Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia chcoli

Daruwala, R.; Meganathan, R.

doi:10.1016/0378-1097(91)90485-s

Cited by 9 publications

(10 citation statements)

References 30 publications

(26 reference statements)

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“…The EcMenA genetic rescue experiments were carried out using a protocol adapted from Suvarna et al [7]. The 10 mL cultures of a glycerol/trimethylamine N-oxide minimal media [50] containing 0.5 mM IPTG and 0.1 mg/mL ampicillin were inoculated with 10 µl of the glycerol stocks and then incubated in an anaerobic chamber at 37°C. At 24 h postinoculation, OD 600 was measured for each culture.…”

Section: Methodsmentioning

confidence: 99%

Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1

et al. 2014

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Section: Methodsmentioning

confidence: 99%

Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1

et al. 2014

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“…Recombinant clones containing inserts in pUC18 or pUC19 and pQF50 vectors were selected on L agar plus 0.004% 5-bromo-4-chloro-3-indolyl-3-D-galactopyranoside and 50 ,ug of ampicillin per ml. Plasmid complementation assays with menB mutants were performed anaerobically on glycerol minimal media containing 50 ,ug of ampicillin per ml and by using trimethylamine N-oxide as the electron acceptor as described previously (6). Enzymatic complementation assays were performed with cell extracts from Trypticase soy broth-grown cultures harvested and prepared as previously described (12).…”

Section: Methodsmentioning

confidence: 99%

Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli

et al. 1992

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In Escherichia coli, the biosynthesis of the electron carrier menaquinone (vitamin K2) involves at least seven identified enzymes. One of these, naphthoate synthase, forms the bicyclic ring system by catalyzing the conversion of o-succinylbenzoyl-coenzyme A to 1,4-dihydroxy-2-naphthoic acid. The gene for this enzyme has been previously identified as menB. By genetic and biochemical tests, a 1.349-kb DNA fragment from the E. coli men locus complements menB mutants. This fragment contains a single 285-codon open reading frame (ORF). Recombinant plasmids containing deletions of either the amino or the carboxy region of the ORF fail to complement the mutants. The ORF is preceded by consensus sequences for a ribosomal binding site and a sigma 70 promoter. menB transcription sufficient to complement the menB mutant in vivo and in vitro can be initiated from the identified putative promoter, and that in the constructs, menB expression, can be made independent of read-through transcription from the lac promoter. However, multicopy plasmids containing menB fail to generate the expected levels of enzymatic activity.

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“…Fnr has an iron-sulfur cluster [4Fe–4S] that senses the presence of oxygen and becomes inactivated when oxidized in the presence of oxygen. It can also be converted into a disulfide form by glutathione or thioredoxin when inactive (Daruwala and Meganathan, 1991). …”

Section: Resultsmentioning

confidence: 99%

“…As Figure 4 shows, E. coli uses N- and S- oxides as the terminal electron acceptors (Daruwala and Meganathan, 1991). …”

Section: Resultsmentioning

confidence: 99%

MIRA: mutual information-based reporter algorithm for metabolic networks

2014

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Motivation: Discovering the transcriptional regulatory architecture of the metabolism has been an important topic to understand the implications of transcriptional fluctuations on metabolism. The reporter algorithm (RA) was proposed to determine the hot spots in metabolic networks, around which transcriptional regulation is focused owing to a disease or a genetic perturbation. Using a z-score-based scoring scheme, RA calculates the average statistical change in the expression levels of genes that are neighbors to a target metabolite in the metabolic network. The RA approach has been used in numerous studies to analyze cellular responses to the downstream genetic changes. In this article, we propose a mutual information-based multivariate reporter algorithm (MIRA) with the goal of eliminating the following problems in detecting reporter metabolites: (i) conventional statistical methods suffer from small sample sizes, (ii) as z-score ranges from minus to plus infinity, calculating average scores can lead to canceling out opposite effects and (iii) analyzing genes one by one, then aggregating results can lead to information loss. MIRA is a multivariate and combinatorial algorithm that calculates the aggregate transcriptional response around a metabolite using mutual information. We show that MIRA’s results are biologically sound, empirically significant and more reliable than RA.Results: We apply MIRA to gene expression analysis of six knockout strains of Escherichia coli and show that MIRA captures the underlying metabolic dynamics of the switch from aerobic to anaerobic respiration. We also apply MIRA to an Autism Spectrum Disorder gene expression dataset. Results indicate that MIRA reports metabolites that highly overlap with recently found metabolic biomarkers in the autism literature. Overall, MIRA is a promising algorithm for detecting metabolic drug targets and understanding the relation between gene expression and metabolic activity.Availability and implementation: The code is implemented in C# language using .NET framework. Project is available upon request.Contact: cicek@cs.cmu.eduSupplementary information: Supplementary data are available at Bioinformatics online

show abstract

Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia chcoli

Cited by 9 publications

References 30 publications

Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1

Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1

Menaquinone (vitamin K2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli

MIRA: mutual information-based reporter algorithm for metabolic networks

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