Characterizing the Staphylococcus aureus fatty acid degradation operon
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ABSTRACT:
PROVIDER: PRJNA1272353 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33838352_1.fastq.gz | Fastqsanger.gz | |||
| SRR33838352_2.fastq.gz | Fastqsanger.gz | |||
| SRR33838353_1.fastq.gz | Fastqsanger.gz | |||
| SRR33838353_2.fastq.gz | Fastqsanger.gz | |||
| SRR33838354_1.fastq.gz | Fastqsanger.gz |
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Project description:Staphylococcus aureus can supplement its endogenous fatty acid synthesis pathway (FASII) with exogenous fatty acids it acquires from the environment through the fatty acid kinase (Fak) complex. While S. aureus has been thought to not degrade fatty acids, it does possess a potential fadXDEBA locus that contains all the genes necessary for -oxidation. Using mRNA analysis, we determined that the fadXDEBA operon can be found on one polycistronic mRNA. Moreover, we identified the fadX promoter and a putative binding site within this region that is consistent with negative regulation by the metabolism-responsive regulator, Carbon Catabolite Protein A (CcpA). Indeed, in the absence of glucose or CcpA, we saw the fadXDEBA operon was derepressed. S. aureus is annotated to lack the crotonase domain of FadB; however, new analysis indicates it is present. To test the functionality of the S. aureus FadB, we performed complementation assays with E. coli fad mutants using minimal media supplemented with single fatty acids. We were able to restore growth of E. coli fad mutants when providing safadBA genes on a plasmid and demonstrate that the SaFadB crotonase domain is required for complementation. Together, these data demonstrate the SaFadBA proteins are functional within a well characterized fatty acid degradation system and the fadXDEBA operon is under strong catabolite repression.
2025-06-05 | GSE299037 | GEO
Project description:Loss of Fatty Acid Degradation by Astrocytic Mitochondria Triggers Neuroinflammation and Neurodegeneration
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Project description:Fatty-acid degrading metagenome
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Project description:S. aureus response to exogenous fatty acid (oleic acid) Gene expression profiles were generated by microarray analysis of S. aureus cells grown in media without or with oleic aicd Comparison of expression profiles after growth of S. aureus in exogenous fatty acid S. aureus was grown in media with and without oleic acid to an OD600nm of 0.5, and RNA was extracted to look at the gobal gene expression.
2012-12-21 | E-GEOD-36231 | biostudies-arrayexpress
Project description:Methicillin-resistant Staphylococcus aureus (MRSA) infections result in more than 200,000 hospitalizations and 10,000 deaths in the United States each year and remain an important medical challenge. A key factor of S. aureus pathogenesis is the production of virulence proteins that are secreted into the extracellular matrix damaging host tissues and forming abscesses that may serve as replicative niches for the bacteria. We recently discovered that host-derived cis-unsaturated fatty acids activate the transcription and translation of EsxA, a protein that plays a central role in abscess formation in clinically relevant MRSA strains. Additionally, we discovered that fatty acid stimulation of EsxA is dependent on fakA, a gene that encodes a protein responsible for the incorporation of exogenous fatty acids into the S. aureus phospholipid membrane. In order to gain a comprehensive understanding of host-fatty-acid-sensing in S. aureus, we performed RNA-Seq analysis on WT Staphylococcus aureus USA300 NRS384, a community-acquired MRSA strain, in the presence and absence of 10μM linoleic acid.
2017-11-15 | GSE101580 | GEO
Project description:Purpose: RNase Y is a major enzyme responsible for mRNA degradation in Streptococcus pyogenes. The goals of this study are to understand whether RNase Y plays a role in operon transcription of S. pyogenes NZ131 by using RNA-seq analysis. Methods: S. pyogenes mRNA profiles of wild type (WT) and RNase Y mutant (∆rny) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. The sequence reads were aligned to the S. pyogenes genome using Bowtie2. The aligned files were sorted to BAM format and indexed using Samtools. The read depth of each base was derived from BAM files using BEDtools. Operon organization of S. pyogenes WT and ∆rny strains were predicted based on base reads. Results: A total of 11 to 12 billion reads were obtained from each sample. More than 99% of these reads were mapped to the S. pyogenes genome. Predictions of operon organization using WT and ∆rny samples showed little difference between the two strains. Conclusions: Our result shows that the mutation of RNase Y does not affect the operon organization of S. pyogenes NZ131.
2017-06-02 | GSE99533 | GEO
Project description:Comparative analysis of changes in gene and protein expression and fatty acid profiles between Escherichia coli K-12 MG1655 ΔfadD ΔaraBAD expressing an acyl-acyl carrier protein thioesterase from Umbellularia californica (BTE) or a non-functional mutant thioesterase (BTE-H204A) to determine the functional basis for losses in cell viability, membrane integrity, or other stresses and metabolic perturbations that may be present. New hypotheses obtained from the study will assist in metabolic engineering efforts of improved strains exhibiting higher fatty acid yields and productivities. Cultures of fatty acid overproducing (BTE-expressing) and negative control (non-functional BTE-H204A-expressing) strains of Escherichia coli K-12 MG1655 delta-fadD delta-araBAD (deficient in beta-oxidation and L-arabinose catabolism) were sampled under two different sets of media/induction/antibiotic conditions. These conditions were shake flasks at 37C, 250 rpm shaking, in EZ rich defined medium supplemented with 0.2% glucose and 0.01 mM biotin (EZglu), and in fermentors at 37C with controlled air sparging, agitation, and pH in EZ rich defined medium supplemented with 0.4% glycerol and 0.01 mM biotin (EZgly). Two strains were analyzed in the EZglu experiment, the background strain harboring either pTrc99A-BTE (fatty acid overproducing) or pTrc99A-BTE-H204A (control phenotype). Three strains were analyzed in the EZgly experiment, with the background strain haboring either pBAD35-BTE and pBAD33 (fatty acid overproducing), pBAD35-BTE and pBAD33-ACC (fatty acid overproducing, ACC are the 4 subunits of E. coli K-12 acetyl-CoA carboxylase expressed as an artificial operon accDABC in plasmid pBAD33), and pBAD35-BTE-H204A and pBAD33 (control phenotype). RNA was extracted from harvested cell pellets from biological triplicates (EZglu) or biological duplicates (EZgly) of each strain at three different sampling times as defined in each sample description. Due to a hybridization or scanning problem, biological duplicates rather than triplicates were analyzed at the mid-stationary phase sampling point in the EZglu experiment for the control strain harboring pTrc99A-BTE-H204A. Multiple technical replicates at either the hybridization or sample level were analyzed from the biological duplicates of the fermentor experiment. The form of technical replicate (sample or hybridization) is specified in each EZgly sample description.
2011-05-24 | E-GEOD-29424 | biostudies-arrayexpress
Project description:Staphylococcus aureus is an opportunistic pathogen that can grow in wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilms forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branch-chained fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branch-chained fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl- CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan.
2020-04-21 | GSE133013 | GEO
Project description:In this study (S)-3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase (H16_A0461/FadB', gene ID: 4247876) from one of two active fatty acid degradation operons of Ralstonia eutropha H16 has been heterologously expressed in Escherichia coli, purified as protein possessing a His-Tag and initially characterized. FadB' is an enzyme with two catalytic domains exhibiting a single monomeric structure and possessing a molecular weight of 86 kDa. The C-terminal part of the enzyme harbors enoyl-CoA hydratase activity and is able to convert trans-crotonyl-CoA to 3-hydroxybutyryl-CoA. The N-terminal part of FadB' comprises an NAD(+) binding site and is responsible for 3-hydroxyacyl-CoA dehydrogenase activity converting (S)-3-hydroxybutyryl-CoA to acetoacetyl-CoA. Enoyl-CoA hydratase activity was detected spectrophotometrically with trans-crotonyl-CoA. (S)-3-Hydroxyacyl-CoA dehydrogenase activity was measured in both directions with acetoacetyl-CoA and 3-hydroxybutyryl-CoA. FadB' was found to be strictly stereospecific to (S)-3-hydroxybutyryl-CoA and to prefer NAD(+). The K m value for acetoacetyl-CoA was 48 μM and V max 149 μmol mg(-1) min(-1). NADP(H) was utilized at a rate of less than 10% in comparison to activity with NAD(H). FadB' exhibited optimal activity at pH 6-7 and the activity decreased at alkaline and acidic pH values. Acetyl-CoA, propionyl-CoA and CoA were found to have an inhibitory effect on FadB'. This study is a first report on biochemical properties of purified (S)-stereospecific 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase with the inverted domain order from R. eutropha H16. In addition to fundamental information about FadB' and fatty acid metabolism, FadB' might be also interesting for biotechnological applications.
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Project description:S. aureus response to exogenous fatty acid (oleic acid) Gene expression profiles were generated by microarray analysis of S. aureus cells grown in media without or with oleic aicd
2012-12-21 | GSE36231 | GEO