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

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.

WRKY22 Transcription Factor from Iris laevigata Regulates Flowering Time and Resistance to Salt and Drought

Iris laevigata Fisch. is an excellent ornamental plant in cold regions due to its unique ornamental ability and strong cold resistance. However, the flowering period of the population is only about 20 days, greatly limiting its potential uses in landscaping and the cutting flower industry. In addition, I. laevigata is often challenged with various abiotic stresses including high salinity and drought in its native habitats. Thus, breeding novel cultivars with delayed flowering time and higher resistance to abiotic stress is of high importance. In this study, we utilized sequencing data from the I. laevigata transcriptome to identify WRKYs and characterized IlWRKY22, a key transcription factor that modulates flowering time and abiotic stress responses. IlWRKY22 is induced by salt and drought stress. We cloned IlWRKY22 and found that it is a Group IIe WRKY localized in the nucleus. Overexpressing IlWRKY22 in Arabidopsis thaliana (L.) Heynh. and Nicotiana tabacum L. resulted in a delayed flowering time in the transgenic plants. We created transgenic N. tabacum overexpressing IlWRKY22, which showed significantly improved resistance to both salt and drought compared to the control plants. Thus, our study revealed a unique dual function of IlWRKY22, an excellent candidate gene for breeding novel Iris cultivars of desirable traits.

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.

CsSPL13A directly binds and positively regulates CsFT and CsBAM to accelerate flowering in cucumber

Flowering is an important developmental transition that greatly affects the yield of many vegetable crops. In cucumber (Cucumis sativus), flowering is regulated by various factors including squamosa promoter-binding-like (SPL) family proteins. However, the role of CsSPL genes in cucumber flowering remains largely unknown. In this study, we cloned the squamosa promoter-binding-like protein 13A (CsSPL13A) gene, which encodes a highly conserved SBP-domain protein that acts as a transcription factor and localizes to the nucleus. Quantitative real-time PCR (qRT-PCR) analysis showed that CsSPL13A was mainly expressed in flowers, and its expression level increased significantly nearing the flowering stage. Additionally, compared with the wild type(WT), CsSPL13A-overexpressing transgenic cucumber plants (CsSPL13A-OE) showed considerable differences in flowering phenotypes, such as early flowering, increased number of male flowers, and longer flower stalks. CsSPL13A upregulated the expression of the flowering integrator gene Flowering Locus T (CsFT) and the sugar-mediated flowering gene β-amylase (CsBAM) in cucumber. Yeast one-hybrid and firefly enzyme reporter assays confirmed that the CsSPL13A protein could directly bind to the promoters of CsFT and CsBAM, suggesting that CsSPL13A works together with CsFT and CsBAM to mediate flowering in cucumber. Overall, our results provide novel insights into the regulatory network of flowering in cucumber as well as new ideas for the genetic improvement of cucumber varieties.

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.

Functional studies of four MiFPF genes in mango revealed their function in promoting flowering in transgenic Arabidopsis

Flowering promoting factor (FPF) genes play a substantial regulatory role in the process of flowering. In the present study, four MiFPF genes, namely, MiFPF1, MiFPF2, MiFPF3a, and MiFPF3b, were obtained from mango (Mangifera indica L.). Tissue expression analysis showed that MiFPFs were expressed in all mango tissues. Specifically, MiFPF1 and MiFPF2 were highly expressed in leaves, while MiFPF3a and MiFPF3b were highly expressed in flowers and buds. The four MiFPF proteins localize to the nucleus. Overexpression of MiFPFs in transgenic Arabidopsis resulted in early flowering and upregulated the expression of APETAL1 (AP1), FLOWERING LOCUS D (FD) and FLOWERING LOCUS T (FT). MiFPF genes increased the root growth of transgenic Arabidopsis plants under gibberellin treatment. BiFC assays showed that MiFPFs can interact with several DELLA proteins. Taken together, our results demonstrate that the MiFPF gene was involved not only in promoting flowering but also in increasing root growth under gibberellin (GA₃) treatment.

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.

Transcriptome analysis of floral bud development and function analysis of a novel CO gene in Paeonia × lemoinei 'High Noon'

Paeonia × lemoinei 'High Noon' is one of the most important cultivars in tree peony (Paeonia sect. Moutan), a traditional horticultural plant in China, with a re-blooming characteristic which was quite different from other cultivars. So, the genetic resources in 'High Noon' were incredibly valuable in flowering-time-modified molecular breeding in tree peony. However, the molecular mechanism underlying the floral bud formation of 'High Noon' was not clear yet. To explore the molecular mechanism in this process, the transcriptomes of three stages during floral bud development were deeply analyzed in this study. As a result, a total of 5816 differentially expressed genes (DEGs) were identified between the three developmental stages, and pathways including ''DNA replication'', ''metabolic pathways'', ''circadian rhythm'', and ''plant hormone signal transduction'' were mostly enriched in the functional enrichment and expression pattern analysis. Furthermore, a total of 584 genes related to the photoperiod pathway were further identified and a novel CO homolog gene PlCO was identified to be a stable hydrophilic protein, which contained both CCT domain and B-box domain. Over-expression of PlCO in Arabidopsis resulted in early flowering, which suggested a promotion role of flowering. The PlCO protein localized in nucleus and possessed a transcription activity ability, which implied that PlCO might function as a transcription factor. The transcriptome analysis revealed pathways involved in floral bud development in tree peony and provided new insight into the regulatory network underlying the floral bud development. The gene identification in 'High Noon' provided new valuable candidate genes for flowering-time-modified molecular breeding in tree peony.

Integrated Metabolites and Transcriptomics at Different Growth Stages Reveal Polysaccharide and Flavonoid Biosynthesis in Cynomorium songaricum

Cynomorium songaricum is a perennial parasitic herb, and its stem is widely used as a traditional Chinese medicine, which largely relies on bioactive compounds (e.g., polysaccharides, flavonoids, and triterpenes). To date, although the optimum harvest time of stems has been demonstrated at the unearthed stage (namely the early flowering stage, EFS), the accumulation mechanism of polysaccharides and flavonoids during growth stages is still limited. In this study, the physiological characteristics (stem fresh weight, contents of soluble sugar and flavonoids, and antioxidant capacity) at four different growth stages (germination stage (GS), vegetative growth stage (VGS), EFS, and flowering stage (FS)) were determined, transcriptomics were analyzed by illumina sequencing, and expression levels of key genes were validated by qRT-PCR at the GS, VGS, and EFS. The results show that the stem biomass, soluble sugar and total flavonoids contents, and antioxidant capacity peaked at EFS compared with GS, VGS, and FS. A total of 6098 and 13,023 differentially expressed genes (DEGs) were observed at VGS and EFS vs. GS, respectively, with 367 genes co-expressed. Based on their biological functions, 109 genes were directly involved in polysaccharide and flavonoid biosynthesis as well as growth and development. The expression levels of key genes involved in polysaccharides (e.g., GLCs, XTHs and PMEs), flavonoids (e.g., 4CLLs, CYPs and UGTs), growth and development (e.g., AC58, TCPs and AP1), hormones biosynthesis and signaling (e.g., YUC8, AIPT and ACO1), and transcription factors (e.g., MYBs, bHLHs and WRKYs) were in accordance with changes of physiological characteristics. The combinational analysis of metabolites with transcriptomics provides insight into the mechanism of polysaccharide and flavonoid biosynthesis in C. songaricum during growth stages.

Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering

Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential for producing I. laevigata of desirable flowering properties. A prerequisite is to identify and characterize key flowering control genes, the identity of which remains largely unknown in I. laevigata due to the lack of genome information. To fill this knowledge gap, we used sequencing data of the I. laevigata transcriptome to identify MADS-box gene-encoding transcription factors that have been shown to play key roles in developmental processes, including flowering. Our data revealed 41 putative MADS-box genes, which consisted of 8 type I (5 Mα and 3 Mβ, respectively) and 33 type II members (2 MIKC* and 31 MIKCC, respectively). We then selected IlSEP3 and IlSVP for functional studies and found that both are localized to the nucleus and that they interact physically in vitro. Ectopic expression of IlSEP3 in Arabidopsis resulted in early flowering (32 days) compared to that of control plants (36 days), which could be mediated by modulating the expression of FT, SOC1, AP1, SVP, SPL3, VRN1, and GA20OX. By contrast, plants overexpressing IlSVP were phenotypically similar to that of wild type. Our functional validation of IlSEP3 was consistent with the notion that SEP3 promotes flowering in multiple plant species and indicated that IlSEP3 regulates flowering in I. laevigata. Taken together, this work provided a systematic identification of MADS-box genes in I. laevigata and demonstrated that the flowering time of I. laevigata can be genetically controlled by altering the expression of key MADS-box genes.

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.

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.

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.