The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.

• MeSH
• Chenopodiaceae * metabolismus   genetika   účinky léků   MeSH
• chlorid sodný farmakologie   metabolismus   MeSH
• endoplazmatické retikulum metabolismus   MeSH
• proteomika MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• rostlinné proteiny * metabolismus   genetika   MeSH
• salinita MeSH
• solný stres MeSH
• tabák metabolismus   genetika   účinky léků   MeSH
• tolerance k soli * genetika   MeSH
• transkriptom MeSH
• vakuoly metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system leading to demyelination and axonal loss. Relapsing-remitting multiple sclerosis (RRMS) is commonly treated by anti-inflammatory drugs, where one of the most effective drugs to date is the monoclonal antibody natalizumab. METHODS: The cerebrospinal fluid (CSF) proteome was analyzed in 56 patients with RRMS before and after natalizumab treatment, using label-free mass spectrometry and a subset of the changed proteins were verified by parallel reaction monitoring in a new cohort of 20 patients, confirming the majority of observed changes. RESULTS: A total of 287 differentially abundant proteins were detected including (i) the decrease of proteins with roles in immunity, such as immunoglobulin heavy constant mu, chitinase-3-like protein 1 and chitotriosidase, (ii) an increase of proteins involved in metabolism, such as lactate dehydrogenase A and B and malate-dehydrogenase cytoplasmic, and (iii) an increase of proteins associated with the central nervous system, including lactadherin and amyloid precursor protein. Comparison with the CSF-PR database provided evidence that natalizumab counters protein changes commonly observed in RRMS. Furthermore, vitamin-D binding protein and apolipoprotein 1 and 2 were unchanged during treatment with natalizumab, implying that these may be involved in disease activity unaffected by natalizumab. CONCLUSIONS: Our study revealed that some of the previously suggested biomarkers for MS were affected by the natalizumab treatment while others were not. Proteins not previously suggested as biomarkers were also found affected by the treatment. In sum, the results provide new information on how the natalizumab treatment impacts the CSF proteome of MS patients, and points towards processes affected by the treatment. These findings ought to be explored further to disclose potential novel disease mechanisms and predict treatment responses.

• MeSH
• antiflogistika terapeutické užití   MeSH
• biologické markery metabolismus   MeSH
• imunologické faktory terapeutické užití   MeSH
• lidé MeSH
• natalizumab terapeutické užití   MeSH
• proteom MeSH
• relabující-remitující roztroušená skleróza * farmakoterapie   mozkomíšní mok   MeSH
• roztroušená skleróza * farmakoterapie   mozkomíšní mok   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antiflogistika MeSH
• biologické markery MeSH
• imunologické faktory MeSH
• natalizumab MeSH
• proteom MeSH

Mycoparasitism is a key feature of Trichoderma (Hypocreales, Ascomycota) biocontrol agents. Recent studies of intracellular signal transduction pathways of the potent mycoparasite Trichoderma atroviride revealed the involvement of Tmk1, a mitogen-activated protein kinase (MAPK), in triggering the mycoparasitic response. We previously showed that mutants missing Tmk1 exhibit reduced mycoparasitic activity against several plant pathogenic fungi. In this study, we identified the most robustly regulated targets that were governed by Tmk1 during mycoparasitism using transcriptome and proteome profiling. Tmk1 mainly exerts a stimulating function for T. atroviride during its mycoparasitic interaction with the fungal plant pathogen Rhizoctonia solani, as reflected by 89% of strongly differently responding genes in the ∆tmk1 mutant compared to the wild type. Specifically, 54% of these genes showed strong downregulation in the response with a deletion of the tmk1 gene, whereas in the wild type the same genes were strongly upregulated during the interaction with the fungal host. These included the gene encoding the mycoparasitism-related proteinase Prb1; genes involved in signal transduction pathways such as a candidate coding for a conserved 14-3-3 protein, and a gene coding for Tmk2, the T. atroviride cell-wall integrity MAP kinase; genes encoding a specific siderophore synthetase, and multiple FAD-dependent oxidoreductases and aminotransferases. Due to the phosphorylating activity of Tmk1, different (phospho-)proteomics approaches were applied and identified proteins associated with cellular metabolism, energy production, protein synthesis and fate, and cell organization. Members of FAD- and NAD/NADP-binding-domain proteins, vesicular trafficking of molecules between cellular organelles, fungal translational, as well as protein folding apparatus were among others found to be phosphorylated by Tmk1 during mycoparasitism. Outstanding downregulation in the response of the ∆tmk1 mutant to the fungal host compared to the wild type at both the transcriptome and the proteome levels was observed for nitrilase, indicating that its defense and detoxification functions might be greatly dependent on Tmk1 during T. atroviride mycoparasitism. An intersection network analysis between the identified transcripts and proteins revealed a strong involvement of Tmk1 in molecular functions with GTPase and oxidoreductase activity. These data suggest that during T. atroviride mycoparasitism this MAPK mainly governs processes regulating cell responses to extracellular signals and those involved in reactive oxygen stress.

• MeSH
• Hypocreales * metabolismus   MeSH
• mitogenem aktivované proteinkinasy genetika   metabolismus   MeSH
• proteom metabolismus   MeSH
• regulace genové exprese u hub MeSH
• signální transdukce MeSH
• Trichoderma * metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mitogenem aktivované proteinkinasy MeSH
• proteom MeSH

BACKGROUND: Structural Maintenance of Chromosomes (SMC) complexes are molecular machines driving chromatin organization at higher levels. In eukaryotes, three SMC complexes (cohesin, condensin and SMC5/6) play key roles in cohesion, condensation, replication, transcription and DNA repair. Their physical binding to DNA requires accessible chromatin. RESULTS: We performed a genetic screen in fission yeast to identify novel factors required for SMC5/6 binding to DNA. We identified 79 genes of which histone acetyltransferases (HATs) were the most represented. Genetic and phenotypic analyses suggested a particularly strong functional relationship between the SMC5/6 and SAGA complexes. Furthermore, several SMC5/6 subunits physically interacted with SAGA HAT module components Gcn5 and Ada2. As Gcn5-dependent acetylation facilitates the accessibility of chromatin to DNA-repair proteins, we first analysed the formation of DNA-damage-induced SMC5/6 foci in the Δgcn5 mutant. The SMC5/6 foci formed normally in Δgcn5, suggesting SAGA-independent SMC5/6 localization to DNA-damaged sites. Next, we used Nse4-FLAG chromatin-immunoprecipitation (ChIP-seq) analysis in unchallenged cells to assess SMC5/6 distribution. A significant portion of SMC5/6 accumulated within gene regions in wild-type cells, which was reduced in Δgcn5 and Δada2 mutants. The drop in SMC5/6 levels was also observed in gcn5-E191Q acetyltransferase-dead mutant. CONCLUSION: Our data show genetic and physical interactions between SMC5/6 and SAGA complexes. The ChIP-seq analysis suggests that SAGA HAT module targets SMC5/6 to specific gene regions and facilitates their accessibility for SMC5/6 loading.

• Klíčová slova
• Ada2, Chromatin accessibility, DNA repair, Gcn5, Gene regions, Genetic and protein–protein interactions, Histone H3K9ac acetylation, Nse3 KITE, SAGA histone acetyltransferase module, SMC5/6 complex targeting, rDNA,
• MeSH
• acetyltransferasy genetika   MeSH
• buněčné jádro metabolismus   MeSH
• chromatin metabolismus   MeSH
• chromozomy metabolismus   MeSH
• DNA metabolismus   MeSH
• histonacetyltransferasy genetika   metabolismus   MeSH
• proteiny buněčného cyklu genetika   metabolismus   MeSH
• Schizosaccharomyces pombe - proteiny * genetika   metabolismus   MeSH
• Schizosaccharomyces * genetika   metabolismus   MeSH
• transportní proteiny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• acetyltransferasy MeSH
• chromatin MeSH
• DNA MeSH
• Gcn5 protein, S pombe MeSH Prohlížeč
• histonacetyltransferasy MeSH
• Nse4 protein, S pombe MeSH Prohlížeč
• proteiny buněčného cyklu MeSH
• Schizosaccharomyces pombe - proteiny * MeSH
• Smc5 protein, S pombe MeSH Prohlížeč
• smc6 protein, S pombe MeSH Prohlížeč
• transportní proteiny MeSH

Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.

• Klíčová slova
• differentially expressed gene, gene duplication, nodule-specific cysteine-rich peptide, transcriptome,
• Publikační typ
• časopisecké články MeSH

Male infertility is a global public health concern. Teratozoospermia is a qualitative anomaly of spermatozoa morphology, contributing significantly to male infertility, whereas azoospermia is the complete absence of spermatozoa in the ejaculate. Thus, there is a serious need for unveiling the common origin and/or connection between both of these diseases, if any. This study aims to identify common potential biomarker genes of these two diseases via an in silico approach using a meta-analysis of microarray data. In this study, a differential expression analysis of genes was performed on four publicly available RNA microarray datasets, two each from teratozoospermia (GSE6872 and GSE6967) and azoospermia (GSE145467 and GSE25518). From the analysis, 118 DEGs were found to be common to teratozoospermia and azoospermia, and, interestingly, sperm autoantigenic protein 17 (SPA17) was found to possess the highest fold change value among all the DEGs (9.471), while coiled-coil domain-containing 90B (CCDC90B) and coiled-coil domain-containing 91 (CCDC91) genes were found to be common among three of analyses, i.e., Network Analyst, ExAtlas, and GEO2R. This observation indicates that SPA17, CCDC90B, and CCDC91 genes might have significant roles to play as potential biomarkers for teratozoospermia and azoospermia. Thus, our study opens a new window of research in this area and can provide an important theoretical basis for the diagnosis and treatment of both these diseases.

• Klíčová slova
• CCDC90B, CCDC91, SPA17, azoospermia, biomarker genes, male infertility, teratozoospermia,
• MeSH
• azoospermie * diagnóza   genetika   MeSH
• biologické markery MeSH
• lidé MeSH
• mužská infertilita * genetika   MeSH
• RNA MeSH
• sperma metabolismus   MeSH
• teratozoospermie * genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• metaanalýza MeSH
• Názvy látek
• biologické markery MeSH
• RNA MeSH

In de novo purine biosynthesis (DNPS), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (EC 2.1.2.3)/inosine monophosphate cyclohydrolase (EC 3.5.4.10) (ATIC) catalyzes the last two reactions of the pathway: conversion of 5-aminoimidazole-4-carboxamide ribonucleotide [aka Z-nucleotide monophosphate (ZMP)] to 5-formamido-4-imidazolecarboxamide ribonucleotide (FAICAR) then to inosine monophosphate (IMP). Mutations in ATIC cause an untreatable and devastating inborn error of metabolism in humans. ZMP is an adenosine monophosphate (AMP) mimetic and a known activator of AMP-activated protein kinase (AMPK). Recently, a HeLa cell line null mutant for ATIC was constructed via CRISPR-Cas9 mutagenesis. This mutant, crATIC, accumulates ZMP during purine starvation. Given that the mutant can accumulate ZMP in the absence of treatment with exogenous compounds, crATIC is likely an important cellular model of DNPS inactivation and ZMP accumulation. In the current study, we characterize the crATIC transcriptome versus the HeLa transcriptome in purine-supplemented and purine-depleted growth conditions. We report and discuss transcriptome changes with particular relevance to Alzheimer's disease and in genes relevant to lipid and fatty acid synthesis, neurodevelopment, embryogenesis, cell cycle maintenance and progression, extracellular matrix, immune function, TGFβ and other cellular processes.

• Klíčová slova
• 5-aminoimidazole-4-carboxamide ribonucleoside, (AICAr), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase, (ATIC), 5-aminoimidazole-4-carboxamide ribonucleotide, (ZMP), 5-formamido-4-imidazolecarboxamide ribonucleotide, (FAICAR), AICA-ribosiduria, AMP-activated protein kinase, (AMPK), Alzheimer's disease, Development, Purine synthesis, RNA-seq, Tuberous Sclerosis Complex 1 and 2, (TSC1 and TSC2), adenine phosphoribosyltransferase, (APRT), adenosine monophosphate, (AMP), adenosine triphosphate, (ATP), adenylosuccinate lyase, (ADSL), arachidonic acid, (AA), cyclooxygenase, (COX), cytochrome, P450 (CYP), cytosolic phospholipase A2, (cPLA2), de novo purine synthesis, (DNPS), differentially expressed gene, (DEG), false discovery rate, (FDR), fatty acid amide hydrolase, (FAAH), fetal calf macroserum, (FCM), fetal calf serum, (FCS), fragments per kilobase of exon per million reads mapped, (FPKM), gene ontology, (GO), guanosine monophosphate, (GMP), inosine monophosphate, (IMP), interferon, (INF), lipoxygenase, (LOX), mammalian Target of Rapamycin, (mTOR), minus adenine crATIC to minus adenine WT comparison, (MM), phospholipase, (PLA), phosphoribosyl pyrophosphate, (PRPP), phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase, (PAICS), plus adenine crATIC to plus adenine WT comparison, (PP), xanthine monophosphate, (XMP),
• Publikační typ
• časopisecké články MeSH

The plant cell wall plays an important role in damage-associated molecular pattern-induced resistance to pathogens and herbivorous insects. Our current understanding of cell wall-mediated resistance is largely based on the degree of pectin methylesterification. However, little is known about the role of pectin acetylesterification in plant immunity. This study describes how one pectin-modifying enzyme, PECTIN ACETYLESTERASE 9 (PAE9), affects the Arabidopsis (Arabidopsis thaliana) transcriptome, secondary metabolome, and aphid performance. Electro-penetration graphs showed that Myzus persicae aphids established phloem feeding earlier on pae9 mutants. Whole-genome transcriptome analysis revealed a set of 56 differentially expressed genes (DEGs) between uninfested pae9-2 mutants and wild-type plants. The majority of the DEGs were enriched for biotic stress responses and down-regulated in the pae9-2 mutant, including PAD3 and IGMT2, involved in camalexin and indole glucosinolate biosynthesis, respectively. Relative quantification of more than 100 secondary metabolites revealed decreased levels of several compounds, including camalexin and oxylipins, in two independent pae9 mutants. In addition, absolute quantification of phytohormones showed that jasmonic acid (JA), jasmonoyl-Ile, salicylic acid, abscisic acid, and indole-3-acetic acid were compromised due to PAE9 loss of function. After aphid infestation, however, pae9 mutants increased their levels of camalexin, glucosinolates, and JA, and no long-term effects were observed on aphid fitness. Overall, these data show that PAE9 is required for constitutive up-regulation of defense-related compounds, but that it is not required for aphid-induced defenses. The signatures of phenolic antioxidants, phytoprostanes, and oxidative stress-related transcripts indicate that the processes underlying PAE9 activity involve oxidation-reduction reactions.

• MeSH
• acetylesterasa metabolismus   MeSH
• Arabidopsis genetika   metabolismus   parazitologie   MeSH
• býložravci fyziologie   MeSH
• down regulace genetika   MeSH
• genové regulační sítě MeSH
• glukosinoláty metabolismus   MeSH
• indoly metabolismus   MeSH
• metabolom genetika   MeSH
• mšice fyziologie   MeSH
• mutace genetika   MeSH
• oxidační stres MeSH
• oxylipiny metabolismus   MeSH
• proteiny huseníčku metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• regulační geny MeSH
• regulátory růstu rostlin metabolismus   MeSH
• sekundární metabolismus MeSH
• thiazoly metabolismus   MeSH
• transkripční faktory metabolismus   MeSH
• transkriptom genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• acetylesterasa MeSH
• camalexin MeSH Prohlížeč
• glukosinoláty MeSH
• indoly MeSH
• oxylipiny MeSH
• PAE9 protein, Arabidopsis MeSH Prohlížeč
• proteiny huseníčku MeSH
• regulátory růstu rostlin MeSH
• thiazoly MeSH
• transkripční faktory MeSH

Adenylosuccinate lyase (ADSL) catalyzes two steps in de novo purine synthesis (DNPS). Mutations in ADSL can result in inborn errors of metabolism characterized by developmental delay and disorder phenotypes, with no effective treatment options. Recently, SAICAR, a metabolic substrate of ADSL, has been found to have alternative roles in the cell, complicating the role of ADSL. crADSL, a CRISPR KO of ADSL in HeLa cells, was constructed to investigate DNPS and ADSL in a human cell line. Here we employ this cell line in an RNA-seq analysis to initially investigate the effect of DNPS and ADSL deficiency on the transcriptome as a first step in establishing a cellular model of ADSL deficiency. We report transcriptome changes in genes relevant to development, vascular development, muscle, and cancer biology, which provide interesting avenues for future research.

• Klíčová slova
• Adenylosuccinate lyase, Purine synthesis, RNA-seq, Transcriptome, adenosine monophosphate, (AMP), adenylosuccinate lyase, (ADSL), aminoimidazole carboxamide ribonucleotide, (AICAR), de novo purine synthesis, (DNPS), differentially expressed gene, (DEG), false discovery rate, (FDR), fetal calf macroserum, (FCM), fragments per kilobase of exon per million reads mapped, (FPKM), gene ontology, (GO), guanosine monophosphate, (GMP), minus adenine crADSL to minus adenine WT comparison, (MM), phosphoribosyl pyrophosphate, (PRPP), phosphoribosylaminoimidazolesuccinocarboxamide, (SAICAR), plus adenine crADSL to plus adenine WT comparison, (PP), succinyladenosine monophosphate, (SAMP),
• Publikační typ
• časopisecké články MeSH

The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 ortholog in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to control flowering through the vernalization pathway via enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the ortholog of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2, we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here, we demonstrate that PEP2 activity prevents the up-regulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY), and APETALA1 (AaAP1), ensuring floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in axillary branches. These multiple roles of PEP2 in the vernalization response contribute to the A. alpina life cycle.

• MeSH
• Arabis genetika   růst a vývoj   metabolismus   MeSH
• květy genetika   růst a vývoj   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• stonky rostlin genetika   růst a vývoj   MeSH
• transkripční faktory genetika   metabolismus   MeSH
• transkriptom * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• rostlinné proteiny MeSH
• transkripční faktory MeSH