Transcriptomic response
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Exposition to pharmaceutical compounds released to the environment is considered as a potential risk for various organisms. We exposed Arabidopsis thaliana plants to naproxen (NAP) and praziquantel (PZQ) in 5 µM concentration for 2 days and recorded transcriptomic response in their roots with the aim to estimate ecotoxicity and to identify gene candidates potentially involved in metabolism of both compounds. Nonsteroidal anti-inflammatory drug NAP up-regulated 105 and down-regulated 29 genes (p-value ≤ 0.1, fold change ≥ 2), while anthelmintic PZQ up-regulated 389 and down-regulated 353 genes with more rigorous p-value ≤ 0.001 (fold change ≥ 2). High number of up-regulated genes coding for heat shock proteins and other genes involved in response to biotic and abiotic stresses as well as down-regulation of genes involved in processes such as cell proliferation, transcription and water transport indicates serious negative effect of PZQ. NAP up-regulated mostly genes involved in various biological processes and signal transduction and down-regulated mainly genes involved in signal transduction and electron transport or energy pathways. Further, two cytochrome P450s (demethylation) and one methyltransferase (methylation of carboxyl group) were identified as candidates for phase I and several glutathione- and glycosyltransferases (conjugation) for phase II of NAP metabolism. Cytochrome P450s, glutathione and glycosyltransferases seem to play role also in metabolism of PZQ. Up-regulation of several ABC and MATE transporters by NAP and PZQ indicated their role in transport of both compounds.
- MeSH
- anthelmintika farmakologie MeSH
- antiflogistika nesteroidní farmakologie MeSH
- Arabidopsis účinky léků metabolismus MeSH
- biologický transport účinky léků MeSH
- down regulace MeSH
- glutathion metabolismus MeSH
- glykosyltransferasy metabolismus MeSH
- kořeny rostlin metabolismus MeSH
- methyltransferasy metabolismus MeSH
- naproxen farmakologie MeSH
- praziquantel farmakologie MeSH
- proliferace buněk účinky léků MeSH
- proteiny teplotního šoku metabolismus MeSH
- regulace genové exprese u rostlin účinky léků MeSH
- signální transdukce účinky léků MeSH
- stanovení celkové genové exprese MeSH
- transkriptom účinky léků MeSH
- transport elektronů účinky léků MeSH
- upregulace MeSH
- Publikační typ
- časopisecké články MeSH
Surface waters in urban areas are contaminated by ibuprofen (IBP), a popular and extensively used anti-inflammatory drug. In this study, we investigated the transcriptomic response in Arabidopsis thaliana (L.) Heynh. roots with the aim of revealing genes that are potentially involved in IBP detoxification and elucidating the effect of IBP on plants. IBP upregulated 63 and downregulated 38 transcripts (p-value < 0.1, fold change ≥2) after 2-day exposure to a 5-µM (1.03 mg/L) concentration of IBP under hydroponic conditions. Although the IBP concentration used in the experiment was highly relative to the concentrations found in rivers and wastewater, the number of genes with transcriptional changes was relatively low. The upregulation of cytochrome P450s, glutathione S-transferases, and UDP-glycosyltransferases indicates the occurrence of IBP oxidation in the first phase, followed by conjugation with glutathione and sugar in the second detoxification phase. ABC transporters could be involved in the transport of IBP and its metabolites. The identification of genes potentially involved in IBP detoxification could be useful in an IBP phytoremediation approach.
Heavy metal pollution is an increasing global concern. Among heavy metals, mercury (Hg) is especially dangerous because of its massive release into the environment and high toxicity, especially for aquatic organisms. The molecular response mechanisms of algae to Hg exposure are mostly unknown. Here, we combine physiological, biochemical, and transcriptomic analysis to provide, for the first time, a comprehensive view on the pathways activated in Chromera velia in response to toxic levels of Hg. Production of hydrogen peroxide and superoxide anion, two reactive oxygen species (ROS), showed opposite patterns in response to Hg2+ while reactive nitrogen species (RNS) levels did not change. A deep RNA sequencing analysis generated a total of 307,738,790 high-quality reads assembled in 122,874 transcripts, representing 89,853 unigenes successfully annotated in databases. Detailed analysis of the differently expressed genes corroborates the biochemical results observed in ROS production and suggests novel putative molecular mechanisms in the algal response to Hg2+. Moreover, we indicated that important transcription factor (TF) families associated with stress responses differentially expressed in C. velia cultures under Hg stress. Our study presents the first in-depth transcriptomic analysis of C. velia, focusing on the expression of genes involved in different detoxification defense systems in response to heavy metal stress.
- MeSH
- Alveolata účinky léků genetika růst a vývoj metabolismus MeSH
- chemické látky znečišťující vodu toxicita MeSH
- chlorofyl metabolismus MeSH
- peroxid vodíku metabolismus MeSH
- reaktivní formy dusíku metabolismus MeSH
- reaktivní formy kyslíku metabolismus MeSH
- rtuť toxicita MeSH
- transkriptom účinky léků MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
This paper aims to identify and describe new genetic markers involved in the processes of protein expression and modification reflected in the change of mitochondrial activity before and after in vitro maturation of the oocyte. Porcine oocytes collected from the ovaries of slaughtered landrace gilts were subjected to the process of in vitro maturation. Transcriptomic changes in the expression profile of oocyte genes involved in response to hypoxia, the transmembrane protein receptor serine threonine kinase signaling pathway, the "transforming growth factor β receptor signaling pathway", "response to protein stimulus", and "response to organic substance" were investigated using microarrays. The expression values of these genes in oocytes was analyzed before (immature) and after (mature) in vitro maturation, with significant differences found. All the significantly altered genes showed downregulation after the maturation process. The most changed genes from these gene ontologies, FOS, ID2, VEGFA, BTG2, CYR61, ESR1, AR, TACR3, CCND2, CHRDL1, were chosen to be further validated, described and related to the literature. Additionally, the mitochondrial activity of the analyzed oocytes was measured using specific dyes. We found that the mitochondrial activity was higher before the maturation process. The analysis of these results and the available literature provides a novel insight on the processes that occur during in vitro oocyte maturation. While this knowledge may prove to be useful in further research of the procedures commonly associated with in vitro fertilization procedures, it serves mostly as a basic reference for further proteomic, in vivo, and clinical studies that are necessary to translate it into practical applications.
- MeSH
- hypoxie buňky genetika MeSH
- IVM techniky MeSH
- kultivované buňky MeSH
- mitochondrie genetika metabolismus MeSH
- oocyty cytologie metabolismus MeSH
- oogeneze genetika MeSH
- prasata MeSH
- signální transdukce MeSH
- transformující růstový faktor beta metabolismus MeSH
- transkriptom * MeSH
- tyrosinkinasové receptory metabolismus MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- Clostridium beijerinckii cytologie genetika MeSH
- fermentace genetika MeSH
- fyziologický stres * genetika MeSH
- glukosa metabolismus MeSH
- kyseliny metabolismus MeSH
- mastné kyseliny metabolismus MeSH
- proteiny teplotního šoku genetika metabolismus MeSH
- regulace genové exprese u bakterií * MeSH
- rozpouštědla metabolismus MeSH
- spory bakteriální metabolismus MeSH
- transkriptom genetika MeSH
- vodík metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The impact of nanosize was evaluated by comparing of the transcriptomic response of Arabidopsis thaliana roots to ZnO nanoparticles (nZnO), bulk ZnO, and ionic Zn(2+). Microarray analyses revealed 416 up- and 961 down-regulated transcripts (expression difference >2-fold, p [FDR] < 0.01) after a seven-day treatment with nZnO (average particle size 20 nm, concentration 4 mg L(-1)). Exposure to bulk ZnO resulted in 816 up- and 2179 down-regulated transcripts. The most dramatic changes (1711 transcripts up- and 3242 down-regulated) were caused by the presence of ionic Zn(2+) (applied as ZnSO4.7H20 at a concentration of 14.14 mg L(-1), corresponding to the amount of Zn contained in 4 mg L(-1) ZnO). Genes involved in stress response (e.g., to salt, osmotic stress or water deprivation) were the most relatively abundant group of gene transcripts up-regulated by all three Zn treatments while genes involved in cell organization and biogenesis (e.g., tubulins, arabinogalactan proteins) and DNA or RNA metabolism (e.g., histones) were the most relatively abundant groups of down-regulated transcripts. The similarity of the transcription profiles and the increasing number of changed transcripts correlating with the increased concentration of Zn(2+) in cultivation medium indicated that released Zn(2+) may substantially contribute to the toxic effect of nZnO because particle size has not demonstrated a decisive role.
- MeSH
- Arabidopsis účinky léků genetika MeSH
- kationty dvojmocné MeSH
- kořeny rostlin účinky léků genetika MeSH
- nanočástice chemie toxicita MeSH
- oxid zinečnatý chemie farmakologie toxicita MeSH
- síran zinečnatý chemie toxicita MeSH
- stanovení celkové genové exprese metody MeSH
- testy toxicity MeSH
- velikost částic MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
Kayviruses are polyvalent broad host range staphylococcal phages with a potential to combat staphylococcal infections. However, the implementation of rational phage therapy in medicine requires a thorough understanding of the interactions between bacteriophages and pathogens at omics level. To evaluate the effect of a phage used in therapy on its host bacterium, we performed differential transcriptomic analysis by RNA-Seq from bacteriophage K of genus Kayvirus infecting two Staphylococcus aureus strains, prophage-less strain SH1000 and quadruple lysogenic strain Newman. The temporal transcriptional profile of phage K was comparable in both strains except for a few loci encoding hypothetical proteins. Stranded sequencing revealed transcription of phage noncoding RNAs that may play a role in the regulation of phage and host gene expression. The transcriptional response of S. aureus to phage K infection resembles a general stress response with differential expression of genes involved in a DNA damage response. The host transcriptional changes involved upregulation of nucleotide, amino acid and energy synthesis and transporter genes and downregulation of host transcription factors. The interaction of phage K with variable genetic elements of the host showed slight upregulation of gene expression of prophage integrases and antirepressors. The virulence genes involved in adhesion and immune evasion were only marginally affected, making phage K suitable for therapy. IMPORTANCE Bacterium Staphylococcus aureus is a common human and veterinary pathogen that causes mild to life-threatening infections. As strains of S. aureus are becoming increasingly resistant to multiple antibiotics, the need to search for new therapeutics is urgent. A promising alternative to antibiotic treatment of staphylococcal infections is a phage therapy using lytic phages from the genus Kayvirus. Here, we present a comprehensive view on the phage-bacterium interactions on transcriptomic level that improves the knowledge of molecular mechanisms underlying the Kayvirus lytic action. The results will ensure safer usage of the phage therapeutics and may also serve as a basis for the development of new antibacterial strategies.
Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host's hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for managing blood meals (storage and digestion) and protecting against host immunity and pathogen infections. Previous transcriptomic studies revealed the complexity of tick sialomes (salivary gland transcriptomes) and mialomes (midgut transcriptomes) which encode for protease inhibitors, lipocalins (histamine-binding proteins), disintegrins, enzymes, and several other tick-specific proteins. Several studies have demonstrated that mammalian hosts acquire tick resistance against repeated tick bites. Consequently, there is an urgent need to uncover how tick sialomes and mialomes respond to resistant hosts, as they may serve to develop novel tick control strategies and applications. Here, we mimicked natural repeated tick bites in a laboratory setting and analyzed gene expression dynamics in the salivary glands and midguts of adult female ticks. Rabbits were subjected to a primary (feeding on a naive host) and a secondary infestation of the same host (we re-exposed the hosts but to other ticks). We used single salivary glands and midguts dissected from individual siblings adult pathogen-free female Ixodes ricinus to reduce genetic variability between individual ticks. The comprehensive analysis of 88 obtained RNA-seq data sets allows us to provide high-quality annotated sialomes and mialomes from individual ticks. Comparisons between fed/unfed, timepoints, and exposures yielded as many as 3000 putative differentially expressed genes (DEG). Interestingly, when classifying the exposure DEGs by means of a clustering approach we observed that the majority of these genes show increased expression at early feeding time-points in the mid-gut of re-exposed ticks. The existence of clearly defined groups of genes with highly similar responses to re-exposure suggests the existence of molecular swiches. In silico functional analysis shows that these early feeding reexposure response genes form a dense interaction network at protein level being related to virtually all aspects of gene expression regulation and glycosylation. The processed data is available through an easy-to-use database-associated webpage (https://arn.ugr.es/IxoriDB/) that can serve as a valuable resource for tick research.
- MeSH
- klíště * genetika MeSH
- kousnutí klíštětem * MeSH
- králíci MeSH
- obratlovci MeSH
- proteiny členovců genetika metabolismus MeSH
- savci genetika MeSH
- slinné žlázy metabolismus MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- králíci MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
As sessile organisms, plants must sense environmental conditions and adjust their growth and development processes accordingly, through adaptive responses regulated by various internal factors, including hormones. A key environmental factor is temperature, but temperature-sensing mechanisms are not fully understood despite intense research. We investigated proteomic responses to temperature shocks (15 min cold or heat treatments) with and without exogenous applications of cytokinin in Arabidopsis. Image and mass spectrometric analysis of the two-dimensionally separated proteins detected 139 differentially regulated spots, in which 148 proteins were identified, most of which have not been previously linked to temperature perception. More than 70% of the temperature-shock response proteins were modulated by cytokinin, mostly in a similar manner as heat shock. Data mining of previous transcriptomic datasets supported extensive interactions between temperature and cytokinin signalling. The biological significance of this finding was tested by assaying an independent growth response of Arabidopsis seedlings to heat stress: hypocotyl elongation. This response was strongly inhibited in mutants with deficiencies in cytokinin signalling or endogenous cytokinin levels. Thus, cytokinins may directly participate in heat signalling in plants. Finally, large proportions of both temperature-shock and cytokinin responsive proteomes co-localize to the chloroplast, which might therefore host a substantial proportion of the temperature response machinery.
- MeSH
- Arabidopsis genetika růst a vývoj MeSH
- biologické modely MeSH
- cytokininy farmakologie MeSH
- fosforylace účinky léků MeSH
- geneticky modifikované rostliny MeSH
- hypokotyl účinky léků genetika růst a vývoj MeSH
- metabolismus sacharidů účinky léků genetika MeSH
- mutace MeSH
- proteiny huseníčku klasifikace genetika metabolismus MeSH
- proteom metabolismus MeSH
- reakce na tepelný šok genetika MeSH
- rostlinné geny MeSH
- teplota * MeSH
- transkriptom účinky léků genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Engineered nanoparticles (ENPs) exhibit unique properties advantageous in a number of applications, but they also represent potential health and environmental risks. In this study, we investigated the phytotoxic mechanism of CuO ENPs using transcriptomic analysis and compared this response with the response to CuO bulk particles and ionic Cu2+. Ionic Cu2+at the concentration of 0.16 mg L-1changed transcription of 2692 genes (p value of <0.001, fold change of ≥2) after 7 days of exposure, whereas CuO ENPs and bulk particles (both in the concentration of 10 mg L-1) altered the expression of 922 and 482 genes in Arabidopsis thaliana roots, respectively. The similarity between transcription profiles of plants exposed to ENPs and ionic Cu2+indicated that the main factor in phytotoxicity was the release of Cu2+ions from CuO ENPs after 7 days of exposure. The effect of Cu2+ions was evident in all treatments, as indicated by the down-regulation of genes involved in metal homeostasis and transport and the up-regulation of oxidative stress response genes. ENPs were more soluble than bulk particles, resulting in the up-regulation of metallochaperone-like genes or the down-regulation of aquaporins and metal transmembrane transporters that was also characteristic for ionic Cu2+exposure.
