EcoCyc: fusing model organism databases with systems biology

Keseler, Ingrid M.; Mackie, Amanda; Peralta-Gil, Martín; Santos-Zavaleta, Alberto; Gama-Castro, Socorro; Bonavides-Martínez, César; Fulcher, Carol A.; Huerta, A.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muñiz-Rascado, Luis; Ong, Quang; Paley, Suzanne M.; Schröder, Imke; Shearer, Alexander G.; Subhraveti, Pallavi; Travers, Michael; Weerasinghe, Deepika; Weiss, Verena; Gunsalus, Robert P.; Paulsen, Ian T.; Karp, Peter D.

doi:10.1093/nar/gks1027

Cited by 518 publications

(665 citation statements)

References 29 publications

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“…As a result of genome-wide expression analysis using the 5¢-end specific RNA-seq approach, a potential s 32 -dependent promoter was suggested 144 bp upstream of the exuR coding sequence (Gama-Castro et al, 2008;Huerta & ColladoVides, 2003;Keseler et al, 2013). A further four possible s 70 promoters have been predicted in silico (Shavkunov et al, 2009;Fig.…”

Section: Identification Of the Exur Transcription Start Sitesmentioning

confidence: 99%

Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation

et al. 2016

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Section: Identification Of the Exur Transcription Start Sitesmentioning

confidence: 99%

Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation

et al. 2016

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“…Functional information was retrieved from the EcoCyc (Keseler et al, 2013), KEEG (Ogata et al, 1999) and BRENDA (Scheer et al, 2011) databases.…”

Section: Westeberhardia Detection and Phylogenomic Analysesmentioning

confidence: 99%

A novel intracellular mutualistic bacterium in the invasive antCardiocondyla obscurior

et al. 2015

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The evolution of eukaryotic organisms is often strongly influenced by microbial symbionts that confer novel traits to their hosts. Here we describe the intracellular Enterobacteriaceae symbiont of the invasive ant Cardiocondyla obscurior, 'Candidatus Westeberhardia cardiocondylae'. Upon metamorphosis, Westeberhardia is found in gut-associated bacteriomes that deteriorate following eclosion. Only queens maintain Westeberhardia in the ovarian nurse cells from where the symbionts are transmitted to late-stage oocytes during nurse cell depletion. Functional analyses of the streamlined genome of Westeberhardia (533 kb, 23.41% GC content) indicate that neither vitamins nor essential amino acids are provided for the host. However, the genome encodes for an almost complete shikimate pathway leading to 4-hydroxyphenylpyruvate, which could be converted into tyrosine by the host. Taken together with increasing titers of Westeberhardia during pupal stage, this suggests a contribution of Westeberhardia to cuticle formation. Despite a widespread occurrence of Westeberhardia across host populations, one ant lineage was found to be naturally symbiont-free, pointing to the loss of an otherwise prevalent endosymbiont. This study yields insights into a novel intracellular mutualist that could play a role in the invasive success of C. obscurior.

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“…Therefore, this increase in biomass was equivalent to an additional ∼1.2 × 10 12 bacteria l −1 . An electron transport chain consisting of NADH dehydrogenase I and TMAO reductase contributes 6 H + to the proton motive force per NADH molecule oxidized (Keseler et al ., 2013). For an H + /ATP ratio of 3.3 (Futai et al ., 2012), 1.8 ATP molecules are produced for every TMAO molecule reduced, which equates to the production of 5 × 10 22 molecules of ATP.…”

Section: Resultsmentioning

confidence: 99%

“…These transcripts were transiently increased in abundance 15–20 min following addition of TMAO to the chemostats before returning to the pre‐TMAO addition level (Table 2; group C). Three of the six transiently induced operons in group C are regulated by MetJ, suggesting that during this period of enhanced biomass production the supply of S ‐adenosylmethionine, a molecule used in methyl transfer reactions, is restricted (Keseler et al ., 2013). Group D contained peptide, C 4 ‐dicarboxylic acid/orotate, galactose and glycerol‐3‐phosphate transport systems (Table 2; group D).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to the changes in transcript abundance that pass an arbitrary ≥ threefold ( t ‐test, P = 0.05) filter (Table 2), there were widespread changes that are components of the transcriptional response that sit below this statistical filter. To capture the breadth of the transcriptional response when the anaerobic fermentative system was perturbed by introduction of the primary signal TMAO, the activities of 167 TFs that are recorded as able to directly regulate target genes in the EcoCyc database (Keseler et al ., 2013) were simultaneously inferred from the transcript profiles using the open access tfinfer software (Asif et al ., 2010). tfinfer is based on a state space model that employs a linear approximation (in log space) to the dynamics of transcription and treats noise in a principled way such that the estimated TF activities are associated with confidence limits (Sanguinetti et al ., 2006).…”

Section: Resultsmentioning

confidence: 99%

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Adaptation of anaerobic cultures of Escherichia coli K‐12 in response to environmental trimethylamine‐N‐oxide

Denby

Rolfe

Crick

et al. 2015

Environmental Microbiology

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SummarySystematic analyses of transcriptional and metabolic changes occurring when E scherichia coli K‐12 switches from fermentative growth to anaerobic respiratory growth with trimethylamine‐N‐oxide (TMAO) as the terminal electron acceptor revealed: (i) the induction of torCAD, but not genes encoding alternative TMAO reductases; (ii) transient expression of frmRAB, encoding formaldehyde dehydrogenase; and (iii) downregulation of copper resistance genes. Simultaneous inference of 167 transcription factor (TF) activities implied that transcriptional re‐programming was mediated by 20 TFs, including the transient inactivation of the two‐component system ArcBA; a prediction validated by direct measurement of phosphorylated ArcA. Induction of frmRAB, detection of dimethylamine in culture medium and formaldehyde production when cell‐free extracts were incubated with TMAO suggested the presence of TMAO demethylase activity. Accordingly, the viability of an frmRAB mutant was compromised upon exposure to TMAO. Downregulation of genes involved in copper resistance could be accounted for by TMAO inhibition of Cu(II) reduction. The simplest interpretation of the data is that during adaptation to the presence of environmental TMAO, anaerobic fermentative cultures of E . coli respond by activating the TorTSR regulatory system with consequent induction of TMAO reductase activity, resulting in net oxidation of menaquinone and inhibition of Cu(II) reduction, responses that are sensed by ArcBA and CusRS respectively.

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EcoCyc: fusing model organism databases with systems biology

Cited by 518 publications

References 29 publications

Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation

Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation

A novel intracellular mutualistic bacterium in the invasive antCardiocondyla obscurior

Adaptation of anaerobic cultures of Escherichia coli K‐12 in response to environmental trimethylamine‐N‐oxide

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