scholarly journals Insertion sequence-related genetic variation in resting Escherichia coli K-12.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 721-730 ◽  
Author(s):  
T Naas ◽  
M Blot ◽  
W M Fitch ◽  
W Arber
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Insertion Sequence ◽  
Ancestral Population ◽  
E Coli ◽  
Rich Media ◽  
Reduced Rate ◽  
K 12 ◽  
High Degree

Abstract Bacterial subclones recovered from an old stab culture of Escherichia coli K-12 revealed a high degree of genetic diversity, which occurred in spite of a very reduced rate of propagation during storage. This conclusion is based on a pronounced restriction fragment length polymorphism (RFLP) detected upon hybridization with internal fragments of eight resident insertion sequences (IS). Genetic diversity was dependent on the IS considered and, in many cases, a clear consequence of IS transposition. IS5 was particularly active in the generation of variation. All subclones in which IS30 had been active testify to a burst of IS30 transposition. This was correlated with a loss of prototrophy and a reduced growth on rich media. A pedigree of the entire clone could be drawn from the RFLP patterns of the subclones. Out of 118 subclones analyzed, 68 different patterns were found but the putative ancestral population had disappeared. A few patterns were each represented by several subclones displaying improved fitness. These results offer insights into the role of IS elements in the plasticity of the E. coli genome, and they further document that enzyme-mediated DNA rearrangements do occur in resting bacterial cultures.

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

2019 ◽  
Vol 9 (1) ◽  
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).

scholarly journals Interaction between complement subcomponent C1q and bacterial lipopolysaccharides

1989 ◽  
Vol 257 (3) ◽  
pp. 865-873 ◽  
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.

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

1979 ◽  
Vol 21 (3) ◽  
pp. 423-428 ◽  
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.

scholarly journals Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

mSystems ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Kaneyoshi Yamamoto ◽  
Yuki Yamanaka ◽  
Tomohiro Shimada ◽  
Paramita Sarkar ◽  
Myu Yoshida ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Small Subunit ◽  
Open Reading Frames ◽  
Pcr Assay ◽  
E Coli ◽  
K 12 ◽  
Chip Chip ◽  
Reading Frames

The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β′, of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP function. After analysis of genomewide distribution of wild-type and RpoZ-defective RNAP by the ChIP-chip method, we found alteration of the RpoZ-defective RNAP inside open reading frames, in particular, of the genes within prophages. For a set of the genes that exhibited altered occupancy of the RpoZ-defective RNAP, transcription was found to be altered as observed by qRT-PCR assay. All the observations here described indicate the involvement of RpoZ in recognition of some of the prophage genes. This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature.

Properties of haemolysin E (HlyE) from a pathogenic Escherichia coli avian isolate and studies of HlyE export

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1495-1505 ◽  
Author(s):  
Neil R. Wyborn ◽  
Angela Clark ◽  
Ruth E. Roberts ◽  
Stuart J. Jamieson ◽  
Svetomir Tzokov ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Blood Cells ◽  
Cell Envelope ◽  
Membrane Integrity ◽  
Intrinsic Property ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
Carboxyl Terminal ◽  
K 12

Haemolysin E (HlyE) is a novel pore-forming toxin first identified in Escherichia coli K-12. Analysis of the 3-D structure of HlyE led to the proposal that a unique hydrophobic β-hairpin structure (the β-tongue, residues 177–203) interacts with the lipid bilayer in target membranes. In seeming contradiction to this, the hlyE sequence from a pathogenic E. coli strain (JM4660) that lacks all other haemolysins has been reported to encode an Arg residue at position 188 that was difficult to reconcile with the proposed role of the β-tongue. Here it is shown that the JM4660 hlyE sequence encodes Gly, not Arg, at position 188 and that substitution of Gly188 by Arg in E. coli K-12 HlyE abolishes activity, emphasizing the importance of the head domain in HlyE function. Nevertheless, 76 other amino acid substitutions were confirmed compared to the HlyE protein of E. coli K-12. The JM4660 HlyE protein was dimeric, suggesting a mechanism for improving toxin solubility, and it lysed red blood cells from many species by forming 36–41 Å diameter pores. However, the haemolytic phenotype of JM4660 was found to be unstable due to defects in HlyE export, indicating that export of active HlyE is not an intrinsic property of the protein but requires additional components. TnphoA mutagenesis of hlyE shows that secretion from the cytoplasm to the periplasm does not require the carboxyl-terminal region of HlyE. Finally, disruption of genes associated with cell envelope function, including tatC, impairs HlyE export, indicating that outer membrane integrity is important for effective HlyE secretion.

scholarly journals Morphological and physiological effects of a single amino acid substitution in the patatin-like phospholipase CapV in Escherichia coli

2020 ◽  
Author(s):  
Fengyang Li ◽  
Heike Bähre ◽  
Manfred Rohde ◽  
Ute Römling
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Biofilm Formation ◽  
Morphological Plasticity ◽  
Single Amino Acid ◽  
E Coli ◽  
Single Amino Acid Change ◽  
Response To Stress ◽  
K 12

AbstractIn rod-shaped bacteria morphological plasticity occurs in response to stress, which blocks cell division to promote filamentation. We demonstrate here that overexpression of the patatin-like phospholipase variant CapVQ329R but not CapV causes pronounced sulA-independent pyridoxine-inhibited cell filamentation and restriction of swimming and flagella production of Escherichia coli K-12 derivative MG1655. Mutational analyses of CapVQ329R indicated conserved amino acids in canonical patatin-like phospholipase A motifs, but not the nucleophilic serine to be required for the observed phenotypes. Furthermore, CapVQ329R alters rdar biofilm formation including expression of the biofilm activator CsgD. Moreover, commensal and pathogenic E. coli strains and Salmonella typhimurium also responded with cell filamentation and alteration in biofilm formation. In conclusion, this work identifies the CapV variant CapVQ329R as a pleiotropic regulator, emphasizes a scaffold function for patatin-like phospholipases and highlights the role of a single amino acid change for the evolution of protein functionality.

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

2005 ◽  
Vol 187 (24) ◽  
pp. 8350-8360 ◽  
Author(s):  
Liang Wang ◽  
Jun Li ◽  
John C. March ◽  
James J. Valdes ◽  
William E. Bentley
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Growth Conditions ◽  
Receptor Protein ◽  
Metabolic Enzyme ◽  
Signal Molecule ◽  
E Coli ◽  
Induced Genes ◽  
K 12

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.

scholarly journals Genetic Diversity among Escherichia coli O157:H7 Isolates and Identification of Genes Linked to Human Infections

2007 ◽  
Vol 76 (2) ◽  
pp. 845-856 ◽  
Author(s):  
Guanghui Wu ◽  
Ben Carter ◽  
Muriel Mafura ◽  
Ernesto Liebana ◽  
Martin J. Woodward ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Comparative Genomic ◽  
Escherichia Coli O157 ◽  
Microarray Hybridization ◽  
E Coli ◽  
Genomic Microarray ◽  
K 12 ◽  
Human Infections ◽  
Dominant Genes

ABSTRACT An Escherichia coli oligonucleotide microarray based on three sequenced genomes was validated for comparative genomic microarray hybridization and used to study the diversity of E. coli O157 isolates from human infections and food and animal sources. Among 26 test strains, 24 (including both Shiga toxin [Stx]-positive and -negative strains) were found to be related to the two sequenced E. coli O157:H7 strains, EDL933 and Sakai. However, these strains showed much greater genetic diversity than those reported previously, and most of them could not be categorized as either lineage I or II. Some genes were found more often in isolates from human than from nonhuman sources; e.g., ECs1202 and ECs2976, associated with stx2AB and stx1AB, were in all isolates from human sources but in only 40% of those from nonhuman sources. Some (but not all) lineage I-specific or -dominant genes were also more frequently associated with isolates from human. The results suggested that it might be more effective to concentrate our efforts on finding markers that are directly related to infection rather than those specific to certain lineages. In addition, two Stx-negative O157 cattle isolates (one confirmed to be H7) were significantly different from other Stx-positive and -negative E. coli O157:H7 strains and were more similar to MG1655 in their gene content. This work demonstrates that not all E. coli O157:H7 strains belong to the same clonal group, and those that were similar to E. coli K-12 might be less virulent.

scholarly journals Mapping Stress-Induced Changes in Autoinducer AI-2 Production in Chemostat-Cultivated Escherichia coli K-12

2001 ◽  
Vol 183 (9) ◽  
pp. 2918-2928 ◽  
Author(s):  
Matthew P. DeLisa ◽  
James J. Valdes ◽  
William E. Bentley
Keyword(s):  
Escherichia Coli ◽  
Steady State ◽  
Quorum Sensing ◽  
Interleukin 2 ◽  
Heterologous Proteins ◽  
Induced Expression ◽  
E Coli ◽  
Chemostat Cultures ◽  
K 12

ABSTRACT Numerous gram-negative bacteria employ a cell-to-cell signaling mechanism, termed quorum sensing, for controlling gene expression in response to population density. Recently, this phenomenon has been discovered in Escherichia coli, and while pathogenicE. coli utilize quorum sensing to regulate pathogenesis (i.e., expression of virulence genes), the role of quorum sensing in nonpathogenic E. coli is less clear, and in particular, there is no information regarding the role of quorum sensing during the overexpression of recombinant proteins. The production of autoinducer AI-2, a signaling molecule employed by E. coli for intercellular communication, was studied in E. coli W3110 chemostat cultures using a Vibrio harveyi AI-2 reporter assay (M. G. Surrette and B. L. Bassler, Proc. Natl. Acad. Sci. USA 95:7046–7050, 1998). Chemostat cultures enabled a study of AI-2 regulation through steady-state and transient responses to a variety of environmental stimuli. Results demonstrated that AI-2 levels increased with the steady-state culture growth rate. In addition, AI-2 increased following pulsed addition of glucose, Fe(III), NaCl, and dithiothreitol and decreased following aerobiosis, amino acid starvation, and isopropyl-β-d-thiogalactopyranoside-induced expression of human interleukin-2 (hIL-2). In general, the AI-2 responses to several perturbations were indicative of a shift in metabolic activity or state of the cells induced by the individual stress. Because of our interest in the expression of heterologous proteins in E. coli, the transcription of four quorum-regulated genes and 20 stress genes was mapped during the transient response to induced expression of hIL-2. Significant regulatory overlap was revealed among several stress and starvation genes and known quorum-sensing genes.

scholarly journals Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays

2003 ◽  
Vol 185 (6) ◽  
pp. 1831-1840 ◽  
Author(s):  
Ulrich Dobrindt ◽  
Franziska Agerer ◽  
Kai Michaelis ◽  
Andreas Janka ◽  
Carmen Buchrieser ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Dna Sequences ◽  
Bacterial Genome ◽  
Distributional Pattern ◽  
Dna Arrays ◽  
E Coli ◽  
Dna Elements ◽  
Presence And Absence ◽  
K 12

ABSTRACT Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.

Sign in / Sign up

Export Citation Format

Share Document