The timing of seed germination is crucial for seed plants and is coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many receptors, signaling cascades, and hormonal control elements. In contrast, seed germination in several other plants is inhibited by light, but the molecular basis of this alternative response is unknown. We describe Aethionema arabicum (Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as this species has accessions with natural variation between light-sensitive and light-neutral responses. Inhibition of germination occurs in red, blue, or far-red light and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination, as in Arabidopsis, but transcriptome comparisons of light- and dark-exposed A. arabicum seeds revealed that, upon light exposure, the expression of genes for key regulators undergo converse changes, resulting in antipodal hormone regulation. These findings illustrate that similar modular components of a pathway in light-inhibited, light-neutral, and light-requiring germination among the Brassicaceae have been assembled in the course of evolution to produce divergent pathways, likely as adaptive traits.

• MeSH
• Brassicaceae fyziologie   účinky záření   MeSH
• exprese genu účinky záření   MeSH
• gibereliny metabolismus   MeSH
• klíčení účinky záření   MeSH
• kyselina abscisová metabolismus   MeSH
• rostlinné geny * MeSH
• sluneční záření * MeSH
• transkriptom účinky léků   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The maintenance of genome integrity over cell divisions is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is the STRUCTURAL MAINTENANCE OF CHROMOSOME5 (SMC5) and SMC6 (SMC5/6) complex, related to the cohesin and condensin complexes that control sister chromatid alignment and chromosome condensation, respectively. Here, we characterize NON-SMC ELEMENT4 (NSE4) paralogs of the SMC5/6 complex in Arabidopsis (Arabidopsis thaliana). NSE4A is expressed in meristems and accumulates during DNA damage repair. Partial loss-of-function nse4a mutants are viable but hypersensitive to DNA damage induced by zebularine. In addition, nse4a mutants produce abnormal seeds, with noncellularized endosperm and embryos that maximally develop to the heart or torpedo stage. This phenotype resembles the defects in cohesin and condensin mutants and suggests a role for all three SMC complexes in differentiation during seed development. By contrast, NSE4B is expressed in only a few cell types, and loss-of-function mutants do not have any obvious abnormal phenotype. In summary, our study shows that the NSE4A subunit of the SMC5-SMC6 complex is essential for DNA damage repair in somatic tissues and plays a role in plant reproduction.

• MeSH
• Arabidopsis embryologie   genetika   imunologie   MeSH
• duplikace genu MeSH
• genom rostlinný MeSH
• oprava DNA * genetika   MeSH
• podjednotky proteinů metabolismus   MeSH
• poškození DNA * genetika   MeSH
• proteiny buněčného cyklu genetika   metabolismus   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• pyl genetika   MeSH
• regulace genové exprese u rostlin MeSH
• semena rostlinná genetika   metabolismus   MeSH
• transkriptom genetika   MeSH
• upregulace genetika   MeSH
• vajíčko rostlin genetika   MeSH
• vazba proteinů MeSH
• vývojová regulace genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Maize is the highest yielding cereal crop grown worldwide for grain or silage. Here, we show that modulating the expression of the maize PLASTOCHRON1 (ZmPLA1) gene, encoding a cytochrome P450 (CYP78A1), results in increased organ growth, seedling vigour, stover biomass and seed yield. The engineered trait is robust as it improves yield in an inbred as well as in a panel of hybrids, at several locations and over multiple seasons in the field. Transcriptome studies, hormone measurements and the expression of the auxin responsive DR5rev:mRFPer marker suggest that PLA1 may function through an increase in auxin. Detailed analysis of growth over time demonstrates that PLA1 stimulates the duration of leaf elongation by maintaining dividing cells in a proliferative, undifferentiated state for a longer period of time. The prolonged duration of growth also compensates for growth rate reduction caused by abiotic stresses.

• MeSH
• biomasa * MeSH
• buněčné dělení genetika   MeSH
• časové faktory MeSH
• geneticky modifikované rostliny MeSH
• kukuřice setá genetika   růst a vývoj   metabolismus   MeSH
• kyseliny indoloctové metabolismus   MeSH
• listy rostlin genetika   růst a vývoj   metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• rostlinné proteiny genetika   MeSH
• semena rostlinná genetika   metabolismus   MeSH
• semenáček růst a vývoj   metabolismus   MeSH
• stanovení celkové genové exprese MeSH
• systém (enzymů) cytochromů P-450 genetika   MeSH
• vývojová regulace genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination.

• MeSH
• endosperm enzymologie   fyziologie   MeSH
• hypokotyl enzymologie   fyziologie   MeSH
• karboxylesterhydrolasy biosyntéza   genetika   fyziologie   MeSH
• klíčení genetika   fyziologie   MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• Lepidium sativum enzymologie   genetika   fyziologie   MeSH
• regulace genové exprese u rostlin genetika   fyziologie   MeSH
• rostlinné proteiny genetika   fyziologie   MeSH
• semena rostlinná enzymologie   fyziologie   MeSH
• stanovení celkové genové exprese MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.

• MeSH
• anotace sekvence MeSH
• Brassicaceae genetika   růst a vývoj   MeSH
• genom rostlinný MeSH
• genová ontologie MeSH
• klíčení MeSH
• regulace genové exprese u rostlin * MeSH
• rostlinné proteiny genetika   MeSH
• semena rostlinná genetika   růst a vývoj   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom * MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH

Background and Aims: Pisum sativum L. (pea) seed is a source of carbohydrate and protein for the developing plant. By studying pea seeds inoculated by the cytokinin-producing bacterium, Rhodococcus fascians , we sought to determine the impact of both an epiphytic (avirulent) strain and a pathogenic strain on source-sink activity within the cotyledons during and following germination. Methods: Bacterial spread was monitored microscopically, and real-time reverse transcription-quantitative PCR was used to determine the expression of cytokinin biosynthesis, degradation and response regulator gene family members, along with expression of family members of SWEET , SUT , CWINV and AAP genes - gene families identified initially in pea by transcriptomic analysis. The endogenous cytokinin content was also determined. Key Results: The cotyledons infected by the virulent strain remained intact and turned green, while multiple shoots were formed and root growth was reduced. The epiphytic strain had no such marked impact. Isopentenyl adenine was elevated in the cotyledons infected by the virulent strain. Strong expression of RfIPT , RfLOG and RfCKX was detected in the cotyledons infected by the virulent strain throughout the experiment, with elevated expression also observed for PsSWEET , PsSUT and PsINV gene family members. The epiphytic strain had some impact on the expression of these genes, especially at the later stages of reserve mobilization from the cotyledons. Conclusions: The pathogenic strain retained the cotyledons as a sink tissue for the pathogen rather than the cotyledon converting completely to a source tissue for the germinating plant. We suggest that the interaction of cytokinins, CWINVs and SWEETs may lead to the loss of apical dominance and the appearance of multiple shoots.

• MeSH
• cytokininy metabolismus   MeSH
• hrách setý genetika   mikrobiologie   MeSH
• interakce hostitele a patogenu MeSH
• klíčení MeSH
• kotyledon růst a vývoj   mikrobiologie   MeSH
• nemoci rostlin mikrobiologie   MeSH
• polymerázová řetězová reakce MeSH
• Rhodococcus fyziologie   MeSH
• semena rostlinná mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH

The plant-specific receptor-like cytoplasmic kinases (RLCKs) form a large, poorly characterized family. Members of the RLCK VI_A class of dicots have a unique characteristic: their activity is regulated by Rho-of-plants (ROP) GTPases. The biological function of one of these kinases was investigated using a T-DNA insertion mutant and RNA interference. Loss of RLCK VI_A2 function resulted in restricted cell expansion and seedling growth. Although these phenotypes could be rescued by exogenous gibberellin, the mutant did not exhibit lower levels of active gibberellins nor decreased gibberellin sensitivity. Transcriptome analysis confirmed that gibberellin is not the direct target of the kinase; its absence rather affected the metabolism and signalling of other hormones such as auxin. It is hypothesized that gibberellins and the RLCK VI_A2 kinase act in parallel to regulate cell expansion and plant growth. Gene expression studies also indicated that the kinase might have an overlapping role with the transcription factor circuit (PIF4-BZR1-ARF6) controlling skotomorphogenesis-related hypocotyl/cotyledon elongation. Furthermore, the transcriptomic changes revealed that the loss of RLCK VI_A2 function alters cellular processes that are associated with cell membranes, take place at the cell periphery or in the apoplast, and are related to cellular transport and/or cell wall reorganisation.

• MeSH
• Arabidopsis účinky léků   enzymologie   genetika   růst a vývoj   MeSH
• DNA bakterií genetika   metabolismus   MeSH
• DNA vazebné proteiny genetika   metabolismus   MeSH
• geneticky modifikované rostliny MeSH
• gibereliny metabolismus   farmakologie   MeSH
• hypokotyl účinky léků   enzymologie   genetika   růst a vývoj   MeSH
• inzerční mutageneze MeSH
• kotyledon účinky léků   enzymologie   genetika   růst a vývoj   MeSH
• kyseliny indoloctové metabolismus   farmakologie   MeSH
• protein-serin-threoninkinasy genetika   metabolismus   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• regulace genové exprese u rostlin * MeSH
• regulátory růstu rostlin farmakologie   MeSH
• semenáček účinky léků   enzymologie   genetika   růst a vývoj   MeSH
• stanovení celkové genové exprese MeSH
• transkripční faktory bHLH genetika   metabolismus   MeSH
• transkripční faktory genetika   metabolismus   MeSH
• transkriptom MeSH
• vývojová regulace genové exprese MeSH
• Publikační typ
• časopisecké články MeSH

The nascent polypeptide-associated (NAC) complex was described in yeast as a heterodimer composed of two subunits, α and β, and was shown to bind to the nascent polypeptides newly emerging from the ribosomes. NAC function was widely described in yeast and several information are also available about its role in plants. The knock down of individual NAC subunit(s) led usually to a higher sensitivity to stress. In Arabidopsis thaliana genome, there are five genes encoding NACα subunit, and two genes encoding NACβ. Double homozygous mutant in both genes coding for NACβ was acquired, which showed a delayed development compared to the wild type, had abnormal number of flower organs, shorter siliques and greatly reduced seed set. Both NACβ genes were characterized in more detail-the phenotype of the double homozygous mutant was complemented by a functional NACβ copy. Then, both NACβ genes were localized to nuclei and cytoplasm and their promoters were active in many organs (leaves, cauline leaves, flowers, pollen grains, and siliques together with seeds). Since flowers were the most affected organs by nacβ mutation, the flower buds' transcriptome was identified by RNA sequencing, and their proteome by gel-free approach. The differential expression analyses of transcriptomic and proteomic datasets suggest the involvement of NACβ subunits in stress responses, male gametophyte development, and photosynthesis.

• MeSH
• alely MeSH
• Arabidopsis fyziologie   MeSH
• fenotyp MeSH
• geneticky modifikované rostliny MeSH
• homozygot MeSH
• klíčení MeSH
• květy fyziologie   MeSH
• molekulární chaperony genetika   metabolismus   MeSH
• mutace MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• proteomika metody   MeSH
• regulace genové exprese u rostlin MeSH
• semena rostlinná MeSH
• transkriptom MeSH
• vývoj rostlin * genetika   MeSH
• Publikační typ
• časopisecké články MeSH

Chromatin is assembled by histone chaperones such as chromatin assembly factor CAF-1. We had noticed that vigor of Arabidopsis thaliana CAF-1 mutants decreased over several generations. Because changes in mutant phenotype severity over generations are unusual, we asked how repeated selfing of Arabidopsis CAF-1 mutants affects phenotype severity. CAF-1 mutant plants of various generations were grown, and developmental phenotypes, transcriptomes and DNA cytosine-methylation profiles were compared quantitatively. Shoot- and root-related growth phenotypes were progressively more affected in successive generations of CAF-1 mutants. Early and late generations of the fasciata (fas)2-4 CAF-1 mutant displayed only limited changes in gene expression, of which increasing upregulation of plant defense-related genes reflects the transgenerational phenotype aggravation. Likewise, global DNA methylation in the sequence context CHG but not CG or CHH (where H = A, T or C) changed over generations in fas2-4. Crossing early and late generation fas2-4 plants established that the maternal contribution to the phenotype severity exceeds the paternal contribution. Together, epigenetic rather than genetic mechanisms underlie the progressive developmental phenotype aggravation in the Arabidopsis CAF-1 mutants and preferred maternal transmission reveals a more efficient reprogramming of epigenetic information in the male than the female germline.

• MeSH
• alely MeSH
• Arabidopsis genetika   MeSH
• epigeneze genetická * MeSH
• fenotyp MeSH
• fyziologický stres genetika   MeSH
• genová ontologie MeSH
• metylace DNA genetika   MeSH
• mutace genetika   MeSH
• neplodnost rostlin MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• sekvence nukleotidů MeSH
• semena rostlinná embryologie   MeSH
• sestřihové faktory genetika   metabolismus   MeSH
• transkriptom genetika   MeSH
• typy dědičnosti genetika   MeSH
• vajíčko rostlin embryologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

To counter environmental cues, cultivated tomato (Solanum lycopersicum L.) has evolved adaptive mechanisms requiring regulation of downstream genes. The dehydration-responsive element-binding protein 2 (DREB2) transcription factors regulate abiotic stresses responses in plants. Herein, we isolated a novel DREB2-type regulator involved in salinity response, named SlDREB2. Spatio-temporal expression profile together with investigation of its promoter activity indicated that SlDREB2 is expressed during early stages of seedling establishment and in various vegetative and reproductive organs of adult plants. SlDREB2 is up-regulated in roots and young leaves following exposure to NaCl, but is also induced by KCl and drought. Its overexpression in WT Arabidopsis and atdreb2a mutants improved seed germination and plant growth in presence of different osmotica. In tomato, SlDREB2 affected vegetative and reproductive organs development and the intronic sequence present in the 5' UTR drives its expression. Physiological, biochemical and transcriptomic analyses showed that SlDREB2 enhanced plant tolerance to salinity by improvement of K(+) /Na(+) ratio, and proline and polyamines biosynthesis. Exogenous hormonal treatments (abscisic acid, auxin and cytokinins) and analysis of WT and 35S::SlDREB2 tomatoes hormonal contents highlighted SlDREB2 involvement in abscisic acid biosynthesis/signalling. Altogether, our results provide an overview of SlDREB2 mode of action during early salt stress response.

• MeSH
• Arabidopsis genetika   fyziologie   MeSH
• chlorid sodný farmakologie   MeSH
• dehydratace MeSH
• fyziologický stres MeSH
• geneticky modifikované rostliny MeSH
• kořeny rostlin genetika   fyziologie   MeSH
• kyselina abscisová farmakologie   MeSH
• molekulární sekvence - údaje MeSH
• mutace MeSH
• období sucha MeSH
• regulace genové exprese u rostlin * MeSH
• regulátory růstu rostlin farmakologie   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• semenáček genetika   fyziologie   MeSH
• Solanum lycopersicum genetika   fyziologie   MeSH
• stanovení celkové genové exprese MeSH
• tolerance k soli MeSH
• transkripční faktory genetika   metabolismus   MeSH
• transkriptom * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH