The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development

Non-cell-autonomous signaling associated with barley ALOG1 specifies spikelet meristem determinacy

Inflorescence architecture and crop productivity are often tightly coupled in our major cereal crops. However, the underlying genetic mechanisms controlling cereal inflorescence development remain poorly understood. Here, we identified recessive alleles of barley (Hordeum vulgare L.) HvALOG1 (Arabidopsis thaliana LSH1 and Oryza G1) that produce non-canonical extra spikelets and fused glumes abaxially to the central spikelet from the upper-mid portion until the tip of the inflorescence. Notably, we found that HvALOG1 exhibits a boundary-specific expression pattern that specifically excludes reproductive meristems, implying the involvement of previously proposed localized signaling centers for branch regulation. Importantly, during early spikelet formation, non-cell-autonomous signals associated with HvALOG1 expression may specify spikelet meristem determinacy, while boundary formation of floret organs appears to be coordinated in a cell-autonomous manner. Moreover, barley ALOG family members synergistically modulate inflorescence morphology, with HvALOG1 predominantly governing meristem maintenance and floral organ development. We further propose that spatiotemporal redundancies of expressed HvALOG members specifically in the basal inflorescence may be accountable for proper patterning of spikelet formation in mutant plants. Our research offers new perspectives on regulatory signaling roles of ALOG transcription factors during the development of reproductive meristems in cereal inflorescences.

The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development

The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.

Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants

The HD superfamily has been studied in detail for several decades. The plant-specific HD-Zip I subfamily attracts the most attention because of its involvement in plant development and stress responses. In this review, we provide a comprehensive insight into the evolutionary events responsible for the functional redundancy and diversification of the HD-Zip I genes in regulating various biological processes. We summarized the evolutionary history of the HD-Zip family, highlighting the important role of WGDs in its expansion and divergence of retained duplicates in the genome. To determine the relationship between the evolutionary origin and functional conservation of HD-Zip I in different species, we performed a phylogenetic analysis, compared their expression profiles in different tissues and under stress and traced the role of orthologs and paralogs in regulating developmental processes. We found that HD-Zip I from different species have similar gene structures with a highly conserved HD and Zip, bind to the same DNA sequences and are involved in similar biological processes. However, they exhibit a functional diversity, which is manifested in altered expression patterns. Some of them are involved in the regulation of species-specific leaf morphology and phenotypes. Here, we discuss the role of changes in functional domains involved in DNA binding and protein interaction of HD-Zip I and in cis-regulated regions of its target genes in promoting adaptive innovations through the formation of de novo regulatory systems. Understanding the role of the HD-Zip I subfamily in organism-environment interactions remains a challenge for evolutionary developmental biology (evo-devo).

Sp1-mediated miR-193b suppresses atopic dermatitis by regulating HMGB1

Atopic dermatitis (AD) is a chronic and recurrent inflammatory skin disease. Keratinocyte dysfunction plays a central role in AD development. MicroRNA is a novel player in many inflammatory and immune skin diseases. In this study, we investigated the potential function and regulatory mechanism of miR-193b in AD. Inflamed human keratinocytes (HaCaT) were established by tumor necrosis factor (TNF)-α/interferon (IFN)-γ stimulation. Cell viability was measured using MTT assay, while the cell cycle was analyzed using flow cytometry. The cytokine levels were examined by enzyme-linked immunosorbent assay. The interaction between Sp1, miR-193b, and HMGB1 was analyzed using dual luciferase reporter and/or chromatin immunoprecipitation (ChIP) assays. Our results revealed that miR-193b upregulation enhanced the proliferation of TNF-α/IFN-γ-treated keratinocytes and repressed inflammatory injury. miR-193b negatively regulated high mobility group box 1 (HMGB1) expression by directly targeting HMGB1. Furthermore, HMGB1 knockdown promoted keratinocyte proliferation and inhibited inflammatory injury by repressing nuclear factor kappa-B (NF-κB) activation. During AD progression, HMGB1 overexpression abrogated increase of keratinocyte proliferation and repression of inflammatory injury caused by miR-193b overexpression. Moreover, transcription factor Sp1 was identified as the biological partner of the miR-193b promoter in promoting miR-193b expression. Therefore, Sp1 upregulation promotes keratinocyte proliferation and represses inflammatory injury during AD development via promoting miR-193b expression and repressing HMGB1/NF-κB activation.

Differential chromatin binding preference is the result of the neo-functionalization of the TB1 clade of TCP transcription factors in grasses

The understanding of neo-functionalization of plant transcription factors (TFs) after gene duplication has been extensively focused on changes in protein-protein interactions, the expression pattern of TFs, or the variation of cis-elements bound by TFs. Yet, the main molecular role of a TF, that is, its specific chromatin binding for the direct regulation of target gene expression, continues to be mostly overlooked. Here, we studied the TB1 clade of the TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) TF family within the grasses (Poaceae). We identified an Asp/Gly amino acid replacement within the TCP domain, originated within a paralog TIG1 clade exclusive for grasses. The heterologous expression of Zea mays TB1 and its two paralogs BAD1 and TIG1 in Arabidopsis mutant plants lacking the TB1 ortholog BRC1 revealed distinct functions in plant development. Notably, the Gly acquired in the TIG1 clade does not impair TF homodimerization and heterodimerization, while it modulates chromatin binding preferences. We found that in vivo TF recognition of target promoters depends on this Asp/Gly mutation and directly impacts downstream gene expression and subsequent plant development. These results provided new insights into how natural selection fine-tunes gene expression regulation after duplication of TFs to define plant architecture.

The upregulated LsKN1 gene transforms pinnately to palmately lobed leaves through auxin, gibberellin, and leaf dorsiventrality pathways in lettuce

Leaf shape represents a vital agronomic trait for leafy vegetables such as lettuce. Some lettuce cultivars produce lobed leaves, varying from pinnately to palmately lobed, but the genetic mechanisms remain unclear. In this study, we cloned one major quantitative trait locus (QTL) controlling palmately lobed leaves. The candidate gene, LsKN1, encodes a homeobox transcription factor, and has been shown previously to be critical for the development of leafy heads in lettuce. The LsKN1 allele that is upregulated by the insertion of a transposon promotes the development of palmately lobed leaves. We demonstrated that LsKN1 upregulated LsCUC2 and LsCUC3 through different mechanisms, and their upregulation was critical for the development of palmately lobed leaves. LsKN1 binds the promoter of LsPID to promote auxin biosynthesis, which positively contributes to the development of palmately lobed leaves. In contrast, LsKN1 suppresses GA biosynthesis to promote palmately lobed leaves. LsKN1 also binds to the promoter of LsAS1, a dorsiventrality gene, to downregulate its expression. Overexpression of the LsAS1 gene compromised the effects of the LsKN1 gene changing palmately to pinnately lobed leaves. Our study illustrated that the upregulated LsKN1 gene led to palmately lobed leaves in lettuce by integrating several downstream pathways, including auxin, gibberellin, and leaf dorsiventrality pathways.

Identification and analysis of HD-Zip genes involved in the leaf development of Liriodendron chinense using multidimensional analysis

Homeodomain-leucine zipper (HD-Zip) proteins are plant-specific transcription factors that play important roles in different biological processes, especially leaf development. However, no studies to date have identified the HD-Zip genes in Liriodendron chinense nor characterized their functions. We identified the HD-Zip genes in L. chinense by analysing the phylogeny, chromosome location, structure, conserved motif, cis-regulatory elements, synteny, post-transcriptional regulation and expression patterns of these genes during leaf development. A total of 36 LcHD-Zip genes were identified and divided into four subfamilies (HD-Zip I to IV). Synteny analysis revealed that segmental duplication was the main force driving the expansion of LcHD-Zip genes. These 36 LcHD-Zip genes exhibited 11 different expression patterns. Pattern 1, 2, 3, 4, 6, 7, 8 and 9 genes may play important roles in leaf development, such as leaf initiation, leaf polarity establishment, leaf shape development, phytohormone-mediated leaf growth and leaf epidermal structure formation. Four HD-Zip III genes were targeted by microRNAs (miRNAs), and the miR165/166a-HD-Zip regulatory module formed regulated leaf initiation and leaf polarity establishment. Overall, LcHD-Zip genes play key roles in leaf development of L. chinense. This work provides a foundation for the functional verification of HD-Zip genes identified in this study.

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

Identification and characterization of stress responsive homeodomain leucine zipper transcription factors in Medicago truncatula

BACKGROUND

Homeodomain leucine zipper (HD-ZIP) transcription factors play roles in regulating plant development and responses to abiotic stresses; however, how HD-ZIP genes in Medicago truncatula are involved in abiotic stress response remains elusive.

METHODS AND RESULTS

The HD-ZIP I genes in Medicago truncatula were identified and characterized, and their expression patterns in different tissues and under different abiotic stresses were analyzed. A total of 15 Medicago truncatula HD-ZIP I genes were identified and a phylogenetic analysis of HD-ZIP I proteins in Arabidopsis thaliana and Medicago truncatula was conducted. Fifteen HD-ZIP I genes showed diverse tissue preferences. Among them, expressions of MtHB22 and MtHB51 were specially detected in vegetative buds. In addition, they responded to various abiotic stresses, including salinity and osmotic stress and abscisic acid (ABA). For instance, MtHB7 and MtHB12 expression levels were found to be positively associated with salt, osmotic stress and ABA in both shoots and roots, while MtHB13 and MtHB23 were negatively associated with these stresses in Medicago truncatula.

CONCLUSION

The HD-ZIP I genes in Medicago truncatula are evolutionarily conserved, but also exhibit gene duplication and gene loss events. Differential expression analysis of Medicago truncatula HD-ZIP I genes indicated their crucial roles in abiotic stress responses. Our genome-wide analysis of the HD-ZIP I transcription factor family in Medicago truncatula provided a valuable reference for further research.

MicroRNA biogenesis and activity in plant cell dedifferentiation stimulated by cell wall removal

BACKGROUND

Despite the frequent use of protoplast-to-plant system in in vitro cultures of plants, the molecular mechanisms regulating the first and most limiting stages of this process, i.e., protoplast dedifferentiation and the first divisions leading to the formation of a microcallus, have not been elucidated.

RESULTS

In this study, we investigated the function of miRNAs in the dedifferentiation of A. thaliana mesophyll cells in a process stimulated by the enzymatic removal of the cell wall. Leaf cells, protoplasts and CDPs (cells derived from protoplasts) cultured for 24, 72 and 120 h (first cell division). In protoplasts, a strong decrease in the amount of AGO1 in both the nucleus and the cytoplasm, as well as dicing bodies (DBs), which are considered to be sites of miRNA biogenesis, was shown. However during CDPs division, the amounts of AGO1 and DBs strongly increased. MicroRNA transcriptome studies demonstrated that lower amount of differentially expressed miRNAs are present in protoplasts than in CDPs cultured for 120 h. Then analysis of differentially expressed miRNAs, selected pri-miRNA and mRNA targets were performed.

CONCLUSION

This result indicates that miRNA function is not a major regulation of gene expression in the initial but in later steps of dedifferentiation during CDPs divisions. miRNAs participate in organogenesis, oxidative stress, nutrient deficiencies and cell cycle regulation in protoplasts and CDPs. The important role played by miRNAs in the process of dedifferentiation of mesophyll cells was confirmed by the increased mortality and reduced cell division of CDPs derived from mutants with defective miRNA biogenesis and miR319b expression.

Knock-down of δ-aminolevulinic acid dehydratase via virus-induced gene silencing alters the microRNA biogenesis and causes stress-related reactions in citrus plants

The δ-aminolevulinic acid (δ-ALA) is an intermediate in the biosynthetic pathway of tetrapyrroles. Tetrapyrroles play vital roles in many biological processes such as photosynthesis, respiration, and light-sensing. ALA-dehydratase (ALAD) combines two molecules of δ-ALA to form porphobilinogen. In citrus, the silencing of ALAD caused discrete yellow spots and necrosis in leaves and stems. Additionally, it caused rapid death in developing new shoots. Herein, we hypothesize that the accumulation of δ-ALA results in severe stress and reduced meristem development. For that reason, we investigated the dynamic changes in the expression profiles of 23 microRNA (miRNA) identified through small RNA sequencing, from CTV-tALAD plants in comparison with healthy C. macrophylla and C. macrophylla infiltrated with CTV-wt. Furthermore, we reported the effect of ALAD silencing on the total phenolics, H₂O_2, and reactive oxygen species (ROS) levels, to examine the possibilities of miRNAs involving the regulation of these pathways. Our results showed that the total phenolics content, H₂O₂, and O₂^- levels were increased in CTV-tALAD plants. Moreover, 63 conserved miRNA members belonging to 23 different miRNA families were differentially expressed in CTV-tALAD plants compared to controls. The identified miRNAs are implicated in auxin biosynthesis and signaling, axillary shoot meristem formation and leaf morphology, starch metabolism, and oxidative stress. Collectively, our findings suggested that ALAD silencing initiates stress on citrus plants. As a result, CTV-tALAD plants exhibit reduced metabolic rate, growth, and development in order to cope with the stress that resulted from the accumulation of δ-ALA. This cascade of events led to leaf, stem, and meristem necrosis and failure of new shoot development.

Beyond Trees: Regulons and Regulatory Motif Characterization

Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a set of target genes regulated by a transcription factor by physically binding to regulatory motifs to accomplish a specific biological function, such as the CO-FT regulon for flowering timing and fall growth cessation in trees. Only with a clear characterization of regulatory motifs, can candidate target genes be experimentally validated, but motif characterization represents the weakest feature of regulon research, especially in tree genetics. I review here relevant experimental and bioinformatics approaches in characterizing transcription factors and their binding sites, outline problems in tree regulon research, and demonstrate how transcription factor databases can be effectively used to aid the characterization of tree regulons.