The anti-sigma factor MucA of Pseudomonas aeruginosa: dramatic differences of mucA22 vs. DmucA mutants in anaerobic acidified nitrite sensitivity of planktonic and biofilm bacteria in vitro and during chronic murine lung infection
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PROVIDER: PRJNA526832 | ENA |
REPOSITORIES: ENA
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Project description:The antimicrobial action of the curing agent NaNO2, which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we applied RNA-sequencing to analyze the acidified NaNO2 shock and adaptive response of Salmonella Typhimurium, a frequent contaminant in raw meat. Upon a 10 minute exposure to 150 mg/l NaNO2 in LB pH 5.5 acidified with lactic acid, genes involved in nitrosative stress protection together with several other stress related genes were induced. To the contrary, genes involved in translation, transcription, replication and motility were down-regulated. Induction of stress tolerance and reduction of cell proliferation obviously promote survival under harsh acidified NaNO2 stress. The subsequent adaptive response was characterized by up-regulation of NsrR-regulated genes and iron-uptake systems and down-regulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite mediated increase of acid stress.
2014-08-25 | GSE57238 | GEO
Project description:The antimicrobial action of the curing agent NaNO2, which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we applied RNA-sequencing to analyze the acidified NaNO2 shock and adaptive response of Salmonella Typhimurium, a frequent contaminant in raw meat. Upon a 10 minute exposure to 150 mg/l NaNO2 in LB pH 5.5 acidified with lactic acid, genes involved in nitrosative stress protection together with several other stress related genes were induced. To the contrary, genes involved in translation, transcription, replication and motility were down-regulated. Induction of stress tolerance and reduction of cell proliferation obviously promote survival under harsh acidified NaNO2 stress. The subsequent adaptive response was characterized by up-regulation of NsrR-regulated genes and iron-uptake systems and down-regulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite mediated increase of acid stress. Transcriptome of Salmonella Typhimurium 14028, treated at OD600 = 0.80-0.85 with 150 mg/l NaNO2 (acidified by lactic acid in the growth medium) for 10 min (shock response) or until an OD600 = 1.45-1.55 is reached (1.5 - 2.0 h, adaptation response), was compared to respective control cultures without NaNO2. Amplified cDNA libraries for sequencing on the SOLiD 5500xl system were prepared from one culture per condition.
2014-08-25 | E-GEOD-57238 | biostudies-arrayexpress
Project description:Macrobrachium nipponense is one of the commonest species threatened by ambient superfluous nitrite. The mechanism of nitrite stress at the molecular level was studied using de novo RNA-Seq to explore the molecular pathways in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24h and the chronic nitrite stress (6.58 mg/L nitrite-N) for 21d. A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1,028.7 bp and N50 of 1,294bp. 2,824 and 2,610 unigenes in the acute and chronic nitrite stress were significantly differentially expressed respectively. Based on the change in GO analysis and KEGG pathway analysis, pathways both in the acute and chronic nitrite stress were glycosphingolipid biosynthesis - ganglio series, alanine aspartate and glutamate metabolism, biotin metabolism and amino sugar and nucleotide sugar metabolism which revealed the commonly functional pathways in acute and chronic nitrite stress. The markedly altered pathways were divided into four sections of immunity, metabolism, cell and others. Immunity section contained the most pathways among the classifications as phagosome, folate biosynthesis, glycerolipid metabolism, glycine, serine and threonine metabolism, selenoamino acid metabolism, cysteine and methionine metabolism, amino sugar and nucleotide sugar metabolism and taurine and hypotaurine metabolism in the acute nitrite stress and lysosome, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, glycosaminoglycan degradation and amino sugar and nucleotide sugar metabolism in the chronic nitrite stress. This is the first report of whole molecular responses of M. nipponense under acute and chronic nitrite stress through de novo transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanisms of the nitrite stress for crustacean species.
2016-11-04 | GSE74684 | GEO
Project description: Not available
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Project description:In this study, the A-NO2- sensitivity of mucA22 mutant bacteria vs. a genome sequence-confirmed mucA deletion (∆mucA) mutant was determined. The ∆mucA is surprisingly more resistant to A-NO2- than mucA22 bacteria. The genes responsible for the disposal of nitric oxide (NO), a by-product of A-NO2-, were found to be near wild-type levels in the ∆mucA mutant yet were dramatically reduced in the mucA22 mutant.
2019-03-14 | GSE128220 | GEO
Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.
2019-07-03 | GSE123406 | GEO
Project description:Unlike all other bacteria, the physiology of cyanobacteria is based on the assimilation of organic matter from inorganic carbon driven by oxygenic photosynthesis. This setting poses special regulatory challenges, particularly in integrating carbon and nitrogen metabolism. Several regulatory factors control the primary nitrogen metabolism, such as the PII protein and proteins interacting with it (PirA, PirC or PipX), or the inactivating factors IF7 and IF17 impacting glutamine synthetase activity. However, regulatory proteins of other enzymes in the nitrogen assimilation pathway have not been described thus far. Here, we show that the 81 amino acids regulatory protein NirP1 in the cyanobacterium Synechocystis sp. PCC 6803 functions as an inhibitor of nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Ectopic overexpression of the nirP1 gene under standard growth conditions led to a pigmentation phenotype and delayed growth, which was correlated by the excretion of nitrite and dramatic changes in metabolite pools. We show that nitrite excretion occurs in Synechocystis wild type cells upon the shift from high CO2 (HC) to low CO2 (LC) conditions when NirP1 expression becomes activated. The expression of nirP1 is controlled by two transcription factors, NtcA, which binds to a recognition site in a repressive position above the transcription start site (TSS), and an activator, which probably binds to an element 60 to 43 nt upstream of the TSS. Therefore, the joint activity of NtcA and this activator leads to the observed induction of NirP1 under LC conditions, whereas it is repressed by shifts to nitrogen starvation. The data demonstrate that NirP1 plays a crucial role in the coordination of C and N primary metabolism in cyanobacteria by targeting the activity of one of the central enzymes. In natural environments, the excreted nitrite will be utilized by other microorganisms; therefore, NirP1 will ultimately impact the activities and composition of the surrounding microbiome.
2024-02-23 | PXD041127 | Pride
Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.
2013-12-30 | GSE24914 | GEO
Project description:Global gene expression was compared between Nitrosomonas europaea wild-type and a nitrite reductase-deficient mutant using a genomic microarray. Keywords: wild-type to mutant global transcriptome comparison
2006-03-23 | GSE4517 | GEO