The genomes of many plants, animals, and fungi frequently comprise dispensable B chromosomes that rely upon various chromosomal drive mechanisms to counteract the tendency of non-essential genetic elements to be purged over time. The B chromosome of rye - a model system for nearly a century - undergoes targeted nondisjunction during first pollen mitosis, favouring segregation into the generative nucleus, thus increasing their numbers over generations. However, the genetic mechanisms underlying this process are poorly understood. Here, using a newly-assembled, ~430 Mb-long rye B chromosome pseudomolecule, we identify five candidate genes whose role as trans-acting moderators of the chromosomal drive is supported by karyotyping, chromosome drive analysis and comparative RNA-seq. Among them, we identify DCR28, coding a microtubule-associated protein related to cell division, and detect this gene also in the B chromosome of Aegilops speltoides. The DCR28 gene family is neo-functionalised and serially-duplicated with 15 B chromosome-located copies that are uniquely highly expressed in the first pollen mitosis of rye.
- MeSH
- Aegilops genetika metabolismus MeSH
- chromozomy rostlin * genetika MeSH
- karyotypizace MeSH
- mitóza * genetika MeSH
- nondisjunkce genetická MeSH
- pyl genetika MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny MeSH
- rostlinné proteiny genetika metabolismus MeSH
- žito * genetika MeSH
- Publikační typ
- časopisecké články MeSH
Despite the widely accepted involvement of DNA methylation in the regulation of rDNA transcription, the relative participation of different cytosine methylation pathways is currently described only for a few model plants. Using PacBio, Bisulfite, and RNA sequencing; PCR; Southern hybridizations; and FISH, the epigenetic consequences of rDNA copy number variation were estimated in two T. porrifolius lineages, por1 and por2, the latter with more than twice the rDNA copy numbers distributed approximately equally between NORs on chromosomes A and D. The lower rDNA content in por1 correlated with significantly reduced (>90%) sizes of both D-NORs. Moreover, two (L and S) prominent rDNA variants, differing in the repetitive organization of intergenic spacers, were detected in por2, while only the S-rDNA variant was detected in por1. Transcriptional activity of S-rDNA in por1 was associated with secondary constriction of both A-NORs. In contrast, silencing of S-rDNA in por2 was accompanied by condensation of A-NORs, secondary constriction on D-NORs, and L-rDNA transcriptional activity, suggesting (i) bidirectional nucleolar dominance and (ii) association of S-rDNAs with A-NORs and L-rDNAs with D-NORs in T. porrifolius. Each S- and L-rDNA array was formed of several sub-variants differentiating both genetically (specific SNPs) and epigenetically (transcriptional efficiency and cytosine methylation). The most significant correlations between rDNA silencing and methylation were detected for symmetric CWG motifs followed by CG motifs. No correlations were detected for external cytosine in CCGs or asymmetric CHHs, where methylation was rather position-dependent, particularly for AT-rich variants. We conclude that variations in rDNA copy numbers in plant diploids can be accompanied by prompt epigenetic responses to maintain an appropriate number of active rDNAs. The methylation dynamics of CWGs are likely to be the most responsible for regulating silent and active rDNA states.
- MeSH
- chromozomy rostlin genetika MeSH
- cytosin * metabolismus MeSH
- epigeneze genetická MeSH
- genetická transkripce MeSH
- metylace DNA * MeSH
- regulace genové exprese u rostlin MeSH
- ribozomální DNA * genetika MeSH
- umlčování genů * MeSH
- variabilita počtu kopií segmentů DNA MeSH
- Publikační typ
- časopisecké články MeSH
The FLOWERING LOCUS T (FT) gene is the essential integrator of flowering regulatory pathways in angiosperms. The paralogs of the FT gene may perform antagonistic functions, as exemplified by BvFT1, that suppresses flowering in Beta vulgaris, unlike the paralogous activator BvFT2. The roles of FT genes in other amaranths were less investigated. Here, we transformed Arabidopsis thaliana with the FLOWERING LOCUS T like (FTL) genes of Chenopodium ficifolium and found that both CfFTL1 and CfFTL2-1 accelerated flowering, despite having been the homologs of the Beta vulgaris floral promoter and suppressor, respectively. The floral promotive effect of CfFTL2-1 was so strong that it caused lethality when overexpressed under the 35S promoter. CfFTL2-1 placed in an inducible cassette accelerated flowering after induction with methoxyphenozide. The spontaneous induction of CfFTL2-1 led to precocious flowering in some primary transformants even without chemical induction. The CqFT2-1 homolog from Chenopodium quinoa had the same impact on viability and flowering as CfFTL2-1 when transferred to A. thaliana. After the FTL gene duplication in Amaranthaceae, the FTL1 copy maintained the role of floral activator. The second copy FTL2 underwent subsequent duplication and functional diversification, which enabled it to control the onset of flowering in amaranths to adapt to variable environments.
- MeSH
- Arabidopsis * genetika metabolismus MeSH
- Chenopodium * genetika metabolismus MeSH
- květy genetika metabolismus MeSH
- proteiny huseníčku * genetika metabolismus MeSH
- regulace genové exprese u rostlin genetika MeSH
- semenáček metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The NGATHA (NGA) transcription factor (TF) belongs to the ABI3/VP1 (RAV) transcriptional subfamily, a subgroup of the B3 superfamily, which is relatively well-studied in Arabidopsis. However, limited data are available on the contributions of NGA TF in other plant species. In this study, 207 NGA gene family members were identified from a genome-wide search against Arabidopsis thaliana in the genome data of 18 dicots and seven monocots. The phylogenetic and sequence alignment analyses divided NGA genes into different clusters and revealed that the numbers of genes varied depending on the species. The phylogeny was followed by the characterization of the Solanaceae (tomato, potato, capsicum, tobacco) and Poaceae (Brachypodium distachyon, Oryza sativa L. japonica, and Sorghum bicolor) family members in comparison with A. thaliana. The gene and protein structures revealed a similar pattern for NGA and NGA-like sequences, suggesting that both are conserved during evolution. Promoter cis-element analysis showed that phytohormones such as abscisic acid, auxin, and gibberellins play a crucial role in regulating the NGA gene family. Gene ontology analysis revealed that the NGA gene family participates in diverse biological processes such as flower development, leaf morphogenesis, and the regulation of transcription. The gene duplication analysis indicates that most of the genes are evolved due to segmental duplications and have undergone purifying selection pressure. Finally, the gene expression analysis implicated that the NGA genes are abundantly expressed in lateral organs and flowers. This analysis has presented a detailed and comprehensive study of the NGA gene family, providing basic knowledge of the gene, protein structure, function, and evolution. These results will lay the foundation for further understanding of the role of the NGA gene family in various plant developmental processes.
- MeSH
- Arabidopsis * genetika metabolismus MeSH
- Brachypodium * genetika MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- multigenová rodina MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- rýže (rod) * genetika metabolismus MeSH
- transkripční faktory genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.
- MeSH
- fyziologická adaptace * MeSH
- kořeny rostlin metabolismus účinky záření MeSH
- regulace genové exprese u rostlin účinky záření MeSH
- rostlinné proteiny genetika metabolismus MeSH
- rostliny metabolismus účinky záření MeSH
- semenáček metabolismus účinky záření MeSH
- světlo * MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
KEY MESSAGE: Multiple origins of Indian dwarf wheat were due to two mutations targeting the same TREE domain of a GSK3-like kinase, and these mutations confer to enhanced drought tolerance and increased phosphate and nitrogen accumulation for adaptation to the dry climate of Indian and Pakistan. Indian dwarf wheat, featured by the short stature, erect leaves, dense spikes, and small, spherical grains, was a staple crop in India and Pakistan from the Bronze Age until the early 1900s. These morphological features are controlled by a single locus Sphaerococcum 1 (S1), but the genetic identity of the locus and molecular mechanisms underlying the selection of this wheat type are unknown. In this study, we showed that the origin of Indian dwarf wheat was due to two independent missense mutations targeting the conserved TREE domain of a GSK3-like kinase, which is homologous to the Arabidopsis BIN2 protein, a negative regulator in brassinosteroid signaling. The S1 protein is involved in brassinosteroid signaling by physical interaction with the wheat BES1/BZR1 proteins. The dwarf alleles are insensitive to brassinosteroid, upregulates brassinosteroid biosynthetic genes, significantly enhanced drought tolerance, facilitated phosphate accumulation, and increased high molecular weight glutenins. It is the enhanced drought tolerance and accumulation of nitrogen and phosphate that contributed to the adaptation of such a small-grain form of wheat to the dry climate of India and Pakistan. Thus, our research not only identified the genetic events underlying the origin of the Indian dwarf wheat, but also revealed the function of brassinosteroid in the regulation of drought tolerance, phosphate homeostasis, and grain quality.
- MeSH
- fenotyp MeSH
- fosfáty metabolismus MeSH
- fosforylace MeSH
- geneticky modifikované rostliny genetika fyziologie MeSH
- kinasa 3 glykogensynthasy genetika metabolismus MeSH
- mutace * MeSH
- období sucha * MeSH
- pšenice genetika fyziologie MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
Structural knowledge of biological macromolecules is essential for understanding their function and for modifying that function by engineering. Protein crystallography is a powerful method for elucidating molecular structures of proteins, but it is essential that the investigator has a basic knowledge of good practices and of the major pitfalls in the technique. Here we describe issues specific for the case of structural studies of strigolactone (SL) receptor structure and function, and in particular the difficulties associated with capturing complexes of SL receptors with the SL hormone ligand in the crystal.
- MeSH
- heterocyklické sloučeniny tricyklické metabolismus MeSH
- konformace proteinů MeSH
- krystalografie rentgenová MeSH
- laktony metabolismus MeSH
- ligandy MeSH
- molekulární modely MeSH
- receptory buněčného povrchu genetika metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- signální transdukce MeSH
- vazba proteinů MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan's molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.
- MeSH
- Arabidopsis fyziologie MeSH
- buněčná stěna metabolismus MeSH
- fluorescenční protilátková technika MeSH
- fyziologie rostlin * MeSH
- glukany chemie metabolismus MeSH
- hrách setý fyziologie MeSH
- kyseliny indoloctové metabolismus MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné buňky metabolismus MeSH
- signální transdukce MeSH
- vývoj rostlin * MeSH
- xylany chemie metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
The transition from vegetative to reproductive phases is the most fundamental and tightly controlled switch in the life of flowering plants. The short-day plant Chenopodium rubrum is a fast cycling annual plant lacking a juvenile phase. It can be induced to flowering at the seedling stage by exposure to a single period of darkness. This floral induction may then be cancelled by a short pulse of red light at midnight called night break (NB), which also inhibits the floral activator FLOWERING LOCUS T LIKE 1 (CrFTL1). We performed a comparative transcriptomic study between C. rubrum seedlings treated by NB and ones growing through uninterrupted night, and found about six hundred differentially expressed genes, including the B-BOX DOMAIN (BBX) genes. We focused on the CrBBX19 and BOLTING TIME CONTROL 1 (BTC1) genes, homologous to the upstream regulators of the BvFT2, a floral inducer in sugar beet. The transcription patterns of the two genes were compatible with their putative role as a sensor of the dark period length optimal for flowering (CrBBX19), and a signal of lights-on (CrBTC1), but the participation of other genes cannot be excluded. The expression profiles of CrBBX19 and the homolog of the core endogenous clock gene LATE ELONGATED HYPOCOTYL (LHY) were highly similar, which suggested their co-regulation.
KEY MESSAGE: The new 4.2-kb transposable insertion in the intron of ZmCCT reversely responded relative to the known 5.1-kb transposable insertion to photoperiods between low- and high-latitude regions. Flowering time is a key trait for cereal adaptation that is controlled by a complex genetic background in maize. The effect of multiple alleles from a quantitative trait locus (QTL) on flowering time remains largely unknown. Here, we fine-mapped a major QTL for flowering time on maize chromosome 10 corresponding to ZmCCT, where a new allele with a 4.2-kilobase (kb) transposable insertion was present in the intron. The known allele with a 5.1-kb transposon insertion in the promoter of ZmCCT enhances flowering in high-latitude regions, but has no effect on flowering time in low-latitude regions in comparison with the null allele lacking this insertion. However, our new allele with a 4.2-kb insertion reduced flowering in the low-latitude region, but produced unchanged flowering time in the high-latitude region relative to the 5.1-kb transposable insertion. Transcription analysis revealed that the new allele with 4.2-kb insertion versus the 5.1-kb insertion repressed and unchanged the transcription of ZmCCT in the low- and high-latitude regions, respectively. Thus, the allele with the 4.2-kb transposable insertion showed a completely opposite response to photoperiods between these two regions. Phylogenetic analysis revealed that the 4.2-kb transposable insertion in the two Northern flint corns originated from tropical maize. RNA-seq analysis and dual-luciferase transient expression assays further identified a conserved gene regulation network of ZmCCT between maize and rice, in which ZmCCT directly repressed the transcription of the florigen gene ZCN8 via ZmEhd1. Our results suggest that transposable elements play an important role in maize adaptation.
- MeSH
- chromozomy rostlin genetika MeSH
- fenotyp MeSH
- fotoperioda * MeSH
- fyziologická adaptace MeSH
- kukuřice setá genetika růst a vývoj účinky záření MeSH
- květy genetika růst a vývoj účinky záření MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů metody MeSH
- promotorové oblasti (genetika) MeSH
- regulace genové exprese u rostlin * MeSH
- rostlinné proteiny genetika metabolismus MeSH
- transpozibilní elementy DNA * MeSH
- Publikační typ
- časopisecké články MeSH
