Characterization of the aegA locus of Escherichia coli: control of gene expression in response to anaerobiosis and nitrate

Cavicchioli, Ricardo; Kolesnikow, Tassia; Chiang, Robin C.; Gunsalus, Robert P.

doi:10.1128/jb.178.23.6968-6974.1996

Cited by 14 publications

(14 citation statements)

References 48 publications

(71 reference statements)

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“…In contrast, transcript levels of aegA, phnA, and ycfH were increased under aerobic conditions in an fnr mutant strain compared to the wild type, although this aerobic effect of FNR was not observed with an aegAЈ-lacZ fusion (12). yfiD expression was anaerobically induced in the wild-type strain, while in the absence of FNR, both the aerobic and anaerobic expression levels were decreased.…”

Section: Strategy For Identifying Genes Regulated By O 2 And/or Fnrmentioning

confidence: 78%

Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function

Kang¹,

Weber

Qiu³

et al. 2005

J Bacteriol

240

221

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The major regulator controlling the physiological switch between aerobic and anaerobic growth conditions in Escherichia coli is the DNA binding protein FNR. To identify genes controlled by FNR, we used Affymetrix Antisense GeneChips to compare global gene expression profiles from isogenic MG1655 wild-type and ⌬fnr strains grown in glucose minimal media under aerobic or anaerobic conditions. We found that 297 genes contained within 184 operons were regulated by FNR and/or by O 2 levels. The expression of many genes known to be involved in anaerobic respiration and fermentation was increased under anaerobic growth conditions, while that of genes involved in aerobic respiration and the tricarboxylic acid cycle were repressed as expected. The expression of nine operons associated with acid resistance was also increased under anaerobic growth conditions, which may reflect the production of acidic fermentation products. Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR. Classification of the 297 genes into eight groups by k-means clustering analysis indicated that genes with common gene expression patterns also had a strong functional relationship, providing clues for studying the function of unknown genes in each group. Six of the eight groups showed regulation by FNR; while some expression groups represent genes that are simply activated or repressed by FNR, others, such as those encoding functions for chemotaxis and motility, showed a more complex pattern of regulation. A computer search for FNR DNA binding sites within predicted promoter regions identified 63 new sites for 54 genes. We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized.

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Section: Strategy For Identifying Genes Regulated By O 2 And/or Fnrmentioning

confidence: 78%

Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function

Kang¹,

Weber

Qiu³

et al. 2005

J Bacteriol

240

221

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“…Although aegA (anaerobically expressed gene A) is reportedly expressed under anaerobic conditions (17), its biological function had not previously been elucidated. AegA is a putative oxidoreductase and has an N-terminal 4Fe-4S dicluster domain, often found within the bacterial ferredoxin, and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain, which shows high similarity with the E. coli glutamate synthase ␤-subunit GltD (18) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification of a Formate-Dependent Uric Acid Degradation Pathway in Escherichia coli

Iwadate

Kato

2019

J Bacteriol

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Purine is a nitrogen-containing compound that is abundant in nature. In organisms that utilize purine as a nitrogen source, purine is converted to uric acid, which is then converted to allantoin. Allantoin is then converted to ammonia. In Escherichia coli, neither urate-degrading activity nor a gene encoding an enzyme homologous to the known urate-degrading enzymes had previously been found.Here, we demonstrate urate-degrading activity in E. coli. We first identified aegA as an E. coli gene involved in oxidative stress tolerance. An examination of gene expression revealed that both aegA and its paralog ygfT are expressed under both microaerobic and anaerobic conditions. The ygfT gene is localized within a chromosomal gene cluster presumably involved in purine catabolism. Accordingly, the expression of ygfT increased in the presence of exogenous uric acid, suggesting that ygfT is involved in urate degradation. Examination of the change of uric acid levels in the growth medium with time revealed urate-degrading activity under microaerobic and anaerobic conditions in the wild-type strain but not in the aegA ygfT double-deletion mutant. Furthermore, AegA-and YgfT-dependent urate-degrading activity was detected only in the presence of formate and formate dehydrogenase H. Collectively, these observations indicate the presence of urate-degrading activity in E. coli that is operational under microaerobic and anaerobic conditions. The activity requires formate, formate dehydrogenase H, and either aegA or ygfT. We also identified other putative genes which are involved not only in formate-dependent but also in formate-independent urate degradation and may function in the regulation or cofactor synthesis in purine catabolism. IMPORTANCE The metabolic pathway of uric acid degradation to date has been elucidated only in aerobic environments and is not understood in anaerobic and microaerobic environments. In the current study, we showed that Escherichia coli, a facultative anaerobic organism, uses uric acid as a sole source of nitrogen under anaerobic and microaerobic conditions. We also showed that formate, formate dehydrogenase H, and either AegA or YgfT are involved in uric acid degradation. We propose that formate may act as an electron donor for a uric acid-degrading enzyme in this bacterium.

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“…Several proteins or domains of proteins whose sequences are now present in data banks are strikingly similar to GltD. The similarities between E. coli aegA gene product (Ec-AegA, [61]) and Rhodobacter capsulatus gltX gene product (Rc-GltX) and GltD have been reported. We recently found that the N-terminal region of dihydropyrimidine dehydrogenase (DPD), another complex Fe/S flavoprotein found in animals, aligns very well with GltD [62].…”

Section: Is the Glts Subunit A Member Of A Novel Family Of Fad-dependmentioning

confidence: 99%

Glutamate synthase: a complex iron-sulfur flavoprotein

Vanoni¹,

Curti²

1999

Cellular and Molecular Life Sciences (CMLS)

110

105

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Glutamate synthase is a complex iron-sulfur flavoprotein that forms L-glutamate from L-glutamine and 2-oxoglutarate. It participates with glutamine synthetase in ammonia assimilation processes. The known structural and biochemical properties of glutamate synthase from Azospirillum brasilense, a nitrogen-fixing bacterium, will be discussed in comparison to those of the ferredoxin-dependent enzyme from photosynthetic tissues and of the eukaryotic reduced pyridine nucleotide-dependent form of glutamate synthase in order to gain insight into the mechanism of the glutamate synthase reaction. Sequence analyses also revealed that the small subunit of bacterial glutamate synthase may be the prototype of a novel class of flavin adenine dinucleotide- and iron-sulfur-containing oxidoreductase widely used as an enzyme subunit or domain to transfer reducing equivalents from NAD(P)H to an acceptor protein or protein domain.

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Characterization of the aegA locus of Escherichia coli: control of gene expression in response to anaerobiosis and nitrate

Cited by 14 publications

References 48 publications

Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function

Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function

Identification of a Formate-Dependent Uric Acid Degradation Pathway in Escherichia coli

Glutamate synthase: a complex iron-sulfur flavoprotein

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