Evolutionary Analysis of the Land Plant-Specific TCP Interactor Containing EAR Motif Protein (TIE) Family of Transcriptional Corepressors.

The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin of the TIE family to the early evolution of the embryophyte, while an earlier diversification in algae cannot be ruled out.

Scalable Approach to Evaluate Plant microRNA Trimming and Tailing from Small RNA-Seq Data.

MicroRNAs are small regulatory RNAs of 20-24 nt, which guide the RNA-induced silencing complex to silence several genes post-transcriptionally. Plant miRNA biogenesis involves many steps, including their 2'-O-methylation at their 3' end, which protects them from degradation. In addition, there are two other types of modifications involved in miRNA turnover: trimming and tailing.

The genome awakens: transposon-mediated gene regulation.

Current progress in plant genomics has uncovered important roles of transposable elements (TEs) in gene regulation and has transformed their perception from 'junk DNA' to key genomic players. Recent advances show how stress conditions trigger TE mobilization, introducing new regulatory sequences that can reshape plant responses to environmental changes. This review explores our current knowledge of how TEs, especially those located in gene-rich regions of plant genomes, regulate gene expression at different mechanistic levels.

Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response.

Infectious diseases drive wild plant evolution and impact crop yield. Plants, like animals, sense biotic threats through pattern recognition receptors (PRRs). Overly robust immune responses can harm plants; thus, understanding the tuning of defense response mechanisms is crucial for developing pathogen-resistant crops.

The HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15-HISTONE DEACETYLASE9 complex associates with HYPONASTIC LEAVES 1 to modulate microRNA expression in response to abscisic acid signaling.

The regulation of microRNA (miRNA) biogenesis is crucial for maintaining plant homeostasis under biotic and abiotic stress. The crosstalk between the RNA polymerase II (Pol-II) complex and the miRNA processing machinery has emerged as a central hub modulating transcription and cotranscriptional processing of primary miRNA transcripts (pri-miRNAs). However, it remains unclear how miRNA-specific transcriptional regulators recognize MIRNA loci.

Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana.

Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable element (TE)-derived inverted repeats (IRs) are commonly found near genes, where they affect host gene expression. However, the molecular mechanisms of such regulation are unclear in most cases.

exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data.

The computational methods for the prediction of gene function annotations aim to automatically find associations between a gene and a set of Gene Ontology (GO) terms describing its functions. Since the hand-made curation process of novel annotations and the corresponding wet experiments validations are very time-consuming and costly procedures, there is a need for computational tools that can reliably predict likely annotations and boost the discovery of new gene functions. This work proposes a novel method for predicting annotations based on the inference of GO similarities from expression similarities.

The underground life of homeodomain-leucine zipper transcription factors.

Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated.

Elucidating carbohydrate metabolism in Euglena gracilis: Reverse genetics-based evaluation of genes coding for enzymes linked to paramylon accumulation.

Euglena gracilis is a eukaryotic single-celled and photosynthetic organism grouped under the kingdom Protista. This phytoflagellate can accumulate the carbon photoassimilate as a linear β-1,3-glucan chain called paramylon. This storage polysaccharide can undergo degradation to provide glucose units to obtain ATP and reducing power both in aerobic and anaerobic growth conditions.

Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover.

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances.

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing.

Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis.

The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity.

In plants, small RNAs are loaded into ARGONAUTE (AGO) proteins to fulfill their regulatory functions. MicroRNAs (miRNAs), one of the most abundant classes of endogenous small RNAs, are preferentially loaded into AGO1. Such loading, long believed to happen exclusively in the cytoplasm, was recently proposed to also occur in the nucleus.

Class I TCP transcription factors regulate trichome branching and cuticle development in Arabidopsis.

Trichomes and the cuticle are two specialized structures of the aerial epidermis that are important for plant organ development and interaction with the environment. In this study, we report that Arabidopsis thaliana plants affected in the function of the class I TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) transcription factors TCP14 and TCP15 show overbranched trichomes in leaves and stems and increased cuticle permeability. We found that TCP15 regulates the expression of MYB106, a MIXTA-like transcription factor involved in epidermal cell and cuticle development, and overexpression of MYB106 in a tcp14 tcp15 mutant reduces trichome branch number.

Light Triggers the miRNA-Biogenetic Inconsistency for De-etiolated Seedling Survivability in Arabidopsis thaliana.

The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels.

CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants.

CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues.

Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower.

Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci.

Alternative use of miRNA-biogenesis co-factors in plants at low temperatures.

Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plant development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs.

A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation.

Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait.

Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids.

The merging of two divergent genomes in a hybrid is believed to trigger a "genomic shock", disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A.

A role for LAX2 in regulating xylem development and lateral-vein symmetry in the leaf.

Background And Aims: The symmetry of venation patterning in leaves is highly conserved within a plant species. Auxins are involved in this process and also in xylem vasculature development. Studying transgenic Arabidopsis plants ectopically expressing the sunflower transcription factor HaHB4, it was observed that there was a significant lateral-vein asymmetry in leaves and in xylem formation compared to wild type plants.

A uORF Represses the Transcription Factor AtHB1 in Aerial Tissues to Avoid a Deleterious Phenotype.

AtHB1 is an Arabidopsis () homeodomain-leucine zipper transcription factor that participates in hypocotyl elongation under short-day conditions. Here, we show that its expression is posttranscriptionally regulated by an upstream open reading frame (uORF) located in its 5' untranslated region. This uORF encodes a highly conserved peptide (CPuORF) that is present in varied monocot and dicot species.

The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus.

Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis-acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A.

The cytochrome c oxidase biogenesis factor AtCOX17 modulates stress responses in Arabidopsis.

COX17 is a soluble protein from the mitochondrial intermembrane space that participates in the transfer of copper for cytochrome c oxidase (COX) assembly in eukaryotic organisms. In this work, we studied the function of both Arabidopsis thaliana AtCOX17 genes using plants with altered expression levels of these genes. Silencing of AtCOX17-1 in a cox17-2 knockout background generates plants with smaller rosettes and decreased expression of genes involved in the response of plants to different stress conditions, including several genes that are induced by mitochondrial dysfunctions.

TCP15 modulates cytokinin and auxin responses during gynoecium development in Arabidopsis.

We studied the role of Arabidopsis thaliana TCP15, a member of the TEOSINTE BRANCHED1-CYCLOIDEA-PCF (TCP) transcription factor family, in gynoecium development. Plants that express TCP15 from the 35S CaMV promoter (35S:TCP15) develop flowers with defects in carpel fusion and a reduced number of stigmatic papillae. In contrast, the expression of TCP15 fused to a repressor domain from its own promoter causes the development of outgrowths topped with stigmatic papillae from the replum.