The EcoCyc Database

Karp, Peter D.; Ong, Wai Kit; Paley, Suzanne M.; Billington, Richard; Caspi, Ron; Fulcher, Carol A.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Midford, Peter E.; Subhraveti, Pallavi; Gama-Castro, Socorro; Muñiz-Rascado, Luis; Bonavides-Martínez, César; Santos-Zavaleta, Alberto; Mackie, Amanda; Keseler, Ingrid M.; Paulsen, Ian T.

doi:10.1128/ecosalplus.esp-0006-2018

Cited by 134 publications

(168 citation statements)

References 98 publications

Supporting

Mentioning

168

Contrasting

Order By: Relevance

“…S3). The nuo operon is positively regulated by cAMP‐Crp, and both nuo operon and ndh are positively regulated by Fis, which is controlled by Crp (Shimada et al ., ; Karp et al ., ). A high (17‐fold) increase in ndh expression in PGRP‐treated bacteria indicates a higher demand for NDH‐2 than NDH‐1 to oxidize the excess of NADH generated in glycolysis and TCA cycle.…”

Section: Resultsmentioning

confidence: 97%

See 1 more Smart Citation

Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

Kashyap

Kuzma

Kowalczyk

et al. 2017

Molecular Microbiology

View full text Add to dashboard Cite

Summary Mammalian Peptidoglycan Recognition Proteins (PGRPs) kill both Gram-positive and Gram-negative bacteria through simultaneous induction of oxidative, thiol, and metal stress responses in bacteria. However, metabolic pathways through which PGRPs induce these bactericidal stress responses are unknown. We screened Keio collection of Escherichia coli deletion mutants and revealed that deleting genes for respiratory chain flavoproteins or for tricarboxylic acid (TCA) cycle resulted in increased resistance of E. coli to PGRP killing. PGRP-induced killing depended on the production of hydrogen peroxide, which required increased supply of NADH for respiratory chain oxidoreductases from central carbon catabolism (glycolysis and TCA cycle), and was controlled by cAMP-Crp. Bactericidal PGRP induced a rapid decrease in respiration, which suggested that the main source of increased production of hydrogen peroxide was a block in respiratory chain and diversion of electrons from NADH oxidoreductases to oxygen. CpxRA two-component system was a negative regulator of PGRP-induced oxidative stress. By contrast, PGRP-induced thiol stress (depletion of thiols) and metal stress (increase in intracellular free Zn2+ through influx of extracellular Zn2+) were mostly independent of oxidative stress. Thus, manipulating pathways that induce oxidative, thiol, and metal stress in bacteria could be a useful strategy to design new approaches to antibacterial therapy.

show abstract

Section: Resultsmentioning

confidence: 97%

“…All of these TCA cycle genes and several glycerol utilization genes are positively controlled by cAMP‐Crp (Fig. and Supporting Information Table S2) (Shimada et al ., ; Karp et al ., ). These results suggest greater utilization of glycerol and increased glycolysis and TCA cycle in PGRP‐treated cells.…”

Section: Resultsmentioning

confidence: 99%

Bactericidal peptidoglycan recognition protein induces oxidative stress in Escherichia coli through a block in respiratory chain and increase in central carbon catabolism

Kashyap

Kuzma

Kowalczyk

et al. 2017

Molecular Microbiology

View full text Add to dashboard Cite

show abstract

“…The K d of the total selected pool was shown to be below 10 nM (Windbichler et al, 2008). To classify the discovered elements, we developed a categorization system according to the genomic location of RAPs with respect to the currently annotated E. coli genes (Karp et al, 2014) (Figure 1A). The majority of identified RAPs (64.3%), termed antisense RAPs, map on the strand opposite to the annotated genes.…”

Section: Resultsmentioning

confidence: 99%

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli

et al. 2017

View full text Add to dashboard Cite

Summary In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

show abstract

“…Since our last publication on EcoCyc in the 2013 NAR Database Issue (2), many improvements to EcoCyc, the Pathway Tools software, the BioCyc family of websites and the display and analysis tools available there have been described elsewhere (3–6). Here, we focus on recent updates to the EcoCyc web site and on additions to the database that reflect new knowledge about E. coli biology.…”

Section: Introductionmentioning

confidence: 99%