Somion occarium is a wood-decaying bracket fungus belonging to an order known to be rich in useful chemical compounds. Despite its widespread distribution, S. occarium has been assessed as endangered on at least 1 national Red List, presumably due to loss of old-growth forest habitat. Here, we present a near-complete, annotated nuclear genome assembly for S. occarium consisting of 31 Mbp arranged in 11 pseudochromosomes-9 of which are telomere-to-telomere-as well as a complete mitochondrial genome assembly of 112.9 Kbp. We additionally performed phylogenomic analysis and annotated carbohydrate-active enzymes (CAZymes) to compare gene and CAZyme content across closely related species. This genome was sequenced as the representative for Kingdom Fungi in the European Reference Genome Atlas Pilot Project.
- Klíčová slova
- cerrenaceae, polyporales, fungal conservation, saprotroph, white-rot,
- MeSH
- dřevo mikrobiologie MeSH
- fylogeneze * MeSH
- genom fungální * MeSH
- genom mitochondriální * MeSH
- ohrožené druhy MeSH
- Publikační typ
- časopisecké články MeSH
Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.
- Klíčová slova
- Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, cytokinins, multistep phosphorelay, osmotic stress, salinity, two-component signaling, type-A response regulator,
- MeSH
- Arabidopsis genetika fyziologie metabolismus MeSH
- Brassica napus genetika fyziologie metabolismus MeSH
- Brassica * genetika fyziologie metabolismus MeSH
- cytokininy * metabolismus MeSH
- fylogeneze MeSH
- fyziologický stres * MeSH
- regulace genové exprese u rostlin MeSH
- regulátory růstu rostlin metabolismus MeSH
- rostlinné proteiny * genetika metabolismus MeSH
- signální transdukce MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- cytokininy * MeSH
- regulátory růstu rostlin MeSH
- rostlinné proteiny * MeSH
Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.
- MeSH
- Arabidopsis * genetika růst a vývoj metabolismus MeSH
- benzamidy MeSH
- buněčná stěna * metabolismus MeSH
- gibereliny metabolismus MeSH
- hypokotyl růst a vývoj genetika metabolismus MeSH
- kyseliny indoloctové * metabolismus MeSH
- mutace genetika MeSH
- pektiny metabolismus MeSH
- proteiny huseníčku * metabolismus genetika MeSH
- regulace genové exprese u rostlin * MeSH
- semenáček * genetika růst a vývoj metabolismus MeSH
- transkripční faktory bHLH * metabolismus genetika MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- benzamidy MeSH
- gibereliny MeSH
- isoxaben MeSH Prohlížeč
- kyseliny indoloctové * MeSH
- pektiny MeSH
- PIF4 protein, Arabidopsis MeSH Prohlížeč
- proteiny huseníčku * MeSH
- transkripční faktory bHLH * MeSH
AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.
- MeSH
- databáze proteinů * MeSH
- internet MeSH
- konformace proteinů MeSH
- molekulární modely MeSH
- proteiny chemie genetika metabolismus MeSH
- proteom * chemie genetika MeSH
- sbalování proteinů MeSH
- software * MeSH
- strojové učení MeSH
- strukturní homologie proteinů MeSH
- vyhledávač MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- proteiny MeSH
- proteom * MeSH
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
- MeSH
- endosperm * genetika metabolismus růst a vývoj MeSH
- epigeneze genetická MeSH
- genové regulační sítě MeSH
- histony metabolismus genetika MeSH
- ječmen (rod) * genetika růst a vývoj metabolismus MeSH
- regulace genové exprese u rostlin * MeSH
- rostlinné proteiny genetika metabolismus MeSH
- semena rostlinná * genetika růst a vývoj metabolismus MeSH
- stanovení celkové genové exprese MeSH
- transkripční faktory genetika metabolismus MeSH
- transkriptom * genetika MeSH
- vývojová regulace genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- histony MeSH
- rostlinné proteiny MeSH
- transkripční faktory MeSH
Isocitrate dehydrogenase is an enzyme converting isocitrate to α-ketoglutarate in the canonical tricarboxylic acid (TCA) cycle. There are three different types of isocitrate dehydrogenase documented in eukaryotes. Our study points out the complex evolutionary history of isocitrate dehydrogenases across kinetoplastids, where the common ancestor of Trypanosomatidae and Bodonidae was equipped with two isoforms of the isocitrate dehydrogenase enzyme: the NADP+-dependent isocitrate dehydrogenase 1 with possibly dual localization in the cytosol and mitochondrion and NADP+-dependent mitochondrial isocitrate dehydrogenase 2. In the extant trypanosomatids, isocitrate dehydrogenase 1 is present only in a few species suggesting that it was lost upon separation of Trypanosoma spp. and replaced by the mainly NADP+-dependent cytosolic isocitrate dehydrogenase 3 of bacterial origin in all the derived lineages. In this study, we experimentally demonstrate that the omnipresent isocitrate dehydrogenase 2 has a dual localization in both mitochondrion and cytosol in at least four species that possess only this isoform. The apparent lack of the NAD+-dependent isocitrate dehydrogenase activity in trypanosomatid mitochondrion provides further support to the existence of the noncanonical TCA cycle across trypanosomatids and the bidirectional activity of isocitrate dehydrogenase 3 when operating with NADP+ cofactor instead of NAD+. This observation can be extended to all 17 species analyzed in this study, except for Leishmania mexicana, which showed only low isocitrate dehydrogenase activity in the cytosol. The variability in isocitrate oxidation capacity among species may reflect the distinct metabolic strategies and needs for reduced cofactors in particular environments.
- Klíčová slova
- Krebs cycle, NAD+, NADP+, TCA cycle, cofactor preference, isocitrate dehydrogenase,
- MeSH
- isocitrátdehydrogenasa * genetika metabolismus MeSH
- isocitráty metabolismus MeSH
- NAD * metabolismus MeSH
- NADP metabolismus MeSH
- protein - isoformy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- isocitrátdehydrogenasa * MeSH
- isocitráty MeSH
- isocitric acid MeSH Prohlížeč
- NAD * MeSH
- NADP MeSH
- protein - isoformy MeSH
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
- Klíčová slova
- Arabidopsis thaliana, auxin, embryogenesis, flowering, meristem, plant, transcription factor, vascularization,
- MeSH
- Arabidopsis * metabolismus MeSH
- DNA vazebné proteiny genetika MeSH
- kyseliny indoloctové metabolismus MeSH
- proteiny huseníčku * genetika metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- transkripční faktory genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- DNA vazebné proteiny MeSH
- kyseliny indoloctové MeSH
- proteiny huseníčku * MeSH
- transkripční faktory MeSH
A series of molybdenum(II) compounds [(η5 -Cp')Mo(CO)2 (L2 )][BF4 ] (Cp'=C5 H4 (CH2 )2 SPh, C9 H6 (CH2 )2 OMe, L2= N,N-chelating ligand) have been synthesized and characterized by spectroscopic and analytical methods including X-ray crystallography. The in vitro assay on human leukemia cells MOLT-4 has shown that the substitution in the π-ligand in combination with suitable N,N-chelating ligand can lead to species with cytotoxicity considerably higher than reported to cisplatin. Unusually high activity was observed for compounds bearing phenanthroline ligands [{η5 -C9 H6 (CH2 )2 OMe}Mo(CO)2 (3,4,7,8-Me4 phen)][BF4 ] (IC50 =0.7±0.3 μM) and [{η5 -C9 H6 (CH2 )2 OMe}Mo(CO)2 (4,7-Ph2 phen)][BF4 ] (IC50 values 0.8±0.4 μM).
- Klíčová slova
- MOLT-4, cyclopentadienyl, cytotoxicity, indenyl, molybdenum,
- Publikační typ
- časopisecké články MeSH
Metal hyperaccumulation is an exclusive evolutionary trait contributing to efficient plant defence against biotic stress. The defence can be based on direct metal toxicity or the joint effects of accumulated metal and organic compounds, the latter being based on integrated signalling networks. While the role of metals in biotic stress defence of hyperaccumulators has been intensively studied, their role in the pathogen immunity of non-accumulator plants is far less understood. New findings show that in metal non-hyperaccumulating plants, localized hot spots of zinc, manganese, and iron increase plant immunity, while manipulation of nutrient availability may be used for priming against subsequent pathogen attack. Recent findings on the role of metals in plant-pathogen interactions are discussed considering the narrow line between deficiency and toxicity, host-pathogen nutrient competition and synergistic effects of simultaneous metal and biotic stress. We discuss the suitability of the direct-defence and joint-effects hypotheses in non-hyperaccumulating plants, and the involvement of metals as active centres of immunity-related enzymes. We also consider future challenges in revealing the mechanisms underlying metal-mediated plant immunity.
- Klíčová slova
- Crop plants, host-pathogen interactions, metal localization, metal transporters, micro X-ray fluorescence, phytohormones, plant immunity, trace metals,
- MeSH
- kovy MeSH
- rostliny MeSH
- stopové prvky * MeSH
- těžké kovy * MeSH
- zinek farmakologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- kovy MeSH
- stopové prvky * MeSH
- těžké kovy * MeSH
- zinek MeSH
Inorganic electrides have been proved to be efficient hosts for incorporating transition metals, which can effectively act as active sites giving an outstanding catalytic performance. Here, it is demonstrated that a reusable and recyclable (for more than 7 times) copper-based intermetallic electride catalyst (LaCu0.67 Si1.33 ), in which the Cu sites activated by anionic electrons with low-work function are uniformly dispersed in the lattice framework, shows vast potential for the selective C-H oxidation of industrially important hydrocarbons and cycloaddition of CO2 with epoxide. This leads to the production of value-added cyclic carbonates under mild reaction conditions. Importantly, the LaCu0.67 Si1.33 catalyst enables much higher turnover frequencies for the C-H oxidation (up to 25 276 h-1 ) and cycloaddition of CO2 into epoxide (up to 800 000 h-1 ), thus exceeding most nonnoble as well as noble metal catalysts. Density functional theory investigations have revealed that the LaCu0.67 Si1.33 catalyst is involved in the conversion of N-hydroxyphthalimide (NHPI) into the phthalimido-N-oxyl (PINO), which then triggers selective abstraction of an H atom from ethylbenzene for the generation of a radical susceptible to further oxygenation in the presence of O2 .
