Differential Analysis of L. buchneri Transcriptomes under anaerobic and aerobic conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Lentilactobacillus buchneri subsp. silagei CD034
PROVIDER: GSE67802 | GEO | 2017/02/10
SECONDARY ACCESSION(S): PRJNA280960
REPOSITORIES: GEO
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Project description:Lacticaseibacillus rhamnosus CM MSU 529 is the O2-tolerant facultative homofermentative lactic acid bacteria realizing respiratory metabolism when grown in a supplemented with hemin and vitamin K2 nutrient medium. This study describes the effect of aerobic and respiratory conditions on biomass and proteome of strain CM MSU 529 grown in a batch culture. Aeration caused the induction of the biosynthesis of 43 proteins, while 14 proteins were down-regulated as detected by label-free LC-MS/MS. Up-regulated proteins are involved in oxygen consumption (Pox, LctO, pyridoxine 5'-phosphate oxidase), xylulose-5-phosphate conversion (Xfp), pyruvate metabolism (PdhD, AlsS, AlsD), reactive oxygen species (ROS) elimination (Tpx, TrxA, Npx), general stress response (GroES, PfpI, universal stress protein, YqiG), antioxidant production (CysK, DkgA), pyrimidine metabolism (CarA, CarB, PyrE, PyrC, PyrB, PyrR), oligopeptide transport and metabolism (OppA, PepO), maturation and stability of ribosomal subunits (RbfA, VicX). Down-regulated proteins participate in ROS defense (AhpC), citrate and pyruvate consumption (CitE, PflB), oxaloacetate production (AvtA), arginine synthesis (ArgG), amino acid transport (GlnQ), and deoxy-nucleoside biosynthesis (RtpR). Overproduction of purine biosynthesis enzyme (PurE) distinguished cells grown under respiratory conditions from cells grown under aerobiosis. The data obtained shed light on mechanisms providing O2-tolerance and adaptation to aerobic/respiratory conditions in strain CM MSU 529.
2023-03-11 | PXD038847 | Pride
Project description:To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions. Dinoroseobacter shibae wild type strain DSM 16493T was grown in a chemostate in saltwater mininmal medium (SWM) mimicking the conditions in the marine habitat under anaerobic conditions. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. Therefore, D. shibae was grown aerobically in the chemostate until the culture reached the exponential phase, than countinuously cultivaion was started. The dilution rate was 0.1 h-1, establishing the approximate half-maximum growth rate of D. shibae in the exponential phase. The anaerobic shift was initialised after 20 hours by stopping the aeration. The samples were harvested before (as reference) and 30 minutes after stopping the airation. Three biological replica were analyzed. Comparison: Identification of genes induced or repressed under aerobic conditions in the Dinoroseobacter shibae wild type strain DSM 16493T. Here we compared the transcriptome profile of D. shibae wild type strain DSM 16493T grown aerobically in the chemostate in exponential phase with the transcriptome profile of the D. shibae wild type strain DSM 16493T which was grown without aeration for 5, 10, 15, 20, 30, 60 and 120 min.
2013-08-30 | E-GEOD-47445 | biostudies-arrayexpress
Project description:The anaerobic metabolism of the opportunistic pathogen Pseudomonas aeruginosa is important for growth and survival during persistent infections. The two Fnr-type transcription factors Anr and Dnr regulate different parts of the underlying network. Both are proposed to bind to a non-distinguishable DNA sequence named Anr box. The aim of this study was the identification of genes induced under anaerobic conditions in the P. aeruginosa wild type and identification of genes under control of the Anr or Dnr regulators. We performed three comparisons to identify genes induced under anaerobic denitrifying conditions in the P. aeruginosa wild type strain and genes which are under control of the Anr or Dnr regulators under these anaerobic conditions. Since the anr and dnr mutant strains do not grow under anaerobic denitrifying conditions, we applied anaerobic shift experiments. Pseudomonas aeruginosa was grown in a modified AB minimal medium, containing 25 µM FeSO4, 20 mM glucose and 50 mM NaNO3. The 200 ml aerobic cultures were grown in 1 l Erlenmeyer flasks at 37 oC and 300 rpm. The aerobic culture was grown to an OD578 of 0.3. For the aerobic culture, cells were harvested at this point. For the anaerobic shift experiments 130 ml of the respective aerobic culture were transferred to a 135 ml sealed serum flask. Control experiments verified that oxygen tension decreased within 3 - 5 min below the detection limit of an oxygen electrode. The cells were harvested after incubation for additional 2h under anaerobic conditions. Within these 2h incubation period no growth of the wild type, the anr mutant or the dnr mutant strain was observed. First comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown under aerobic conditions up to an OD578 of 0.3 with the transcriptome profile of the PAO1 strain, which was first grown under aerobic conditions up to an OD578 of 0.3 and than shifted to anaerobic conditions by transfer to a sealed serum flask and further incubated for two hours under anaerobic conditions. Second comparison: Identification of genes regulated differently in the anr mutant strain PAO6261. Here we compared the transcriptome profile of the P. aeruginosa wild type PAO1 with the transcriptome profile of the P. aeruginosa anr mutant strain PAO6261. Both strains were harvested after 2h incubation under anaerobic conditions. Third comparison: Identification of genes regulated differently in the dnr mutant strain RM536. Here we compared the transcriptome profile of the P. aeruginosa wild type PAO1 with the transcriptome profile of the P. aeruginosa dnr mutant strain RM536. Both strains were harvested after 2h incubation under anaerobic conditions.
2010-07-07 | E-GEOD-17179 | biostudies-arrayexpress
Project description:The goal of this study was to study this interaction by analyzing genome-wide transcriptional responses to four different nutrient-limitation regimes under aerobic and anaerobic conditions in chemostat cultures of S. cerevisiae. This ‘two-dimensional’ approach resulted in a new, robust set of ‘anaerobic’ and ‘aerobic’ signature transcripts for S. cerevisiae, as well as to a refinement of previous reports on nutrient-responsive genes. Moreover, the identification of genes regulated both by nutrient and oxygen availability provided new insight in cross-regulated network and hierarchy in the control of gene expression. Keywords = S. cerevisiae Keywords = oxygen availability Keywords = anaerobiosis Keywords = chemostat Keywords = transcriptome Keywords = nutrient limitation Keywords = carbon Keywords = nitrogen Keywords = sulfur Keywords = phosphorus. Keywords: other
2004-09-03 | GSE1723 | GEO
Project description:During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, and the global RNA profile of rice genes can be affected by their availabilities. In the aerobically germinating rice embryos, most sugar-regulated genes are responsive to low energy and anaerobic conditions, indicating that sugar-regulation is closely associated with energy and anaerobic signaling. The interference pattern of sugar-regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for the alteration in the expression of sugar-regulated genes in aerobically germinating rice embryos. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar-regulated gene expression. Anaerobically responsive genes are highly overlapped with low-energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those induced by low energy-conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It was noted that abscisic acid (ABA)-responsive genes were over-representative of the genes upregulated under low energy conditions, in contrast to the downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.
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Project description:HRE1 and HRE2 are two ERF transcription factors induced by low oxygen. In this work we analyzed the effect of ectopic expression of HRE1 and HRE2 on the arabidopsis transcriptome in aerobic and hypoxic (1% O2) conditions. While HRE1 has a moderate effect on the expression of anaerobic genes under hypoxia, HRE2 does not affect them either under aerobic or hypoxic conditions.
2009-10-31 | GSE17099 | GEO
Project description:Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response A total of 24 samples were analyzed. These consisted of two times points, (3 hours and 26 hours) under two conditions (anaerobic and aerobic). There were 3 biological replicates and two dye swaps. Each microarray containted one to two probes per predicted coding sequence.
2010-05-18 | E-GEOD-10302 | biostudies-arrayexpress
Project description:Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry worldwide. Oxygen deprivation is a stress that A. pleuropneumoniae will encounter during both early infection and the later, persistent stage. To understand modulation of A. pleuropneumoniae gene expression in response to the stress caused by anaerobic conditions, gene expression profiles under anaerobic and aerobic conditions were compared in this study. The microarray results showed that 631 genes (27.7% of the total ORFs) were differentially expressed in anaerobic conditions. Many genes encoding proteins involved in glycolysis, carbon source uptake systems, pyruvate metabolism, fermentation and the electron respiration transport chain were up-regulated. These changes led to an increased amount of pyruvate, lactate, ethanol and acetate in the bacterial cells as confirmed by metabolite detection. Genes encoding proteins involved in cell surface structures, especially biofilm formation, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis were up-regulated as well. Biofilm formation was significantly enhanced under anaerobic conditions. These results indicate that induction of central metabolism is important for basic survival of A. pleuropneumoniae after a shift to an anaerobic environment. Enhanced biofilm formation may contribute to the persistence of this pathogen in the damaged anaerobic host tissue and also in the early colonization stage. These discoveries give new insights into adaptation mechanisms of A. pleuropneumoniae in response to environmental stress. Transcriptional profiles were analyzed using microarray to compare the gene expressions of A. pleuropneumoniae cultured under aerobic and anaerobic condition. The bacteria was cultured under aerobic condition to mid-log phase (3 hours) and then divided into two separate groups, one group was continually cultured under aerobic condition for 1 hour (OD600nm = 0.417 M-BM-1 0.008) and the other group was cultured under anaerobic condition for 1 hour (OD600nm = 0.333 M-BM-1 0.015). Three independent biological replicates were performed. The total RNA were extracted and hybridized with the whole genome microarray of A. pleuropneumoniae. The signal intensities were normalized and transformed into log2 values. The genes with P-value < 0.05 were selected as differentially expressed genes.
2014-06-30 | E-GEOD-39801 | biostudies-arrayexpress
Project description:In Escherichia coli, Lon is an ATP-dependent protease which degrades misfolded proteins and certain rapidly-degraded regulatory proteins. Given that oxidatively damaged proteins are generally degraded rather than repaired, we anticipated that Lon deficient cells would exhibit decreased viability during aerobic, but not anaerobic, carbon starvation. We found that the opposite actually occurs. Wild-type and Lon deficient cells survived equally well under aerobic conditions, but Lon deficient cells died more rapidly than the wild-type under anaerobiosis. Microarray analysis revealed that genes of the Clp family of ATP-dependent proteases were induced during aerobic growth but not during anaerobic growth. Thus, Clp may compensate for loss of Lon when cells are in an oxygen containing atmosphere. Under anaerobic carbon starvation conditions, Lon must be active to support survival. Keywords: Other
2007-11-01 | GSE6609 | GEO
Project description:Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response
2008-10-10 | GSE10302 | GEO