Glucan Biosynthesis Protein G Is a Suitable Reference Gene in <i>Escherichia coli</i> K-12

Heng, Sean S. J.; Chan, Oliver Y. W.; Keng, Bryan M. H.; Ling, Maurice Ht

doi:10.5402/2011/469053

Cited by 25 publications

(30 citation statements)

References 38 publications

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“…Measured values of log(R HK ) = −4.98 and log(L X /L Bol )=-6 (Canto et al 2011) both suggest ages of 4-5 Gyr (Maldonado et al 2010;Mamajek & Hillenbrand 2008). At such an advanced age, Heng (2011) agrees that a steady state model is hard to defend and that a transient origin for the HD 69830's excess is more likely.…”

Section: Limits On Outburstsmentioning

confidence: 93%

Multi-Epoch Observations of Hd 69830: High-Resolution Spectroscopy and Limits to Variability

Beichman

Lisse

Tanner

et al. 2011

ApJ

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The main-sequence solar-type star HD69830 has an unusually large amount of dusty debris orbiting close to three planets found via the radial velocity technique. In order to explore the dynamical interaction between the dust and planets, we have performed multi-epoch photometry and spectroscopy of the system over several orbits of the outer dust. We find no evidence for changes in either the dust amount or its composition, with upper limits of 5-7% (1 σ per spectral element) on the variability of the dust spectrum over 1 year, 3.3% (1 σ) on the broad-band disk emission over 4 years, and 33% (1 σ) on the broad-band disk emission over 24 years. Detailed modeling of the spectrum of the emitting dust arXiv:1108.4704v1 [astro-ph.GA] 23 Aug 2011 -2indicates that the dust is located outside of the orbits of the three planets and has a composition similar to main-belt, C-type asteroids asteroids in our solar system. Additionally, we find no evidence for a wide variety of gas species associated with the dust. Our new higher SNR spectra do not confirm our previously claimed detection of H 2 O ice leading to a firm conclusion that the debris can be associated with the break-up of one or more C-type asteroids formed in the dry, inner regions of the protoplanetary disk of the HD69830 system. The modeling of the spectral energy distribution and high spatial resolution observations in the mid-infrared are consistent with a ∼ 1 AU location for the emitting material.

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Section: Limits On Outburstsmentioning

confidence: 93%

Multi-Epoch Observations of Hd 69830: High-Resolution Spectroscopy and Limits to Variability

Beichman

Lisse

Tanner

et al. 2011

ApJ

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“…For example, several studies had analyzed published microarray datasets for reference genes [63,64] and other biologically significant features [65]. Moreover, most of the 30 microarrays originated from studies that were representative of the type of experimental studies which we expect our predictor to be useful in.…”

Section: Resultsmentioning

confidence: 99%

A predictor for predicting Escherichia colitranscriptome and the effects of gene perturbations

Ling

Poh

2014

BMC Bioinformatics

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BackgroundA means to predict the effects of gene over-expression, knockouts, and environmental stimuli in silico is useful for system biologists to develop and test hypotheses. Several studies had predicted the expression of all Escherichia coli genes from sequences and reported a correlation of 0.301 between predicted and actual expression. However, these do not allow biologists to study the effects of gene perturbations on the native transcriptome.ResultsWe developed a predictor to predict transcriptome-scale gene expression from a small number (n = 59) of known gene expressions using gene co-expression network, which can be used to predict the effects of over-expressions and knockdowns on E. coli transcriptome. In terms of transcriptome prediction, our results show that the correlation between predicted and actual expression value is 0.467, which is similar to the microarray intra-array variation (p-value = 0.348), suggesting that intra-array variation accounts for a substantial portion of the transcriptome prediction error. In terms of predicting the effects of gene perturbation(s), our results suggest that the expression of 83% of the genes affected by perturbation can be predicted within 40% of error and the correlation between predicted and actual expression values among the affected genes to be 0.698. With the ability to predict the effects of gene perturbations, we demonstrated that our predictor has the potential to estimate the effects of varying gene expression level on the native transcriptome.ConclusionWe present a potential means to predict an entire transcriptome and a tool to estimate the effects of gene perturbations for E. coli, which will aid biologists in hypothesis development. This study forms the baseline for future work in using gene co-expression network for gene expression prediction.

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“…Fold induction was calculated using the R ϭ 2 Ϫ⌬⌬CT method (16). The glucan biosynthesis protein gene mdoG was used as a reference gene for normalization (17). RNA of the Z5905 homolog of E. coli K-12 was analyzed nine times for the qPCR analysis.…”

Section: Methodsmentioning

confidence: 99%

Unexpected Diversity of Escherichia coli Sialate O -Acetyl Esterase NanS

2016

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The sialic acids (N-acylneuraminates) are a group of nine-carbon keto-sugars existing mainly as terminal residues on animal glycoprotein and glycolipid carbohydrate chains. Bacterial commensals and pathogens exploit host sialic acids for nutrition, adhesion, or antirecognition, where N-acetyl-or N-glycolylneuraminic acids are the two predominant chemical forms of sialic acids. Each form may be modified by acetyl esters at carbon position 4, 7, 8, or 9 and by a variety of less-common modifications. Modified sialic acids produce challenges for colonizing bacteria, because the chemical alterations to N-acetylneuraminic acid (Neu5Ac) confer increased resistance to sialidase and aldolase activities essential for the catabolism of host sialic acids. Bacteria with O-acetyl sialate esterase(s) utilize acetylated sialic acids for growth, thereby gaining a presumed metabolic advantage over competitors lacking this activity. Here, we demonstrate the esterase activity of Escherichia coli NanS after purifying it as a C-terminal HaloTag fusion. Using a similar approach, we show that E. coli strain O157:H7 Stx prophage or prophage remnants invariably include paralogs of nanS often located downstream of the Shiga-like toxin genes. These paralogs may include sequences encoding N-or C-terminal domains of unknown function where the NanS domains can act as sialate O-acetyl esterases, as shown by complementation of an E. coli strain K-12 nanS mutant and the unimpaired growth of an E. coli O157 nanS mutant on Oacetylated sialic acid. We further demonstrate that nanS homologs in Streptococcus spp. also encode active esterase, demonstrating an unexpected diversity of bacterial sialate O-acetyl esterase. IMPORTANCEThe sialic acids are a family of over 40 naturally occurring 9-carbon keto-sugars that function in a variety of host-bacterium interactions. These sugars occur primarily as terminal carbohydrate residues on host glycoproteins and glycolipids. Available evidence indicates that diverse bacterial species use host sialic acids for adhesion or as sources of carbon and nitrogen. Our results show that the catabolism of the diacetylated form of host sialic acid requires a specialized esterase, NanS. Our results further show that nanS homologs exist in bacteria other than Escherichia coli, as well as part of toxigenic E. coli prophage. The unexpected diversity of these enzymes suggests new avenues for investigating host-bacterium interactions. Therefore, these original results extend our previous studies of nanS to include mucosal pathogens, prophage, and prophage remnants. This expansion of the nanS superfamily suggests important, although as-yet-unknown, functions in host-microbe interactions.O ur laboratory discovered (1, 2) and later characterized the transport and metabolism of exogenous N-acetylneuraminic acid (Neu5Ac) in Escherichia coli, Haemophilus influenzae, and Pasteurella multocida (3-6), providing also the first evidence that these processes are essential for animal disease. The essential role of sialic acid trans...

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Glucan Biosynthesis Protein G Is a Suitable Reference Gene in Escherichia coli K-12

Cited by 25 publications

References 38 publications

Multi-Epoch Observations of Hd 69830: High-Resolution Spectroscopy and Limits to Variability

Multi-Epoch Observations of Hd 69830: High-Resolution Spectroscopy and Limits to Variability

A predictor for predicting Escherichia colitranscriptome and the effects of gene perturbations

Unexpected Diversity of Escherichia coli Sialate O -Acetyl Esterase NanS

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