Quantitative polymerase chain reaction revealed that gene transcripts of SWEET2, but not SWEET16 and 17, were significantly induced in seedling roots after 12 h of BS inoculation. Particularly, SWEET2-β-glucuronidase fusion proteins accumulated in the apical mature zone where BS abundantly colonized. Yet, enhanced BS colonization in sweet2 mutant roots suggested a specific role for SWEET2 to constrain BS propagation, probably by limiting hexose secretion. By employing yeast one-hybrid screening and ectopic expression in Arabidopsis protoplasts, the transcription factor AHL29 was identified to function as a repressor of SWEET2 expression through the AT-hook motif. Repression occurred despite immunity signals. Additionally, enhanced SWEET2 expression and reduced colonies were specifically detected in roots of BS-colonized ahl29 mutant. Taken together, we propose that BS colonization may activate repression of AHL29 on SWEET2 transcription that would be enhanced by immunity signals, thereby maintaining adequate sugar secretion for a beneficial Bacillus association.

Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.

Phosphatidyl Ethanolamine Binding Protein FLOWERING LOCUS T-like 12 (OsFTL12) Regulates the Rice Heading Date under Different Day-Length Conditions

Plant FLOWERING LOCUS T-Like (FTL) genes often redundantly duplicate on chromosomes and functionally diverge to modulate reproductive traits. Rice harbors thirteen FTL genes, the functions of which are still not clear, except for the Hd3a and RFT genes. Here, we identified the molecular detail of OsFTL12 in rice reproductive stage. OsFTL12 encoding protein contained PEBP domain and localized into the nucleus, which transcripts specifically expressed in the shoot and leaf blade with high abundance. Further GUS-staining results show the OsFTL12 promoter activity highly expressed in the leaf and stem. OsFTL12 knock-out concurrently exhibited early flowering phenotype under the short- and long-day conditions as compared with wild-type and over-expression plants, which independently regulates flowering without an involved Hd1/Hd3a and Ehd1/RFT pathway. Further, an AT-hook protein OsATH1 was identified to act as upstream regulator of OsFTL12, as the knock-out OsATH1 elevated the OsFTL12 expression by modifying Histone H3 acetylation abundance. According to the dissection of OsFTL12 molecular functions, our study expanded the roles intellectual function of OsFTL12 in the mediating of a rice heading date.

Plant-TFClass: a structural classification for plant transcription factors

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.

Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo

In the monoecious Cucurbita pepo, the transition to female flowering is the time at which the plant starts the production of female flowers after an initial male phase of development. Ethylene plays an essential role in this process since some ethylene deficient and ethylene-insensitive mutants are androecious and only produce male flowers. To gain insight into the molecular mechanisms regulating the specification and early development of female flowers, we have compared the transcriptomic changes occurring in the shoot apices of WT and androecious ethylene-insensitive etr1b mutant plants upon female flowering transition. There were 1160 female flowering-specific DEGs identified in WT plants upon female flowering, and 284 of them were found to be modulated by the ethylene-insensitive etr1b mutation. The function of these DEGs indicated that female flower specification depends on the adoption of a transcriptional program that includes previously identified sex-determining genes in the ethylene pathway, but also genes controlling the biosynthesis and signaling pathways of other phytohormones, and those encoding for many different transcription factors. The transcriptomic changes suggested that gibberellins play a negative role in female flowering, while ethylene, auxins, ABA and cytokinins are positive regulators. Transcription factors from 34 families, including NAC, ERF, bHLH, bZIP, MYB and C2H2/CH3, were found to be regulating female flowering in an ethylene-dependent or -independent manner. Our data open a new perspective of the molecular mechanisms that control the specification and development of female flowers in C. pepo.

The central role of stem cells in determining plant longevity variation

Vascular plants display a huge variety of longevity patterns, from a few weeks for several annual species up to thousands of years for some perennial species. Understanding how longevity variation is structured has long been considered a fundamental aspect of the life sciences in view of evolution, species distribution, and adaptation to diverse environments. Unlike animals, whose organs are typically formed during embryogenesis, vascular plants manage to extend their life by continuously producing new tissues and organs in apical and lateral directions via proliferation of stem cells located within specialized tissues called meristems. Stem cells are the main source of plant longevity. Variation in plant longevity is highly dependent on the activity and fate identity of stem cells. Multiple developmental factors determine how stem cells contribute to variation in plant longevity. In this review, we provide an overview of the genetic mechanisms, hormonal signaling, and environmental factors involved in controlling plant longevity through long-term maintenance of stem cell fate identity.

Identification of tomato AHL gene families and functional analysis their roles in fruit development and abiotic stress response

The AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) transcription factors play important roles in regulating plant development and stress response. However, the AHL family genes have not been identified in tomato (Solanum lycopersicum) and their biological functions have not been elucidated. In this work, the gene families encoding AHLs were identified in tomato genome, and their physical and chemical characteristics, subcellular localization, gene expression profiles during fruit development and upon abiotic stimulus were investigated. Overall, a total of 18 AHL members were identified in tomato genome, phylogenetic analysis classified these SlAHL members into two clades, clade A (SlAHL1-8) and clade B (SlAHL9-18). Six clade A SlAHLs were detected to be subcellular localized in the nucleus. The transcripts of the representative clade A SlAHLs predominantly accumulated 10 days post anthesis (dpa) in tomato fruits, revealing an involvement of these SlAHLs in early fruit development. Furthermore, compared with clade B members, the transcripts of the clade A SlAHLs were more responsive to heat, drought, cold and salt stresses, suggesting that these SlAHLs may play major roles in response to abiotic stresses. Moreover, overexpression of SlAHL1 and SlAHL7 in Arabidopsis increased the sensitivity to ABA during seed germination and seedling stages. Overexpression of SlAHL1 inhibited seed germination while increased primary root elongation upon salt and drought stresses. Together, our work suggested that the clade A SlAHL genes may play an important role in response to abiotic stresses, which paving the way for future functional analysis of AHL genes in tomato and other Solanaceae species.

Genome-Wide Identification and Expression Analysis under Abiotic Stress of BrAHL Genes in Brassica rapa

The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factor critical for the growth, development, and stress tolerance of plants. However, the function of the AHL gene family in Brassica rapa (B. rapa) remains unclear. In this study, 42 AHL family members were identified from the B. rapa genome and mapped to nine B. rapa chromosomes. Two clades have formed in the evolution of the AHL gene family. The results showed that most products encoded by AHL family genes are located in the nucleus. Gene duplication was common and expanded the BrAHL gene family. According to the analysis of cis-regulatory elements, the genes interact with stress responses (osmotic, cold, and heavy metal stress), major hormones (abscisic acid), and light responses. In addition, the expression profiles revealed that BrAHL genes are widely expressed in different tissues. BrAHL16 was upregulated at 4 h under drought stress, highly expressed under cadmium conditions, and downregulated in response to cold conditions. BrAHL02 and BrAHL24 were upregulated at the initial time point and peaked at 12 h under cold and cadmium stress, respectively. Notably, the interactions between AHL genes and proteins under drought, cold, and heavy metal stresses were observed when predicting the protein-protein interaction network.

AGAMOUS regulates various target genes via cell cycle-coupled H3K27me3 dilution in floral meristems and stamens

The MADS domain transcription factor AGAMOUS (AG) regulates floral meristem termination by preventing maintenance of the histone modification lysine 27 of histone H3 (H3K27me3) along the KNUCKLES (KNU) coding sequence. At 2 d after AG binding, cell division has diluted the repressive mark H3K27me3, allowing activation of KNU transcription prior to floral meristem termination. However, how many other downstream genes are temporally regulated by this intrinsic epigenetic timer and what their functions are remain unknown. Here, we identify direct AG targets regulated through cell cycle-coupled H3K27me3 dilution in Arabidopsis thaliana. Expression of the targets KNU, AT HOOK MOTIF NUCLEAR LOCALIZED PROTEIN18 (AHL18), and PLATZ10 occurred later in plants with longer H3K27me3-marked regions. We established a mathematical model to predict timing of gene expression and manipulated temporal gene expression using the H3K27me3-marked del region from the KNU coding sequence. Increasing the number of del copies delayed and reduced KNU expression in a polycomb repressive complex 2- and cell cycle-dependent manner. Furthermore, AHL18 was specifically expressed in stamens and caused developmental defects when misexpressed. Finally, AHL18 bound to genes important for stamen growth. Our results suggest that AG controls the timing of expression of various target genes via cell cycle-coupled dilution of H3K27me3 for proper floral meristem termination and stamen development.

Overexpression of AHL proteins enhances root hair production by altering the transcription of RHD6-downstream genes

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins occur in all sequenced plant species. They bind to the AT-rich DNA sequences in chromosomes and regulate gene transcription related to diverse biological processes. However, the molecular mechanism underlying how AHL proteins regulate gene transcription is poorly understood. In this research, we used root hair production as a readout to study the function of two Arabidopsis AHL proteins, AHL17, and its closest homolog AHL28. Overexpression of AHL17 or AHL28 greatly enhanced root hair production by increasing the transcription of an array of genes downstream of RHD6. RHD6 is a key transcription factor that regulates root hair development. Mutation of RHD6 completely suppressed the overproduction of root hairs by blocking the transcription of AHL17-activated genes. The overexpression of AHL17 or AHL28, however, neither affected the transcription of RHD6 nor the accumulation of RHD6 protein. These two AHL proteins also did not directly interact with RHD6. Furthermore, we found that three members of the Heat Shock Protein70 family, which have been annotated as the subunits of the plant Mediator complex, could form a complex with both AHL17 and RHD6. Our research might reveal a previously unrecognized mechanism of how AHL proteins regulate gene transcription.

Genome-wide identification and analyses of the AHL gene family in rice (Oryza sativa)

AHL (AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED) family members play a critical role in stress resistance regulation by DNA-protein and protein-protein interactions in a number of plant biological processes. Using genomic data, an attempt was made to evaluate AHL genes in rice. Using a genome database, we performed in silico detection and characterization of AHL family genes in rice. The data of the gene were obtained from the Rice Genome Annotation Project (RGAP) database. The rice genome data were analyzed using bioinformatics software. The main objectives of the research are genome-wide recognition, expression, structural examination, phylogenetic analysis of AHL gene family, classification of AHL proteins into different classes based on motif and domain composition, analysis of promoter regions to identify stress and phytohormone-associated cis-elements, expression analysis of OsAHL genes in diverse tissues and stressful situations and understanding the roles of AHLs in controlling rice plant development. The genome-wide recognition, expression, and structural examination of the AHL gene family were undertaken in this research to evaluate the structural activities of AHLs in rice. From the Oryza sativa genome, 26 AHL genes have been identified. WoLF PSORT analysis predicted different subcellular localizations for these proteins, including nuclear, cytoplasmic, chloroplast, and endoplasmic reticulum. According to a phylogenetic study, rice AHLs resulted in two clades: Clade-A with no introns (excluding OsAHL15 and OsAHL21) and Clade-B with four introns. Depending on the AT-hook motif (s) (AHM) and PPC/DUF 296 domain composition, the AHL proteins are categorized into the following three classes: Type-I, Type-II, and Type-III, among Type-I AHLs constituting Clade-A, Type-II, and Type-III creating Clade-B. Type-I was the largest gene family, representing 57.69% of OsAHL genes. The exon-intron organization within clades of OsAHL genes was similar. Multiple sequence alignment identified 15 conserved motifs, including AT-hook motifs and the PPC domain, suggesting DNA-binding functionality. OsAHL genes were distributed across 12 chromosomes, with chromosome 2 and 8 harboring the highest number of genes. Gene duplication analysis revealed eight paralogous pairs, indicating evolutionary divergence between 13.32 and 35.59 million years ago. The emergence of OsAHL paralogous pairs was favored by purifying selection. Synteny analysis between rice and Arabidopsis demonstrated collinearity among AHL gene pairs, implying comparable structure and function in the two species. The role of stress- and phytohormone-associated cis-elements in the OsAHL genes was discovered by promoter analysis. OsAHL genes participated in various biological processes, with a prominent involvement in cellular and metabolic processes. They exhibited a significant enrichment in binding functions, including a substantial proportion of transcription regulators. OsAHL genes displayed diverse expression patterns in different tissues and under abiotic stress conditions. According to their expression patterns, the majority of OsAHLs of Clade-B were expressed mainly in the pistil indicating their roles in flower formation, while Clade-A OsAHLs had the minimal expression in pistil and highly expressed in embryos, indicating that the AHLs within each clade had the same expression patterns. Some OsAHL genes were also expressed in stressful situations, such as cold, salt, and drought. Protein interaction analysis revealed networks involving AHL proteins and other proteins, suggesting their participation in phytohormone responses, abiotic stress, and plant development. In this work, 26 OsAHL genes were found in the genome of rice. Rice OsAHLs were grouped into two phylogenetic groups. It is further divided into three types on the basis of the motif and domain composition. At various phases of development, the expression analysis of OsAHLs showed numerous variations in expression levels in diverse tissues and stress situations. Our findings shed light on the significant roles of AHLs in controlling rice plant development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03666-0.

Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate-Tropical Introgression Lines of Maize (Zea mays L.)

Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F₇ recombinant inbred line (RIL) populations were created using a temperate-tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.

Systematical Characterization of the AT-Hook Gene Family in Juglans regia L. and the Functional Analysis of the JrAHL2 in Flower Induction and Hypocotyl Elongation

AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the walnut genome. Based on the evolutionary analysis, JrAHL genes were grouped into two clades, and their expansion may occur due to segmental duplication. The stress-responsive nature and driving of developmental activities of JrAHL genes were revealed by cis-acting elements and transcriptomic data, respectively. Tissue-specific expression analysis showed that JrAHLs had a profound transcription in flower and shoot tip, JrAHL2 in particular. Subcellular localization showed that JrAHL2 is anchored to the nucleus. Overexpression of JrAHL2 in Arabidopsis adversely affected hypocotyl elongation and delayed flowering. Our study, for the first time, presented a detailed analysis of JrAHL genes in walnut and provided theoretical knowledge for future genetic breeding programs.

Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis

Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states; yet, how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PIF4. Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with ELF7, a critical component of the transcription elongator PAF1 complex. H3.3 promotes thermomorphogenesis and the high temperature-enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal-induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature-induced H3.3 enrichment at PIF4 targets. Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation.

Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago

Symbiotic nitrogen fixation by Rhizobium bacteria in the cells of legume root nodules alleviates the need for nitrogen fertilizers. Nitrogen fixation requires the endosymbionts to differentiate into bacteroids which can be reversible or terminal. The latter is controlled by the plant, it is more beneficial and has evolved in multiple clades of the Leguminosae family. The plant effectors of terminal differentiation in inverted repeat-lacking clade legumes (IRLC) are nodule-specific cysteine-rich (NCR) peptides, which are absent in legumes such as soybean where there is no terminal differentiation of rhizobia. It was assumed that NCRs co-evolved with specific transcription factors, but our work demonstrates that expression of NCR genes does not require NCR-specific transcription factors. Introduction of the Medicago truncatula NCR169 gene under its own promoter into soybean roots resulted in its nodule-specific expression, leading to bacteroid changes associated with terminal differentiation. We identified two AT-Hook Motif Nuclear Localized (AHL) transcription factors from both M. truncatula and soybean nodules that bound to AT-rich sequences in the NCR169 promoter inducing its expression. Whereas mutation of NCR169 arrested bacteroid development at a late stage, the absence of MtAHL1 or MtAHL2 completely blocked bacteroid differentiation indicating that they also regulate other NCR genes required for the development of nitrogen-fixing nodules. Regulation of NCRs by orthologous transcription factors in non-IRLC legumes opens up the possibility of increasing the efficiency of nitrogen fixation in legumes lacking NCRs.

A histone deacetylase inhibitor enhances rice immunity by derepressing the expression of defense-related genes

Histone deacetylase (HDAC) inhibitors (HDACis) have been widely used in plants to investigate the role of histone acetylation, particularly the function of HDACs, in the regulation of development and stress response. However, how histone acetylation is involved in rice (Oryza sativa L.) disease resistance has hardly been studied. In this paper, four HDACis including Sodium butyrate (NaBT), Suberoylanilide Hydroxamic Acid (SAHA), LBH-589 and Trichostatin A (TSA) were used to treat rice seedlings at different concentrations before inoculation of Magnaporthe oryzae. We found that only 10mM NaBT treatment can significantly enhanced rice blast resistance. However, treatment of the four HDACis all increased global histone acetylation but at different sites, suggesting that the inhibition selectivity of these HDACis is different. Notably, the global H3K9ac level was dramatically elevated after both NaBT and LBH589 treatment although LBH589 could not enhance rice blast resistance. This indicates that the HDACs they inhibit target different genes. In accordance with the phenotype, transcriptomic analysis showed that many defense-related genes were up-regulated by NaBT treatment. Up-regulation of the four genes bsr-d1, PR10B, OsNAC4, OsKS4 were confirmed by RT-qPCR. ChIP-qPCR results revealed that H3K9ac level on these genes was increased after NaBT treatment, suggesting that these defense-related genes were repressed by HDACs. In addition, by promoter motif analysis of the genes that induced by both NaBT treatment and rice blast infection, we found that the motifs bound by ERF and AHL transcription factors (TFs) were the most abundant, which demonstrates that ERF and AHL proteins may act as the candidate TFs that recruit HDACs to defense-related genes to repress their expression when plants are not infected by rice blast.

Two AT-Hook proteins regulate A/NINV7 expression to modulate sucrose catabolism for cold tolerance in Poncirus trifoliata

Invertase (INV)-mediated sucrose (Suc) hydrolysis, leading to the irreversible production of glucose (Glc) and fructose (Frc), plays an essential role in abiotic stress tolerance of plants. However, the regulatory network associated with the Suc catabolism in response to cold environment remains largely elusive. Herein, the cold-induced alkaline/neutral INV gene PtrA/NINV7 of trifoliate orange (Poncirus trifoliata (L.) Raf.) was shown to function in cold tolerance via mediating the Suc hydrolysis. Meanwhile, a nuclear matrix-associated region containing A/T-rich sequences within its promoter was indispensable for the cold induction of PtrA/NINV7. Two AT-Hook Motif Containing Nuclear Localized (AHL) proteins, PtrAHL14 and PtrAHL17, were identified as upstream transcriptional activators of PtrA/NINV7 by interacting with the A/T-rich motifs. PtrAHL14 and PtrAHL17 function positively in the cold tolerance by modulating PtrA/NINV7-mediated Suc catabolism. Furthermore, both PtrAHL14 and PtrAHL17 could form homo- and heterodimers between each other, and interacted with two histone acetyltransferases (HATs), GCN5 and TAF1, leading to elevated histone3 acetylation level under the cold stress. Taken together, our findings unraveled a new cold-responsive signaling module (AHL14/17-HATs-A/NINV7) for orchestration of Suc catabolism and cold tolerance, which shed light on the molecular mechanisms underlying Suc catabolism catalyzed by A/NINVs under cold stress.

miR156-independent repression of the ageing pathway by longevity-promoting AHL proteins in Arabidopsis

Plants age by developmental phase changes. In Arabidopsis, the juvenile to adult vegetative phase change (VPC) is marked by clear heteroblastic changes in leaves. VPC and the subsequent vegetative to reproductive phase change are promoted by SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE (SPL) transcription factors and repressed by miR156/157 targeting SPL transcripts. By genetic, phenotypic, and gene expression analyses, we studied the role of the longevity-promoting AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) and family members in SPL-driven plant ageing. Arabidopsis ahl loss-of-function mutants showed accelerated VPC and flowering, whereas AHL15 overexpression delayed these phase changes. Expression analysis and tissue-specific AHL15 overexpression revealed that AHL15 affects VPC and flowering time directly through its expression in the shoot apical meristem and young leaves, and that AHL15 represses SPL2/9/13/15 gene expression in a miR156/157-independent manner. The juvenile traits of spl loss-of-function mutants appeared to depend on enhanced expression of the AHL15 gene, whereas SPL activity prevented vegetative growth from axillary meristem by repressing AHL15 expression. Our results place AHL15 and close family members together with SPLs in a reciprocal regulatory feedback loop that modulates VPC, flowering time, and axillary meristem development in response to both internal and external signals.

Using a high density bin map to analyze quantitative trait locis of germination ability of maize at low temperatures

Low temperatures in the spring often lead to a decline in the emergence rate and uniformity of maize, which can affect yield in northern regions. This study used 365 recombinant inbred lines (RILs), which arose from crossing Qi319 and Ye478, to identify low-temperature resistance during the germination stage by measuring eight low-temperature-related traits. The quantitative trait locis (QTLs) were mapped using R/qtl software by combining phenotypic data, and the genotyping by sequencing (GBS) method to produce a high-density genetic linkage map. Twenty QTLs were detected during QTL mapping, of which seven QTLs simultaneously detected a consistent 197.10-202.30 Mb segment on chromosome 1. The primary segment was named cQTL1-2, with a phenotypic variation of 5.18-25.96% and a physical distance of 5.2 Mb. This combines the phenotype and genotype with the identification of seven chromosome segment substitution lines (CSSLs), which were derived from Ye478*Qi319 and related to cQTL1-2. The physical distance of cQTL1-2 was reduced to approximately 1.9 Mb. The consistent meta-QTL mQTL1 was located at 619.06 cM on chromosome 1, had a genetic distance of 7.27 cM, and overlapped with cQTL1-2. This was identified by combining the results of previous QTL studies assessing maize tolerance to low temperatures at the germination stage. An assessment of the results of the RIL population, CSSLs, and mQTL1 found the consistent QTL to be LtQTL1-1. It was identified in bin1.06-1.07 at a confidence interval of between 200,400,148 and 201,775,619 bp. In this interval, qRT-PCR found that relative expression of the candidate genes GRMZM2G082630 and GRMZM2G115730 were both up-regulated in low-temperature tolerant lines and down-regulated in sensitive lines (P < 0.01).

SUPPRESSOR OF PHYTOCHROME B-4 #3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days

SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.

AaZFP3, a Novel CCCH-Type Zinc Finger Protein from Adonis amurensis, Promotes Early Flowering in Arabidopsis by Regulating the Expression of Flowering-Related Genes

CCCH-type zinc finger proteins (ZFP) are a large family of proteins that play various important roles in plant growth and development; however, the functions of most proteins in this family are uncharacterized. In this study, a CCCH-type ZFP, AaZFP3, was identified in the floral organ of Adonis amurensis. Quantitative real-time PCR (qPCR) analysis revealed that AaZFP3 was widely expressed in the flowers of A.amurensis. Subcellular localization analysis showed that the AaZFP3 protein was mainly localized to the cytoplasm in tobacco and Arabidopsis. Furthermore, the overexpression of AaZFP3 promoted early flowering in Arabidopsis under both normal and relatively low-temperature conditions. RNA-sequencing and qPCR analyses revealed that the expression of multiple key flowering-time genes was altered in transgenic Arabidopsis overexpressing AaZFP3 compared to wild-type. Of these genes, FLOWERING LOCUS T (AtFT) expression was most significantly up-regulated, whereas FLOWERING LOCUS C (AtFLC) was significantly down-regulated. These results suggest that the overexpression of AaZFP3 promotes early flowering in Arabidopsis by affecting the expression of flowering-time genes. Overall, our study indicates that AaZFP3 may be involved in flowering regulation in A.amurensis and may represent an important genetic resource for improving flowering-time control in other ornamental plants or crops.

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions

AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.

Genome-Wide Analysis of the MADS-Box Gene Family in Holoparasitic Plants (Balanophora subcupularis and Balanophora fungosa var. globosa)

MADS-box is an important transcription factor family that is involved in the regulation of various stages of plant growth and development, especially flowering regulation and flower development. Being a holoparasitic plant, the body structure of Balanophoraceae has changed dramatically over time, and its vegetative and reproductive organs have been extensively modified, with rudimentary flower organs. Meanwhile, extraordinary gene losses have been identified in holoparasitic plants compared with autotrophs. Our study reveals that the MADS-box gene family contracted sharply in Balanophora subcupularis and Balanophora fungosa var. globosa, and some subfamilies were lost, exhibiting reduced redundancy in both. The genes that functioned in the transition from the vegetative to floral production stages suffered a significant loss, but the ABCE model genes remained intact. We further investigated genes related to flowering regulation in B. subcupularis and B. fungosa var. globosa, vernalization and autonomous ways of regulating flowering time remained comparatively integrated, while genes in photoperiod and circadian clock pathways were almost lost. Convergent gene loss in flowering regulation occurred in Balanophora and another holoparasitic plant Sapria himalayana (Rafflesiaceae). The genome-wide analysis of the MADS-box gene family in Balanophora species provides valuable information for understanding the classification, gene loss pattern, and flowering regulation mechanism of MADS-box gene family in parasitic plants.

Overexpression of AHL9 accelerates leaf senescence in Arabidopsis thaliana

BACKGROUND

Leaf senescence, the final stage of leaf growth and development, is regulated by numerous internal factors and environmental cues. Ethylene is one of the key senescence related hormones, but the underlying molecular mechanism of ethylene-induced leaf senescence remains poorly understood.

RESULTS

In this study, we identified one AT-hook like (AHL) protein, AHL9, as a positive regulator of leaf senescence in Arabidopsis thaliana. Overexpression of AHL9 significantly accelerates age-related leaf senescence and promotes dark-induced leaf chlorosis. The early senescence phenotype observed in AHL9 overexpressing lines is inhibited by the ethylene biosynthesis inhibitor aminooxyacetic acid suggesting the involvement of ethylene in the AHL9-associated senescence. RNA-seq and quantitative reverse transcription PCR (qRT-PCR) data identified numerous senescence-associated genes differentially expressed in leaves of AHL9 overexpressing transgenic plants.

CONCLUSIONS

Our investigation demonstrates that AHL9 functions in accelerating the leaf senescence process via ethylene synthesis or signalling.

AHLs' life in plants: Especially their potential roles in responding to Fusarium wilt and repressing the seed oil accumulation

Members of the AT-hook motif nuclear localized (AHL) family contain diverse but poorly understood biological functions. We identified 371 AHLs in 20 land plants, varying from the early diverging lycophyte Selagineila moellendorfi to a variety of higher plants. The AHLs were divided into two clades (Clade-A and Clade-B) with three different types (Type-I, Type-II, and Type-III AHLs). The divergence between Clade-A and Clade-B likely occurred before the separation of S. moellendorfi from the vascular plant lineages. Members of the AHLs family expanded with the specific whole-genome duplication (WGD)/segmental duplication in some genomes, such as Hevea brasiliensis. The ortholog (Vf00G1914/Amo018442) exhibited opposite expression patterns between two Vernicia species (V. fordii and V. montana), indicating that it was implicated in resistance to Fusarium wilt disease. The expression of Vf09G2138 exhibited a negative correlation with lipid biosynthesis in V. fordii seeds during different stages of development, suggesting that this gene might repress the seed oil accumulation. The core AT-hook motif and PPC domain were responsible for guiding the localization of AHL in the nucleus. This study helps us to understand the evolution of AHLs in multiple plants, further highlight their functions during V. fordii seed development and response to Fusarium wilt disease.

Characteristics of the AT-Hook Motif Containing Nuclear Localized (AHL) Genes in Carrot Provides Insight into Their Role in Plant Growth and Storage Root Development

The AT-hook motif containing nuclear localized (AHL) gene family, controlling various developmental processes, is conserved in land plants. They comprise Plant and Prokaryote Conserved (PPC) domain and one or two AT-hook motifs. DcAHLc1 has been proposed as a candidate gene governing the formation of the carrot storage root. We identified and in-silico characterized carrot AHL proteins, performed phylogenetic analyses, investigated their expression profiles and constructed gene coexpression networks. We found 47 AHL genes in carrot and grouped them into two clades, A and B, comprising 29 and 18 genes, respectively. Within Clade-A, we distinguished three subclades, one of them grouping noncanonical AHLs differing in their structure (two PPC domains) and/or cellular localization (not nucleus). Coexpression network analysis attributed AHLs expressed in carrot roots into four of the 72 clusters, some of them showing a large number of interactions. Determination of expression profiles of AHL genes in various tissues and samples provided basis to hypothesize on their possible roles in the development of the carrot storage root. We identified a group of rapidly evolving noncanonical AHLs, possibly differing functionally from typical AHLs, as suggested by their expression profiles and their predicted cellular localization. We pointed at several AHLs likely involved in the development of the carrot storage root.

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.

RESULTS

To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.

CONCLUSION

Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.

Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa

The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.

The Class III peroxidase gene OsPrx30, transcriptionally modulated by the AT-hook protein OsATH1, mediates rice bacterial blight-induced ROS accumulation

Class III peroxidases (CIII Prxs) play critical roles in plant immunity by scavenging reactive oxygen species (ROS). However, the functions of CIII Prxs in rice (Oryza sativa L.) immunity are largely unexplored. Here, we report a Prx precursor, OsPrx30, that is responsive to the bacterial blight Xanthomonas oryzae pv. oryzae (Xoo). OsPrx30 was primarily expressed in rice roots, leaves, and stems, and its protein product was mainly localized at the endoplasmic reticulum. Overexpression of OsPrx30 enhanced the plant's susceptibility to Xoo by maintaining a high level of peroxidase (POD) activity and reducing the content of H₂ O₂ , whereas depletion of OsPrx30 had the opposite effects. Furthermore, we identified an AT-hook transcription factor, OsATH1, that is specifically bound to the OsPrx30 promoter. As observed in plants overexpressing OsPrx30, depletion of OsATH1 enhanced susceptibility to Xoo. Finally, we demonstrated that depletion of OsATH1 increased histone H3 acetylation at the AT-rich region of the OsPrx30 promoter. Taken together, these results reveal a mechanism underlying the POD-induced natural resistance to bacterial diseases and suggest a model for transcription regulation of Prx genes in rice.

Dissection of Functional Modules of AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 4 in the Development of the Root Xylem

Xylem development in the Arabidopsis root apical meristem requires a complex cross talk between plant hormone signaling and transcriptional factors (TFs). The key processes involve fine-tuning between neighboring cells, mediated via the intercellular movement of signaling molecules. As an example, we previously reported that AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN (AHL) 4 (AHL4), a member of the 29 AT-hook family TFs in Arabidopsis, moves into xylem precursors from their neighbors to determine xylem differentiation. As part of the effort to understand the molecular functions of AHL4, we performed domain swapping analyses using AHL1 as a counterpart, finding that AHL4 has three functionally distinctive protein modules. The plant and prokaryotes conserved (PPC) domain of AHL4 acts as a mediator of protein-protein interactions with AHL members. The N-terminus of AHL4 is required for the regulation of xylem development likely via its unique DNA-binding activity. The C-terminus of AHL4 confers intercellular mobility. Our characterization of modules in the AHL4 protein will augment our understanding of the complexity of regulation and the evolution of intercellular mobility in AHL4 and its relatives.

Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression

BACKGROUND

The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored.

RESULTS

Transgenic plants overexpressing AtAHL20 flowered later than the wild type under both short and long days. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20's orthologue in Camelina sativa, Arabidopsis' closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain's highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL19, AtAHL22 and AtAHL29.

CONCLUSION

We showed via gain-of-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Our results demonstrate that AtAHL20 acts as a photoperiod-independent negative regulator of transition to flowering.

Overexpression of a Novel Arabidopsis Gene SUPA Leads to Various Morphological and Abiotic Stress Tolerance Alternations in Arabidopsis and Poplar

With the development of sequencing technology, the availability of genome data is rapidly increasing, while functional annotation of genes largely lags behind. In Arabidopsis, the functions of nearly half of the proteins are unknown and this remains one of the main challenges in current biological research. In an attempt to identify novel and rapid abiotic stress responsive genes, a number of salt-up (SUP) regulated genes were isolated by analyzing the public transcriptomic data, and one of them, SUPA, was characterized in this study. The expression of SUPA transcripts was rapidly up-regulated by various abiotic stress factors (<15 min), and SUPA protein is mainly localized in the peroxisome. Overexpression of SUPA in Arabidopsis leads to the elevated accumulation of reactive oxygen species (ROS), strong morphological changes and alternations in abiotic stress tolerance. The transcriptome analysis showed changes in expression of genes involved in stress response and plant development. Interestingly, ectopic overexpression of SUPA in poplar leads to a dwarf phenotype with severely curved leaves and changes in the plant tolerance of abiotic stresses. Our study reinforces the potential roles of SUPA in normal plant growth and the abiotic stress response.

The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation

Plants tightly control gene transcription to adapt to environmental conditions and steer growth and development. Different types of epigenetic modifications are instrumental in these processes. In recent years, an important role for the chromatin-modifying RPD3/HDA1 class I HDAC HISTONE DEACETYLASE 9 (HDA9) emerged in the regulation of a multitude of plant traits and responses. HDACs are widely considered transcriptional repressors and are typically part of multiprotein complexes containing co-repressors, DNA, and histone-binding proteins. By catalyzing the removal of acetyl groups from lysine residues of histone protein tails, HDA9 negatively controls gene expression in many cases, in concert with interacting proteins such as POWERDRESS (PWR), HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15), WRKY53, ELONGATED HYPOCOTYL 5 (HY5), ABA INSENSITIVE 4 (ABI4), and EARLY FLOWERING 3 (ELF3). However, HDA9 activity has also been directly linked to transcriptional activation. In addition, following the recent breakthrough discovery of mutual negative feedback regulation between HDA9 and its interacting WRKY-domain transcription factor WRKY53, swift progress in gaining understanding of the biology of HDA9 is expected. In this review, we summarize knowledge on this intriguing versatile-and long under-rated-protein and propose novel leads to further unravel HDA9-governed molecular networks underlying plant development and environmental biology.

Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next-generation sequencing in diverse aspects of plant research, genome-wide transcriptome and epigenome profiling during the vernalization response has not been conducted. In this work, to our knowledge, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold exposure. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, which resulted in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.

Transcriptional Regulation of Lipid Catabolism during Seedling Establishment

Lipid catabolism in germinating seeds provides energy and substrates for initial seedling growth, but how this process is regulated is not well understood. Here, we show that an AT-hook motif-containing nuclear localized (AHL) protein regulates lipid mobilization and fatty acid β-oxidation during seed germination and seedling establishment. AHL4 was identified to directly interact with the lipid mediator phosphatidic acid (PA). Knockout (KO) of AHL4 enhanced, but overexpression (OE) of AHL4 attenuated, triacylglycerol (TAG) degradation and seedling growth. Normal seedling growth of the OE lines was restored by sucrose supplementation to the growth medium. AHL4-OE seedlings displayed decreased expression of genes involved in TAG hydrolysis and fatty acid oxidation, whereas the opposite was observed in AHL4-KOs. These genes contained AHL4-binding cis elements, and AHL4 was shown to bind to the promoter regions of genes encoding the TAG lipases SDP1 and DALL5 and acyl-thioesterase KAT5. These AHL4-DNA interactions were suppressed by PA species that bound to AHL4. These results indicate that AHL4 suppresses lipid catabolism by repressing the expression of specific genes involved in TAG hydrolysis and fatty acid oxidation, and that PA relieves AHL4-mediated suppression and promotes TAG degradation. Thus, AHL4 and PA together regulate lipid degradation during seed germination and seedling establishment.

Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis

In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.