Effect of vibration, as a factor associated with cosmic flight on a lysogenic culture of E. coli K-12 (λ)

ABSTRACT Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O2-dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

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Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties

Database ◽

10.1093/database/baaa109 ◽

2020 ◽

Vol 2020 ◽

Author(s):

Carlos-Francisco Méndez-Cruz ◽

Antonio Blanchet ◽

Alan Godínez ◽

Ignacio Arroyo-Fernández ◽

Socorro Gama-Castro ◽

...

Keyword(s):

Transcriptional Regulation ◽

Knowledge Extraction ◽

Biomedical Literature ◽

Main Role ◽

E Coli ◽

Bacterial Transcription ◽

Manual Curation ◽

New Knowledge ◽

Serovar Typhimurium ◽

K 12

Abstract Transcription factors (TFs) play a main role in transcriptional regulation of bacteria, as they regulate transcription of the genetic information encoded in DNA. Thus, the curation of the properties of these regulatory proteins is essential for a better understanding of transcriptional regulation. However, traditional manual curation of article collections to compile descriptions of TF properties takes significant time and effort due to the overwhelming amount of biomedical literature, which increases every day. The development of automatic approaches for knowledge extraction to assist curation is therefore critical. Here, we show an effective approach for knowledge extraction to assist curation of summaries describing bacterial TF properties based on an automatic text summarization strategy. We were able to recover automatically a median 77% of the knowledge contained in manual summaries describing properties of 177 TFs of Escherichia coli K-12 by processing 5961 scientific articles. For 71% of the TFs, our approach extracted new knowledge that can be used to expand manual descriptions. Furthermore, as we trained our predictive model with manual summaries of E. coli, we also generated summaries for 185 TFs of Salmonella enterica serovar Typhimurium from 3498 articles. According to the manual curation of 10 of these Salmonella typhimurium summaries, 96% of their sentences contained relevant knowledge. Our results demonstrate the feasibility to assist manual curation to expand manual summaries with new knowledge automatically extracted and to create new summaries of bacteria for which these curation efforts do not exist. Database URL: The automatic summaries of the TFs of E. coli and Salmonella and the automatic summarizer are available in GitHub (https://github.com/laigen-unam/tf-properties-summarizer.git).

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Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12.

Genetics ◽

10.1093/genetics/125.4.691 ◽

1990 ◽

Vol 125 (4) ◽

pp. 691-702 ◽

Cited By ~ 6

Author(s):

B L Berg ◽

V Stewart

Keyword(s):

Escherichia Coli ◽

Nitrate Reductase ◽

Formate Dehydrogenase ◽

Recombinant Dna ◽

Structural Genes ◽

Respiratory Pathway ◽

E Coli ◽

Formate Oxidation ◽

Operon Expression ◽

K 12

Abstract Formate oxidation coupled to nitrate reduction constitutes a major anaerobic respiratory pathway in Escherichia coli. This respiratory chain consists of formate dehydrogenase-N, quinone, and nitrate reductase. We have isolated a recombinant DNA clone that likely contains the structural genes, fdnGHI, for the three subunits of formate dehydrogenase-N. The fdnGHI clone produced proteins of 110, 32 and 20 kDa which correspond to the subunit sizes of purified formate dehydrogenase-N. Our analysis indicates that fdnGHI is organized as an operon. We mapped the fdn operon to 32 min on the E. coli genetic map, close to the genes for cryptic nitrate reductase (encoded by the narZ operon). Expression of phi(fdnG-lacZ) operon fusions was induced by anaerobiosis and nitrate. This induction required fnr+ and narL+, two regulatory genes whose products are also required for the anaerobic, nitrate-inducible activation of the nitrate reductase structural gene operon, narGHJI. We conclude that regulation of fdnGHI and narGHJI expression is mediated through common pathways.

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Microbial computational genomics of gene regulation

Pure and Applied Chemistry ◽

10.1351/pac200274060899 ◽

2002 ◽

Vol 74 (6) ◽

pp. 899-905 ◽

Cited By ~ 3

Author(s):

Julio Collado-Vides ◽

Gabriel Moreno-Hagelsieb ◽

Arturo Medrano-Soto

Keyword(s):

Transcription Initiation ◽

Transcription Unit ◽

Microbial Genomes ◽

E Coli ◽

Regulatory Interactions ◽

Living Bacterium ◽

Complete Set ◽

Operon Organization ◽

Unit Organization ◽

K 12

Escherichia coli is a free-living bacterium that condensates a large legacy of knowledge as a result of years of experimental work in molecular biology. It represents a point of departure for analyses and comparisons with the ever-increasing number of finished microbial genomes. For years, we have been gathering knowledge from the literature on transcriptional regulation and operon organization in E. coli K-12, and organizing it in a relational database, RegulonDB. RegulonDB contains information of 2025 % of the expected total sets of regulatory interactions at the level of transcription initiation. We have used this knowledge to generate computational methods to predict the missing sets in the genome of E. coli, focusing on prediction of promoters, regulatory sites, regulatory proteins, operons, and transcription units. These predictions constitute separate pieces of a single puzzle. By putting them all together, we shall be able to predict the complete set of regulatory interactions and transcription unit organization of E. coli. Orthologous genes in other genomes of known co-regulated sets of genes in E. coli, along with their corresponding predicted operons, and their predicted transcriptional regulators, shall permit the extension of the previous goal to many more microbial genomes.

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INACTIVATION OF PHAGE C21 BY VARIOUS PREPARATIONS FROM LIPOPOLYSACCHARIDE OF E. COLI K-12

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.56.6.1852 ◽

1966 ◽

Vol 56 (6) ◽

pp. 1852-1858 ◽

Cited By ~ 6

Author(s):

H. M. Kalckar ◽

P. Laursen ◽

A. M. C. Rapin

Keyword(s):

E Coli ◽

K 12

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Potentiation by L-cysteine of the bactericidal effect of hydrogen peroxide in Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.152.1.81-88.1982 ◽

1982 ◽

Vol 152 (1) ◽

pp. 81-88

Author(s):

E H Berglin ◽

M B Edlund ◽

G K Nyberg ◽

J Carlsson

Keyword(s):

Escherichia Coli ◽

Hydrogen Peroxide ◽

Metal Ion ◽

Chelating Agent ◽

Fold Increase ◽

Bactericidal Effect ◽

Anaerobic Conditions ◽

Dna Breakage ◽

E Coli ◽

K 12

Under anaerobic conditions an exponentially growing culture of Escherichia coli K-12 was exposed to hydrogen peroxide in the presence of various compounds. Hydrogen peroxide (0.1 mM) together with 0.1 mM L-cysteine or L-cystine killed the organisms more rapidly than 10 mM hydrogen peroxide alone. The exposure of E. coli to hydrogen peroxide in the presence of L-cysteine inhibited some of the catalase. This inhibition, however, could not fully explain the 100-fold increase in hydrogen peroxide sensitivity of the organism in the presence of L-cysteine. Of other compounds tested only some thiols potentiated the bactericidal effect of hydrogen peroxide. These thiols were effective, however, only at concentrations significantly higher than 0.1 mM. The effect of L-cysteine and L-cystine could be annihilated by the metal ion chelating agent 2,2'-bipyridyl. DNA breakage in E. coli K-12 was demonstrated under conditions where the organisms were killed by hydrogen peroxide.

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Antibacterial Effects of Long-Chain Polyphosphates on Selected Spoilage and Pathogenic Bacteria

Journal of Food Protection ◽

10.4315/0362-028x-71.7.1401 ◽

2008 ◽

Vol 71 (7) ◽

pp. 1401-1405 ◽

Cited By ~ 18

Author(s):

JEREMY A. OBRITSCH ◽

DOJIN RYU ◽

LUCINA E. LAMPILA ◽

LLOYD B. BULLERMAN

Keyword(s):

Food Industry ◽

Pathogenic Bacteria ◽

Antimicrobial Activities ◽

Lag Phase ◽

E Coli ◽

Inhibition Of Growth ◽

K 12 ◽

Chain Lengths ◽

And Staphylococcus Aureus ◽

Long Chain

The antimicrobial activities of four long-chain food-grade polyphosphates were studied at concentrations allowed in the food industry (<5,000 ppm) in defined basal media by determining the inhibition of growth of three gram-negative and four gram-positive spoilage and pathogenic bacteria. Both generation time and lag phase of Escherichia coli K-12, E. coli O157: H7, and Salmonella Typhimurium were increased with all of the polyphosphates tested. Bacillus subtilis and Staphylococcus aureus were more sensitive to polyphosphates, but not in all cases, with multiphased growth. The growth of Lactobacillus plantarum was inhibited by polyphosphates at concentrations above 750 ppm, but the lag time of Listeria monocytogenes was shortened by the presence of polyphosphates. No single polyphosphate was maximally inhibitory against all bacteria. Polyphosphates with chain lengths of 12 to 15 were significantly different from those with chain lengths of 18 to 21 depending on the organism and concentrations of polyphosphate used. Overall, higher polyphosphate concentrations resulted in greater inhibition of bacterial growth.

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pH-Dependent Catabolic Protein Expression during Anaerobic Growth of Escherichia coli K-12

Journal of Bacteriology ◽

10.1128/jb.186.1.192-199.2004 ◽

2004 ◽

Vol 186 (1) ◽

pp. 192-199 ◽

Cited By ~ 65

Author(s):

Elizabeth Yohannes ◽

D. Michael Barnhart ◽

Joan L. Slonczewski

Keyword(s):

Escherichia Coli ◽

Ph Regulation ◽

Metabolic Enzymes ◽

Anaerobic Growth ◽

High Ph ◽

E Coli ◽

Catabolic Enzymes ◽

Periplasmic Proteins ◽

Ph Dependent ◽

K 12

ABSTRACT During aerobic growth of Escherichia coli, expression of catabolic enzymes and envelope and periplasmic proteins is regulated by pH. Additional modes of pH regulation were revealed under anaerobiosis. E. coli K-12 strain W3110 was cultured anaerobically in broth medium buffered at pH 5.5 or 8.5 for protein identification on proteomic two-dimensional gels. A total of 32 proteins from anaerobic cultures show pH-dependent expression, and only four of these proteins (DsbA, TnaA, GatY, and HdeA) showed pH regulation in aerated cultures. The levels of 19 proteins were elevated at the high pH; these proteins included metabolic enzymes (DhaKLM, GapA, TnaA, HisC, and HisD), periplasmic proteins (ProX, OppA, DegQ, MalB, and MglB), and stress proteins (DsbA, Tig, and UspA). High-pH induction of the glycolytic enzymes DhaKLM and GapA suggested that there was increased fermentation to acids, which helped neutralize alkalinity. Reporter lac fusion constructs showed base induction of sdaA encoding serine deaminase under anaerobiosis; in addition, the glutamate decarboxylase genes gadA and gadB were induced at the high pH anaerobically but not with aeration. This result is consistent with the hypothesis that there is a connection between the gad system and GabT metabolism of 4-aminobutanoate. On the other hand, 13 other proteins were induced by acid; these proteins included metabolic enzymes (GatY and AckA), periplasmic proteins (TolC, HdeA, and OmpA), and redox enzymes (GuaB, HmpA, and Lpd). The acid induction of NikA (nickel transporter) is of interest because E. coli requires nickel for anaerobic fermentation. The position of the NikA spot coincided with the position of a small unidentified spot whose induction in aerobic cultures was reported previously; thus, NikA appeared to be induced slightly by acid during aeration but showed stronger induction under anaerobic conditions. Overall, anaerobic growth revealed several more pH-regulated proteins; in particular, anaerobiosis enabled induction of several additional catabolic enzymes and sugar transporters at the high pH, at which production of fermentation acids may be advantageous for the cell.

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