luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling

ABSTRACT The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions.

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The Escherichia coli K-12 NarL and NarP Proteins Insulate the nrf Promoter from the Effects of Integration Host Factor

Journal of Bacteriology ◽

10.1128/jb.00975-06 ◽

2006 ◽

Vol 188 (21) ◽

pp. 7449-7456 ◽

Cited By ~ 21

Author(s):

Douglas F. Browning ◽

David J. Lee ◽

Alan J. Wolfe ◽

Jeffrey A. Cole ◽

Stephen J. W. Busby

Keyword(s):

Escherichia Coli ◽

Response Regulator ◽

Regulatory Region ◽

Enteric Bacteria ◽

Integration Host Factor ◽

Host Factor ◽

Receptor Protein ◽

E Coli ◽

Serovar Typhimurium ◽

K 12

ABSTRACT The Escherichia coli K-12 nrf operon promoter can be activated fully by the FNR protein (regulator of fumarate and nitrate reduction) binding to a site centered at position −41.5. FNR-dependent transcription is suppressed by integration host factor (IHF) binding at position −54, and this suppression is counteracted by binding of the NarL or NarP response regulator at position −74.5. The E. coli acs gene is transcribed from a divergent promoter upstream from the nrf operon promoter. Transcription from the major acsP2 promoter is dependent on the cyclic AMP receptor protein and is modulated by IHF and Fis binding at multiple sites. We show that IHF binding to one of these sites, located at position −127 with respect to the nrf promoter, has a positive effect on nrf promoter activity. This activation is dependent on the face of the DNA helix, independent of IHF binding at other locations, and found only when NarL/NarP are not bound at position −74.5. Binding of NarL/NarP appears to insulate the nrf promoter from the effects of IHF. The acs-nrf regulatory region is conserved in other pathogenic E. coli strains and related enteric bacteria but differs in Salmonella enterica serovar Typhimurium.

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Escherichia coli NsrR Regulates a Pathway for the Oxidation of 3-Nitrotyramine to 4-Hydroxy-3-Nitrophenylacetate

Journal of Bacteriology ◽

10.1128/jb.00508-08 ◽

2008 ◽

Vol 190 (18) ◽

pp. 6170-6177 ◽

Cited By ~ 25

Author(s):

Linda D. Rankin ◽

Diane M. Bodenmiller ◽

Jonathan D. Partridge ◽

Shirley F. Nishino ◽

Jim C. Spain ◽

...

Keyword(s):

Escherichia Coli ◽

Physiological Role ◽

Growth Conditions ◽

Growth Defect ◽

E Coli ◽

Mutant Phenotypes ◽

Culture Supernatants ◽

Chip Chip

ABSTRACT Chromatin immunoprecipitation and microarray (ChIP-chip) analysis showed that the nitric oxide (NO)-sensitive repressor NsrR from Escherichia coli binds in vivo to the promoters of the tynA and feaB genes. These genes encode the first two enzymes of a pathway that is required for the catabolism of phenylethylamine (PEA) and its hydroxylated derivatives tyramine and dopamine. Deletion of nsrR caused small increases in the activities of the tynA and feaB promoters in cultures grown on PEA. Overexpression of nsrR severely retarded growth on PEA and caused a marked repression of the tynA and feaB promoters. Both the growth defect and the promoter repression were reversed in the presence of a source of NO. These results are consistent with NsrR mediating repression of the tynA and feaB genes by binding (in an NO-sensitive fashion) to the sites identified by ChIP-chip. E. coli was shown to use 3-nitrotyramine as a nitrogen source for growth, conditions which partially induce the tynA and feaB promoters. Mutation of tynA (but not feaB) prevented growth on 3-nitrotyramine. Growth yields, mutant phenotypes, and analyses of culture supernatants suggested that 3-nitrotyramine is oxidized to 4-hydroxy-3-nitrophenylacetate, with growth occurring at the expense of the amino group of 3-nitrotyramine. Accordingly, enzyme assays showed that 3-nitrotyramine and its oxidation product (4-hydroxy-3-nitrophenylacetaldehyde) could be oxidized by the enzymes encoded by tynA and feaB, respectively. The results suggest that an additional physiological role of the PEA catabolic pathway is to metabolize nitroaromatic compounds that may accumulate in cells exposed to NO.

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Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

Scientific Reports ◽

10.1038/s41598-019-56886-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Tomohiro Shimada ◽

Yui Yokoyama ◽

Takumi Anzai ◽

Kaneyoshi Yamamoto ◽

Akira Ishihama

Keyword(s):

Escherichia Coli ◽

Genetic System ◽

Regulatory Role ◽

E Coli ◽

Warm Blooded Animal ◽

Plant Utilization ◽

K 12

AbstractOutside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization).

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Adaptation in a Mouse Colony Monoassociated with Escherichia coli K-12 for More than 1,000 Days

Applied and Environmental Microbiology ◽

10.1128/aem.00358-10 ◽

2010 ◽

Vol 76 (14) ◽

pp. 4655-4663 ◽

Cited By ~ 13

Author(s):

Sean M. Lee ◽

Aaron Wyse ◽

Aaron Lesher ◽

Mary Lou Everett ◽

Linda Lou ◽

...

Keyword(s):

Escherichia Coli ◽

Growth Rates ◽

Bacterial Species ◽

Intestinal Flora ◽

Average Density ◽

Host Bacterium ◽

E Coli ◽

K 12

ABSTRACT Although mice associated with a single bacterial species have been used to provide a simple model for analysis of host-bacteria relationships, bacteria have been shown to display adaptability when grown in a variety of novel environments. In this study, changes associated with the host-bacterium relationship in mice monoassociated with Escherichia coli K-12 over a period of 1,031 days were evaluated. After 80 days, phenotypic diversification of E. coli was observed, with the colonizing bacteria having a broader distribution of growth rates in the laboratory than the parent E. coli. After 1,031 days, which included three generations of mice and an estimated 20,000 generations of E. coli, the initially homogeneous bacteria colonizing the mice had evolved to have widely different growth rates on agar, a potential decrease in tendency for spontaneous lysis in vivo, and an increased tendency for spontaneous lysis in vitro. Importantly, mice at the end of the experiment were colonized at an average density of bacteria that was more than 3-fold greater than mice colonized on day 80. Evaluation of selected isolates on day 1,031 revealed unique restriction endonuclease patterns and differences between isolates in expression of more than 10% of the proteins identified by two-dimensional electrophoresis, suggesting complex changes underlying the evolution of diversity during the experiment. These results suggest that monoassociated mice might be used as a tool for characterizing niches occupied by the intestinal flora and potentially as a method of targeting the evolution of bacteria for applications in biotechnology.

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Interaction between complement subcomponent C1q and bacterial lipopolysaccharides

Biochemical Journal ◽

10.1042/bj2570865 ◽

1989 ◽

Vol 257 (3) ◽

pp. 865-873 ◽

Cited By ~ 13

Author(s):

A Zohair ◽

S Chesne ◽

R H Wade ◽

M G Colomb

Keyword(s):

Escherichia Coli ◽

Chemical Modification ◽

Essential Role ◽

Wild Strain ◽

E Coli ◽

Diethyl Pyrocarbonate ◽

Direct Binding ◽

Bacterial Lipopolysaccharides ◽

K 12

The heptose-less mutant of Escherichia coli, D31m4, bound complement subcomponent C1q and its collagen-like fragments (C1qCLF) with Ka values of 1.4 x 10(8) and 2.0 x 10(8) M-1 respectively. This binding was suppressed by chemical modification of C1q and C1qCLF using diethyl pyrocarbonate (DEPC). To investigate the role of lipopolysaccharides (LPS) in this binding, biosynthetically labelled [14C]LPS were purified from E. coli D31m4 and incorporated into liposomes prepared from phosphatidylcholine (PC) and phosphatidylethanolamine (PE) [PC/PE/LPS, 2:2:1, by wt.]. Binding of C1q or its collagen-like fragments to the liposomes was estimated via a flotation test. These liposomes bound C1q and C1qCLF with Ka values of 8.0 x 10(7) and 2.0 x 10(7) M-1; this binding was totally inhibited after chemical modification of C1q and C1qCLF by DEPC. Liposomes containing LPS purified from the wild-strain E. coli K-12 S also bound C1q and C1qCLF, whereas direct binding of C1q or C1qCLF to the bacteria was negligible. Diamines at concentrations which dissociate C1 into C1q and (C1r, C1s)2, strongly inhibited the interaction of C1q or C1qCLF with LPS. Removal of 3-deoxy-D-manno-octulosonic acid (2-keto-3-deoxyoctonic acid; KDO) from E. coli D31m4 LPS decreases the binding of C1qCLF to the bacteria by 65%. When this purified and modified LPS was incorporated into liposomes, the C1qCLF binding was completely abolished. These results show: (i) the essential role of the collagen-like moiety and probably its histidine residues in the interaction between C1q and the mutant D31m4; (ii) the contribution of LPS, particularly the anionic charges of KDO, to this interaction.

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THE INFLUENCE OF THE PO1A1 MUTATION UPON RECOMBINATION IN ESCHERICHIA COLI K12

Canadian Journal of Genetics and Cytology ◽

10.1139/g79-046 ◽

1979 ◽

Vol 21 (3) ◽

pp. 423-428 ◽

Cited By ~ 2

Author(s):

Barry W. Glickman ◽

Tineke Rutgers

Keyword(s):

Escherichia Coli ◽

Dna Polymerase ◽

Genetic Recombination ◽

Dna Polymerase I ◽

Multiple Gene ◽

E Coli ◽

Recombinational Process ◽

K 12 ◽

Polymerase I

Genetic recombination in Escherichia coli is a highly regulated process involving multiple gene products. We have investigated the role of DNA polymerase I in this process by studying the effect of the po1A1 mutation upon DNA transfer and conjugation in otherwise isogenic suppressor-free strains of E. coli K-12. It was found that the po1A1 mutation greatly reduces recombination in Hfr crosses (a factor of 20 in Po1+ × Po1A1 crosses and more than a factor of 100 in Po1A1 × Po1A1 crosses). However, since the po1A1 mutation reduces the strains capacity to act as a recipient for an F-prime and the analysis of recombination transfer gradients revealed no differences between Po1+ and Po1− strains, it is concluded that DNA polymerase I probably affects the transfer and/or stability of donor DNA rather than the recombinational process itself.

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Metagenome-wide association study of gut microbiome features for myositis

10.1101/2021.12.15.21267821 ◽

2021 ◽

Author(s):

Yimin Li ◽

Jun Xu ◽

Zijun Li ◽

Yixue Guo ◽

Xiaoyan Xing ◽

...

Keyword(s):

Escherichia Coli ◽

Interstitial Lung Disease ◽

Lung Disease ◽

Gut Microbiome ◽

Association Studies ◽

Bacterial Species ◽

Biological Pathways ◽

Healthy Controls ◽

E Coli

Objective: The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS). Methods We conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD). Our MWAS consisted of both overall distribution level of the bacteria analysis and pathway analysis. Receiver operating characteristic curve (ROC) analysis was performed to identify novel gut bacterial species associated with myositis or myositis-associated RP-ILD, and to evaluate their diagnostic values. Results Apparent discrepancy in β diversities of metagenome was found in the comparison of myositis and HC, RP-ILD and C-ILD in myositis. Analysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases. A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from Healthy controls effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis paitents. Conclusion Our MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.

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Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli: TABLE 1

Journal of Bacteriology ◽

10.1128/jb.00424-15 ◽

2015 ◽

Vol 198 (1) ◽

pp. 7-11 ◽

Cited By ~ 48

Author(s):

Regine Hengge ◽

Michael Y. Galperin ◽

Jean-Marc Ghigo ◽

Mark Gomelsky ◽

Jeffrey Green ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Mechanisms ◽

Bacterial Species ◽

Content Type ◽

E Coli ◽

Diguanylate Cyclases ◽

Genes Encoding ◽

Systematic Nomenclature ◽

K 12 ◽

Encoding Genes

In recent years,Escherichia colihas served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely usedE. coliK-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenicE. colistrains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling inE. coli, we now propose a general and systematicdgcandpdenomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains ofE. coliin future studies.

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O-Antigen-Dependent Colicin Insensitivity of UropathogenicEscherichia coli

Journal of Bacteriology ◽

10.1128/jb.00545-18 ◽

2018 ◽

Vol 201 (4) ◽

Cited By ~ 12

Author(s):

Connor Sharp ◽

Christine Boinett ◽

Amy Cain ◽

Nicholas G. Housden ◽

Sandip Kumar ◽

...

Keyword(s):

Escherichia Coli ◽

Outer Membrane ◽

Growth Conditions ◽

Membrane Receptors ◽

Cell Surface Receptor ◽

Dominant Factor ◽

Content Type ◽

E Coli ◽

O Antigen ◽

K 12

ABSTRACTThe outer membrane of Gram-negative bacteria presents a significant barrier for molecules entering the cell. Nevertheless, colicins, which are antimicrobial proteins secreted byEscherichia coli, can target otherE. colicells by binding to cell surface receptor proteins and activating their import, resulting in cell death. Previous studies have documented high rates of nonspecific resistance (insensitivity) of variousE. colistrains toward colicins that is independent of colicin-specific immunity and is instead associated with lipopolysaccharide (LPS) in the outer membrane. This observation poses a contradiction: why doE. colistrains have colicin-expressing plasmids, which are energetically costly to retain, if cells around them are likely to be naturally insensitive to the colicin they produce? Here, using a combination of transposon sequencing and phenotypic microarrays, we show that colicin insensitivity of uropathogenicE. colisequence type 131 (ST131) is dependent on the production of its O-antigen but that minor changes in growth conditions render the organism sensitive toward colicins. The reintroduction of O-antigen intoE. coliK-12 demonstrated that it is the density of O-antigen that is the dominant factor governing colicin insensitivity. We also show, by microscopy of fluorescently labelled colicins, that growth conditions affect the degree of occlusion by O-antigen of outer membrane receptors but not the clustered organization of receptors. The result of our study demonstrate that environmental conditions play a critical role in sensitizingE. colitoward colicins and that O-antigen in LPS is central to this role.IMPORTANCEEscherichia coliinfections can be a major health burden, especially with the organism becoming increasingly resistant to “last-resort” antibiotics such as carbapenems. Although colicins are potent narrow-spectrum antimicrobials with potential as future antibiotics, high levels of naturally occurring colicin insensitivity have been documented which could limit their efficacy. We identify O-antigen-dependent colicin insensitivity in a clinically relevant uropathogenicE. colistrain and show that this insensitivity can be circumvented by minor changes to growth conditions. The results of our study suggest that colicin insensitivity amongE. coliorganisms has been greatly overestimated, and as a consequence, colicins could in fact be effective species-specific antimicrobials targeting pathogenicE. colisuch as uropathogenicE. coli(UPEC).

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Unexpected Diversity of Escherichia coli SialateO-Acetyl Esterase NanS

Journal of Bacteriology ◽

10.1128/jb.00189-16 ◽

2016 ◽

Vol 198 (20) ◽

pp. 2803-2809 ◽

Cited By ~ 8

Author(s):

Ariel Rangel ◽

Susan M. Steenbergen ◽

Eric R. Vimr

Keyword(s):

Escherichia Coli ◽

Sialic Acid ◽

Bacterial Species ◽

Sialic Acids ◽

Host Bacterium ◽

Acetyl Esterase ◽

Content Type ◽

E Coli ◽

Host Microbe Interactions ◽

K 12

ABSTRACTThe 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, whereN-acetyl- orN-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 toN-acetylneuraminic acid (Neu5Ac) confer increased resistance to sialidase and aldolase activities essential for the catabolism of host sialic acids. Bacteria withO-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 ofEscherichia coliNanS after purifying it as a C-terminal HaloTag fusion. Using a similar approach, we show thatE. colistrain O157:H7 Stx prophage or prophage remnants invariably include paralogs ofnanSoften 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 sialateO-acetyl esterases, as shown by complementation of anE. colistrain K-12nanSmutant and the unimpaired growth of anE. coliO157nanSmutant onO-acetylated sialic acid. We further demonstrate thatnanShomologs inStreptococcusspp. also encode active esterase, demonstrating an unexpected diversity of bacterial sialateO-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 thatnanShomologs exist in bacteria other thanEscherichia coli, as well as part of toxigenicE. coliprophage. The unexpected diversity of these enzymes suggests new avenues for investigating host-bacterium interactions. Therefore, these original results extend our previous studies ofnanSto include mucosal pathogens, prophage, and prophage remnants. This expansion of thenanSsuperfamily suggests important, although as-yet-unknown, functions in host-microbe interactions.

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