scholarly journals Global Regulation of the Response to Sulfur Availability in the Cheese-Related BacteriumBrevibacterium aurantiacum

2010 ◽  
Vol 77 (4) ◽  
pp. 1449-1459 ◽  
Author(s):  
Marie-Pierre Forquin ◽  
Agnès Hébert ◽  
Aurélie Roux ◽  
Julie Aubert ◽  
Caroline Proux ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Metabolic Reconstruction ◽  
Sulfate Assimilation ◽  
Sulfur Starvation ◽  
Expression Of Genes ◽  
Transsulfuration Pathway ◽  
Sulfate Assimilation Pathway ◽  
Genes Encoding ◽  
Sulfur Containing

ABSTRACTIn this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability inBrevibacterium aurantiacum. In agreement with the growth ofB. aurantiacumin the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysEandcysK) or homocysteine (metXandmetY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles ofB. aurantiacumATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression ofmetX,metY,metE1,metE2, andBL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.

scholarly journals Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13

2020 ◽  
Vol 8 (6) ◽  
pp. 888
Author(s):  
Justas Vaitekūnas ◽  
Renata Gasparavičiūtė ◽  
Jonita Stankevičiūtė ◽  
Gintaras Urbelis ◽  
Rolandas Meškys
Keyword(s):  
Recombinant Expression ◽  
Expression Profiles ◽  
Peptide Mass Fingerprinting ◽  
Sole Source ◽  
Open Reading Frames ◽  
Expression Of Genes ◽  
Peptide Mass ◽  
Genes Encoding ◽  
Protein Expression Profiles ◽  
Reading Frames

N-Heterocyclic compounds are widely spread in the biosphere, being constituents of alkaloids, cofactors, allelochemicals, and artificial substances. However, the fate of such compounds including a catabolism of hydroxylated pyridines is not yet fully understood. Arthrobacter sp. IN13 is capable of using 4-hydroxypyridine as a sole source of carbon and energy. Three substrate-inducible proteins were detected by comparing protein expression profiles, and peptide mass fingerprinting was performed using MS/MS. After partial sequencing of the genome, we were able to locate genes encoding 4-hydroxypyridine-inducible proteins and identify the kpi gene cluster consisting of 16 open reading frames. The recombinant expression of genes from this locus in Escherichia coli and Rhodococcus erytropolis SQ1 allowed an elucidation of the biochemical functions of the proteins. We report that in Arthrobacter sp. IN13, the initial hydroxylation of 4-hydroxypyridine is catalyzed by a flavin-dependent monooxygenase (KpiA). A product of the monooxygenase reaction is identified as 3,4-dihydroxypyridine, and a subsequent oxidative opening of the ring is performed by a hypothetical amidohydrolase (KpiC). The 3-(N-formyl)-formiminopyruvate formed in this reaction is further converted by KpiB hydrolase to 3-formylpyruvate. Thus, the degradation of 4-hydroxypyridine in Arthrobacter sp. IN13 was analyzed at genetic and biochemical levels, elucidating this catabolic pathway.

scholarly journals The Recovery from Sulfur Starvation is Independent from the mRNA Degradation Initiation Enzyme PARN in Arabidopsis

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 380 ◽  
Author(s):  
Armbruster ◽  
Uslu ◽  
Wirtz ◽  
Hell
Keyword(s):  
Stress Responses ◽  
Splice Variants ◽  
Marker Genes ◽  
Sulfate Assimilation ◽  
Sulfur Deficiency ◽  
Protective Measures ◽  
Sulfur Starvation ◽  
Sulfate Assimilation Pathway ◽  
Growth Promoting

When plants are exposed to sulfur limitation, they upregulate the sulfate assimilation pathway at the expense of growth-promoting measures. Upon cessation of the stress, however, protective measures are deactivated, and growth is restored. In accordance with these findings, transcripts of sulfur-deficiency marker genes are rapidly degraded when starved plants are resupplied with sulfur. Yet it remains unclear which enzymes are responsible for the degradation of transcripts during the recovery from starvation. In eukaryotes, mRNA decay is often initiated by the cleavage of poly(A) tails via deadenylases. As mutations in the poly(A) ribonuclease PARN have been linked to altered abiotic stress responses in Arabidopsis thaliana, we investigated the role of PARN in the recovery from sulfur starvation. Despite the presence of putative PARN-recruiting AU-rich elements in sulfur-responsive transcripts, sulfur-depleted PARN hypomorphic mutants were able to reset their transcriptome to pre-starvation conditions just as readily as wildtype plants. Currently, the subcellular localization of PARN is disputed, with studies reporting both nuclear and cytosolic localization. We detected PARN in cytoplasmic speckles and reconciled the diverging views in literature by identifying two PARN splice variants whose predicted localization is in agreement with those observations.

scholarly journals Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12424
Author(s):  
Alexandra Cucaita ◽  
Marianne Piochon ◽  
Richard Villemur
Keyword(s):  
Expression Profiles ◽  
Lag Phase ◽  
Rna Seq ◽  
Expression Of Genes ◽  
N Assimilation ◽  
Genes Encoding ◽  
Potential Synergy ◽  
Pure Cultures

Background Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized-bed marine denitrification system. Strain NL23 possesses the complete denitrification pathway, but cannot grow under marine conditions in pure cultures. Strain JAM1 is a marine bacterium that lacks genes encoding a dissimilatory nitrite (NO2−) reductase and therefore cannot reduce NO2−. Here, we report the characterization of some of their physiological traits that could influence their co-habitation. We also perform co-cultures to assess the potential synergy between the two strains under marine and denitrifying conditions. Methodology Anoxic planktonic pure cultures of both strains were grown with different concentrations of nitrate (NO3−). Anoxic planktonic co-cultures could only be cultured on low NaCl concentrations for strain NL23 to grow. Biofilm co-cultures were achieved in a 500-mL bioreactor, and operated under denitrifying conditions with increasing concentrations of NaCl. NO3− and NO2− concentrations and the protein content were measured to derive the denitrification rates. The concentrations of both strains in co-cultures were determined by quantitative PCR (qPCR). Ectoine concentration was measured by mass spectrometry in the biofilm co-culture. The biofilm was visualized by fluorescence in situ hybridization. Reverse-transcription-qPCR and RNA-seq approaches were used to assess changes in the expression profiles of genes involved in the nitrogen pathways in the biofilm cultures. Results Planktonic pure cultures of strain JAM1 had a readiness to reduce NO3− with no lag phase for growth in contrast to pure cultures of strain NL23, which had a 2-3 days lag phase before NO3− starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher µmax for growth and higher specific NO3− reduction rates. Denitrification rates were twice higher in the planktonic co-cultures than those measured in strain NL23 pure cultures. The biofilm co-cultures showed sustained denitrifying activities and surface colonization by both strains under marine conditions. Increase in ectoine concentrations was observed in the biofilm co-culture with the increase of NaCl concentrations. Changes in the relative transcript levels were observed in the biofilm culture with genes encoding NapA and NapGH in strain NL23. The type of medium had a great impact on the expression of genes involved in the N-assimilation pathways in both strains. Conclusions These results illustrate the capacity of both strains to act together in performing sustainable denitrifying activities under marine conditions. Although strain JAM1 did not contribute in better specific denitrifying activities in the biofilm co-cultures, its presence helped strain NL23 to acclimate to medium with NaCl concentrations >1.0%.

scholarly journals Sky1 regulates the expression of sulfur metabolism genes in response to cisplatin

Microbiology ◽  
2014 ◽  
Vol 160 (7) ◽  
pp. 1357-1368 ◽  
Author(s):  
Silvia Rodríguez-Lombardero ◽  
Ángel Vizoso-Vázquez ◽  
Luis J. Lombardía ◽  
Manuel Becerra ◽  
M. Isabel González-Siso ◽  
...  
Keyword(s):  
Amino Acids ◽  
Cellular Response ◽  
Dna Microarrays ◽  
Sulfur Metabolism ◽  
Yeast Cells ◽  
Genes Encoding ◽  
Cisplatin Sensitivity ◽  
Transcriptional Changes ◽  
Upregulated Genes ◽  
Sulfur Containing

Cisplatin is commonly used in cancer therapy and yeast cells are also sensitive to this compound. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin treatment, which are dependent on or independent of SKY1 function – a gene whose deletion increases resistance to the drug. Gene expression changes produced by addition of cisplatin to W303 and W303-Δsky1 cells were recorded using DNA microarrays. The data, validated by quantitative PCR, revealed 122 differentially expressed genes: 69 upregulated and 53 downregulated. Among the upregulated genes, those related to sulfur metabolism were over-represented and partially dependent on Sky1. Deletions of MET4 or other genes encoding co-regulators of the expression of sulfur-metabolism-related genes, with the exception of MET28, did not modify the cisplatin sensitivity of yeast cells. One of the genes with the highest cisplatin-induced upregulation was SEO1, encoding a putative permease of sulfur compounds. We also measured the platinum, sulfur and glutathione content in W303, W303-Δsky1 and W303-Δseo1 cells after cisplatin treatment, and integration of the data suggested that these transcriptional changes might represent a cellular response that allowed chelation of cisplatin with sulfur-containing amino acids and also helped DNA repair by stimulating purine biosynthesis. The transcription pattern of stimulation of sulfur-containing amino acids and purine synthesis decreased, or even disappeared, in the W303-Δsky1 strain.

scholarly journals A network of olfactory receptors is differentially expressed in CD24+ CD73+ Vγ2+ γδ-T cells

2019 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
T Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Γδ T Cells ◽  
Olfactory Receptors ◽  
Global Gene Expression ◽  
Differentially Expressed ◽  
Expression Of Genes ◽  
Vomeronasal Receptors ◽  
Genes Encoding

To evaluate the transcriptional consequences of differential Vγ chain usage in γδ-T cells, I used a publicly available dataset to compare the global gene expression profiles of immature, committed CD24+ CD73+ γδ-T cells bearing either Vγ1.1+ or Vγ2+ at the γδTCR. I found that thirty-nine genes encoding olfactory receptors were among the most differentially expressed in Vγ2+ CD24+ CD73+ cells. Four vomeronasal receptors (proteins involved in pheromone detection) were also transcriptionally up-regulated in Vγ2+ CD24+ CD73+ cells compared to their Vγ1.1+ counterparts. Analysis of two further datasets revealed two other olfactory genes that were differentially expressed in γδ-T cells, in these cases not based on Vγ chain usage but in a stage-selective pattern. To my knowledge this is the first report documenting the differential expression of genes encoding olfactory receptors during γδ-T development and based on Vγ chain usage.

scholarly journals Pseudomonas syringae pv. tomato OxyR Is Required for Virulence in Tomato and Arabidopsis

2016 ◽  
Vol 29 (2) ◽  
pp. 119-131 ◽  
Author(s):  
Yasuhiro Ishiga ◽  
Yuki Ichinose
Keyword(s):  
Oxidative Stress ◽  
Pseudomonas Syringae ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
High Sensitivity ◽  
Defense Responses ◽  
Bacterial Populations ◽  
Disease Symptoms ◽  
Expression Of Genes ◽  
Genes Encoding

Reactive oxygen species (ROS) have been shown to have a crucial role in plant defense responses and signaling pathways. In addition, ROS also have direct toxicity against pathogens. However, the molecular mechanisms of plant ROS in the direct effects against pathogens is still unclear. To investigate the function of plant ROS in the interactions of plant and bacterial pathogens, we focused on oxyR, encoding an oxidative stress-regulated transcription factor in Pseudomonas syringae pv. tomato DC3000 (DC3000), and generated an ΔoxyR mutant. The DC3000 ΔoxyR mutant showed high sensitivity to oxidative stress in comparison with wild type and the complemented line. The host plants of DC3000, including tomato and Arabidopsis inoculated with the ΔoxyR mutant, clearly showed reduced disease symptoms as well as reduced bacterial populations. Expression profiles of DC3000 genes revealed that OxyR could regulate the expression of genes encoding ROS-detoxifying enzymes, including catalases (KatB and KatG), in response to ROS. We also demonstrated that the expression of katB could be regulated by OxyR during the infection of DC3000 in Arabidopsis. These results suggest that OxyR has an important role in the virulence of DC3000 by regulating the expression of genes related to oxidative stress.

Cold-modulated expression of genes encoding for key enzymes of the sugar metabolism in spring and autumn cvs. of Beta vulgaris L.

2011 ◽  
Vol 9 (2) ◽  
pp. 268-271 ◽  
Author(s):  
D. Pacifico ◽  
C. Onofri ◽  
G. Mandolino
Keyword(s):  
Gene Expression ◽  
Beta Vulgaris ◽  
Expression Profiles ◽  
Transcriptional Response ◽  
Sugar Metabolism ◽  
Transcript Level ◽  
Integrated Approach ◽  
Pcr Analysis ◽  
Expression Of Genes ◽  
Genes Encoding

An integrated approach based on the use of bioinformatics and gene expression analysis tools was carried out to evaluate the organ-specific transcription modulation of nine genes relevant to sugar metabolism of Beta vulgaris L. plantlets of the autumn cv. Franca and spring cv. Bianca, in response to low-temperature (LT) treatments. Different growth cycles imply different plant capability to adapt to the environment that includes variations in gene expression of key metabolic enzymes. The transcriptional response was evaluated by quantitative PCR analysis before, during and after the LT treatments. The results were correlated with the LT-induced electrolyte leakage measure and the carbohydrate content. Stress-induced transcript level alterations were detected in the two cultivars, suggesting a modulation of sucrose synthesis and carbohydrate partitioning. Cold stress induced deep changes in the autumn cultivar, especially in fructose-1,6-biphosphatase gene expression, irrespective of temperature or exposure time. These differential features of expression profiles constitute first clues on the molecular basis of the differential LT response of sugarbeet autumn and spring cultivars.

scholarly journals Nitric Oxide-Induced Dormancy Removal of Apple Embryos Is Linked to Alterations in Expression of Genes Encoding ABA and JA Biosynthetic or Transduction Pathways and RNA Nitration

2019 ◽  
Vol 20 (5) ◽  
pp. 1007 ◽  
Author(s):  
Paulina Andryka-Dudek ◽  
Katarzyna Ciacka ◽  
Anita Wiśniewska ◽  
Renata Bogatek ◽  
Agnieszka Gniazdowska
Keyword(s):  
Seed Dormancy ◽  
Expression Profiles ◽  
Transduction Pathway ◽  
Short Term ◽  
Embryonic Axes ◽  
No Donors ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Stimulation Of

Short-term (3 h) treatment of embryos isolated from dormant apple (Malus domestica Borkh.) seeds with NO donors stimulates their transition from dormancy to germination. Seed dormancy is maintained by ABA, while germination is controlled mainly by gibberellins (GAs) and jasmonic acid (JA). NO-induced dormancy removal correlates with low ABA concentration in embryonic axes and reduced embryo sensitivity to ABA. We analyzed the expression of genes encoding key enzymes of ABA degradation (CYP707A1, CYP707A2), biosynthesis (NCED3, NCED9), and elements of the ABA transduction pathway (PYL1, PYL2, RCAR1, RCAR3, PP2CA, ABI1, ABI2, SNRK2, ABI5, AREB3, ABF). A role for JA in the regulation of germination led us to investigate the expression of genes encoding enzymes of JA biosynthesis (AOS1, JMT, JAR1) and the transduction pathway (COI1, MYC2, JAZ3, JAZ12). The expression profiles of the genes were estimated in embryonic axes isolated from dormant or NO fumigated apple embryos. The analyzed genes were differentially regulated during dormancy alleviation, the main modifications in the transcription level were detected for NCED3, NCED9, CYP707A2, RCAR1, ABF, AOS1, JMT, JAR1 and JAZ3. A regulatory role of NO in the removal of seed dormancy is associated with the stimulation of expression of genes related to ABA degradation, down-regulation of genes responsible for ABA synthesis, an increase of expression level of genes engaged in JA synthesis and modification of the expression of genes engaged in signaling pathways of the hormones. To confirm a signaling role of NO during dormancy breakage, an increased RNA nitration level in embryonic axes was demonstrated.

scholarly journals Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ngoot-Chin Ting ◽  
Katrina Sherbina ◽  
Jia-Shiun Khoo ◽  
Katialisa Kamaruddin ◽  
Pek-Lan Chan ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Oil Palm ◽  
Interspecific Hybrids ◽  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Transcriptome Data ◽  
Triacylglycerol Synthesis ◽  
Expression Of Genes ◽  
Genes Encoding

Abstract Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.

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