scholarly journals Identification and Characterization of the Locus for Diffuse Adherence, Which Encodes a Novel Afimbrial Adhesin Found in Atypical Enteropathogenic Escherichia coli

2005 ◽  
Vol 73 (8) ◽  
pp. 4753-4765 ◽  
Author(s):  
Isabel C. A. Scaletsky ◽  
Jane Michalski ◽  
Alfredo G. Torres ◽  
Michelle V. Dulguer ◽  
James B. Kaper
Keyword(s):  
Escherichia Coli ◽  
Genomic Region ◽  
Open Reading Frames ◽  
E Coli ◽  
Atypical Epec ◽  
Structural Subunit ◽  
K 12 ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT The O26 serogroup of enteropathogenic Escherichia coli (EPEC) is one of the serogroups most frequently implicated in infant diarrhea and is also common among enterohemorrhagic E. coli (EHEC) strains. The most common O26 strains belong to EPEC/EHEC serotype O26:H11 and are generally Shiga toxin (Stx) positive. Stx-negative E. coli strains that are negative for the EPEC EAF plasmid and bundle-forming pilus (Bfp) are classified as atypical EPEC. Here, we report a novel adhesin present in an stx-negative bfpA-negative atypical EPEC O26:H11 strain isolated from an infant with diarrhea. A cloned 15-kb genomic region from this strain, designated the locus for diffuse adherence (lda), confers diffuse adherence on HEp-2 cells when expressed in E. coli K-12. Sequence analysis of lda revealed a G+C content of 46.8% and 15 open reading frames sharing homology with the E. coli K88 fae and CS31A clp fimbrial operons. The lda region is part of a putative 26-kb genomic island inserted into the proP gene of the E. coli chromosome. Hybridization studies have demonstrated the prevalence of the minor structural subunit gene, ldaH, across E. coli serogroups O5, O26, O111, and O145. A second plasmid-encoded factor that contributed to the Hep-2 adherence of this strain was also identified but was not characterized. Null mutations that abolish adherence to HEp-2 cells can be restored by plasmid complementation. Antiserum raised against the major structural subunit, LdaG, recognizes a 25-kDa protein from crude heat-extracted protein preparations and inhibits the adherence of the E. coli DH5α lda + clone to HEp-2 cells. Electron microscopy revealed a nonfimbrial structure surrounding the bacterial cell.

scholarly journals afa-8 Gene Cluster Is Carried by a Pathogenicity Island Inserted into the tRNAPhe of Human and Bovine Pathogenic Escherichia coli Isolates

2001 ◽  
Vol 69 (2) ◽  
pp. 937-948 ◽  
Author(s):  
Lila Lalioui ◽  
Chantal Le Bouguénec
Keyword(s):  
Escherichia Coli ◽  
Direct Repeat ◽  
Pathogenicity Island ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Blood Isolate ◽  
Distinctive Features ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
K 12

ABSTRACT We recently described a new afimbrial adhesin, AfaE-VIII, produced by animal strains associated with diarrhea and septicemia and by human isolates associated with extraintestinal infections. Here, we report that the afa-8 operon, encoding AfaE-VIII adhesin, from the human blood isolate Escherichia coli AL862 is carried by a 61-kb genomic region with characteristics typical of a pathogenicity island (PAI), including a size larger than 10 kb, the presence of an integrase-encoding gene, the insertion into a tRNA locus (pheR), and the presence of a small direct repeat at each extremity. Moreover, the G+C content of the afa-8 operon (46.4%) is lower than that of the E. coli K-12/MG1655 chromosome (50.8%). Within this PAI, designated PAI IAL862, we identified open reading frames able to code for products similar to proteins involved in sugar utilization. Four probes spanning these sequences hybridized with 74.3% of pathogenicafa-8-positive E. coli strains isolated from humans and animals, 25% of human pathogenic afa-8-negativeE. coli strains, and only 8% of fecal strains (P = 0.05), indicating that these sequences are strongly associated with the afa-8 operon and that this genetic association may define a PAI widely distributed among human and animal afa-8-positive strains. One of the distinctive features of this study is that E. coli AL862 also carries another afa-8-containing PAI (PAI IIAL862), which appeared to be similar in size and genetic organization to PAI IAL862 and was inserted into the pheV gene. We investigated the insertion sites of afa-8-containing PAI in human and bovine pathogenic E. coli strains and found that this PAI preferentially inserted into the pheV gene.

scholarly journals Identification and Characterization of a New Lipoprotein, NlpI, in Escherichia coli K-12

1999 ◽  
Vol 181 (14) ◽  
pp. 4318-4325 ◽  
Author(s):  
Masaru Ohara ◽  
Henry C. Wu ◽  
Krishnan Sankaran ◽  
Paul D. Rick
Keyword(s):  
Escherichia Coli ◽  
Direct Consequence ◽  
Insertion Mutant ◽  
Polynucleotide Phosphorylase ◽  
Wild Type ◽  
E Coli ◽  
K 12 ◽  
Identification And Characterization ◽  
Lines Of Evidence

ABSTRACT We report here the identification of a new lipoprotein, NlpI, inEscherichia coli K-12. The NlpI structural gene (nlpI) is located between the genes pnp(polynucleotide phosphorylase) and deaD (RNA helicase) at 71 min on the E. coli chromosome. The nlpI gene encodes a putative polypeptide of approximately 34 kDa, and multiple lines of evidence clearly demonstrate that NlpI is indeed a lipoprotein. An nlpI::cm mutation rendered growth of the cells osmotically sensitive, and incubation of the insertion mutant at an elevated temperature resulted in the formation of filaments. The altered phenotype of the mutant was a direct consequence of the mutation in nlpI, since it was complemented by the wild-type nlpI gene alone. Overexpression of the unaltered nlpI gene in wild-type cells resulted in the loss of the rod morphology and the formation of single prolate ellipsoids and pairs of prolate ellipsoids joined by partial constrictions. NlpI may be important for an as-yet-undefined step in the overall process of cell division.

scholarly journals The Iron- and Temperature-RegulatedcjrBC Genes of Shigella and Enteroinvasive Escherichia coli Strains Code for Colicin Js Uptake

2001 ◽  
Vol 183 (13) ◽  
pp. 3958-3966 ◽  
Author(s):  
David Šmajs ◽  
George M. Weinstock
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frames ◽  
Cosmid Library ◽  
E Coli ◽  
Order Of Magnitude ◽  
Fur Protein ◽  
The Difference ◽  
K 12 ◽  
Reading Frames ◽  
Made In

ABSTRACT A cosmid library of DNA from colicin Js-sensitive enteroinvasiveEscherichia coli (EIEC) strain O164 was made in colicin Js-resistant strain E. coli VCS257, and colicin Js-sensitive clones were identified. Sensitivity to colicin Js was associated with the carriage of a three-gene operon upstream of and partially overlapping senB. The open reading frames were designated cjrABC (for colicin Js receptor), coding for proteins of 291, 258, and 753 amino acids, respectively. Tn7 insertions in any of them led to complete resistance to colicin Js. A near-consensus Fur box was found upstream ofcjrA, suggesting regulation of the cjroperon by iron levels. CjrA protein was homologous to iron-regulatedPseudomonas aeruginosa protein PhuW, whose function is unknown; CjrB was homologous to the TonB protein fromPseudomonas putida; and CjrC was homologous to a putative outer membrane siderophore receptor from Campylobacter jejuni. Cloning experiments showed that the cjrBand cjrC genes are sufficient for colicin Js sensitivity. Uptake of colicin Js into sensitive bacteria was dependent on the ExbB protein but not on the E. coli K-12 TonB and TolA, -B, and -Q proteins. Sensitivity to colicin Js is positively regulated by temperature via the VirB protein and negatively controlled by the iron source through the Fur protein. Among EIEC strains, two types of colicin Js-sensitive phenotypes were identified that differed in sensitivity to colicin Js by 1 order of magnitude. The difference in sensitivity to colicin Js is not due to differences between the sequences of the CjrB and CjrC proteins.

scholarly journals Identification and Characterization of Spontaneous Deletions within the Sp11-Sp12 Prophage Region of Escherichia coli O157:H7 Sakai

2013 ◽  
Vol 79 (6) ◽  
pp. 1934-1941 ◽  
Author(s):  
Chun Chen ◽  
Carrie R. Lewis ◽  
Kakolie Goswami ◽  
Elisabeth L. Roberts ◽  
Chitrita DebRoy ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Iii Secretion ◽  
Genomic Region ◽  
Escherichia Coli O157 ◽  
Content Type ◽  
E Coli ◽  
Food Borne ◽  
Genes Encoding ◽  
Identification And Characterization

ABSTRACTProphages make up 12% of the enterohemorrhagicEscherichia coligenome and play prominent roles in the evolution and virulence of this food-borne pathogen. Acquisition and loss of and rearrangements within prophage regions are the primary causes of differences in pulsed-field gel electrophoresis (PFGE) patterns among strains ofE. coliO157:H7. Sp11 and Sp12 are two tandemly integrated and putatively defective prophages carried byE. coliO157:H7 strain Sakai. In this study, we identified 3 classes of deletions that occur within the Sp11-Sp12 region, at a frequency of ca. 7.74 × 10−4. One deletion resulted in a precise excision of Sp11, and the other two spanned the junction of Sp11 and Sp12. All deletions resulted in shifts in the XbaI fragment pattern observed by PFGE. We sequenced the inducible prophage pool of Sakai but did not identify any mature phage particles corresponding to either Sp11 or Sp12. Deletions containingpchBandpsrC, which are Sp11-carried genes encoding proteins known or suspected to regulate type III secretion, did not affect the secretion levels of the EspA or EspB effector. Alignment of the Sp11-Sp12 DNA sequence with its corresponding regions in otherE. coliO157:H7 and O55:H7 strains suggested that homologous recombination rather than integrase-mediated excision is the mechanism behind these deletions. Therefore, this study provides a mechanism behind the previously observed genetic instability of this genomic region ofE. coliO157:H7.

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.

scholarly journals Differential Expression of over 60 Chromosomal Genes in Escherichia coli by Constitutive Expression of MarA

2000 ◽  
Vol 182 (12) ◽  
pp. 3467-3474 ◽  
Author(s):  
Teresa M. Barbosa ◽  
Stuart B. Levy
Keyword(s):  
Escherichia Coli ◽  
Northern Blot Analysis ◽  
Constitutive Expression ◽  
Complete Characterization ◽  
Open Reading Frames ◽  
Altered Expression ◽  
E Coli ◽  
Chromosomal Genes ◽  
Reading Frames

ABSTRACT In Escherichia coli, the MarA protein controls expression of multiple chromosomal genes affecting resistance to antibiotics and other environmental hazards. For a more-complete characterization of the mar regulon, duplicate macroarrays containing 4,290 open reading frames of the E. coli genome were hybridized to radiolabeled cDNA populations derived frommar-deleted and mar-expressing E. coli. Strains constitutively expressing MarA showed altered expression of more than 60 chromosomal genes: 76% showed increased expression and 24% showed decreased expression. Although some of the genes were already known to be MarA regulated, the majority were newly determined and belonged to a variety of functional groups. Some of the genes identified have been associated with iron transport and metabolism; other genes were previously known to be part of thesoxRS regulon. Northern blot analysis of selected genes confirmed the results obtained with the macroarrays. The findings reveal that the mar locus mediates a global stress response involving one of the largest networks of genes described.

scholarly journals A Gene Encoding l-Methionine γ-Lyase Is Present in Enterobacteriaceae Family Genomes: Identification and Characterization of Citrobacter freundiil-Methionine γ-Lyase

2005 ◽  
Vol 187 (11) ◽  
pp. 3889-3893 ◽  
Author(s):  
Ilya V. Manukhov ◽  
Daria V. Mamaeva ◽  
Sergei M. Rastorguev ◽  
Nicolai G. Faleev ◽  
Elena A. Morozova ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
High Sequence Identity ◽  
E Coli ◽  
The Family ◽  
Serovar Typhimurium ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Citrobacter freundii cells produce l-methionine γ-lyase when grown on a medium containing l-methionine. The nucleotide sequence of the hybrid plasmid with a C. freundii EcoRI insert of about 3.0 kbp contained two open reading frames, consisting of 1,194 nucleotides and 1,296 nucleotides, respectively. The first one (denoted megL) encoded l-methionine γ-lyase. The enzyme was overexpressed in Escherichia coli and purified. The second frame encoded a protein belonging to the family of permeases. Regions of high sequence identity with the 3′-terminal part of the C. freundii megL gene located in the same regions of Salmonella enterica serovar Typhimurium, Shigella flexneri, E. coli, and Citrobacter rodentium genomes were found.

scholarly journals Identification and Characterization of a Novel ABC Iron Transport System, fit, in Escherichia coli

2006 ◽  
Vol 74 (12) ◽  
pp. 6949-6956 ◽  
Author(s):  
Zhiming Ouyang ◽  
Richard Isaacson
Keyword(s):  
Escherichia Coli ◽  
Growth Promotion ◽  
Hypothetical Protein ◽  
Bidirectional Promoter ◽  
Intracellular Iron ◽  
E Coli ◽  
K 12 ◽  
Identification And Characterization

ABSTRACT A putative ABC transporter, fit, with significant homology to several bacterial iron transporters was identified in Escherichia coli. The E. coli fit system consists of six genes designated fitA, -B, -C, -D, -E, and -R. Based on DNA sequence analysis, fit encodes an outer membrane protein (FitA), a periplasmic binding protein (FitE), two permease proteins (FitC and -D), an ATPase (FitB), and a hypothetical protein (FitR). Introduction of the E. coli fit system into E. coli strain K-12 increased intracellular iron content and transformed bacteria were more sensitive to streptonigrin, which suggested that fit transports iron in E. coli. Expression of fit was studied using a lacZ reporter assay. A functional, bidirectional promoter was identified in the intergenic region between genes fitA and fitB. The expression of the E. coli fit system was found to be induced by iron limitation and repressed when Fe2+ was added to minimal medium. Several fit mutants were created in E. coli using an in vitro transposon mutagenesis strategy. Mutations in fit did not affect bacterial growth in iron-restricted media. Using a growth promotion test, it was found that fit was not able to transport enterobactin, ferrichrome, transferrin, and lactoferrin in E. coli.

scholarly journals Genomic Interspecies Microarray Hybridization: Rapid Discovery of Three Thousand Genes in the Maize Endophyte,Klebsiella pneumoniae 342, by Microarray Hybridization with Escherichia coli K-12 Open Reading Frames

2001 ◽  
Vol 67 (4) ◽  
pp. 1911-1921 ◽  
Author(s):  
Yuemei Dong ◽  
Jeremy D. Glasner ◽  
Frederick R. Blattner ◽  
Eric W. Triplett
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Acid Metabolism ◽  
Open Reading Frames ◽  
Regulatory Proteins ◽  
Close Relative ◽  
Microarray Hybridization ◽  
E Coli ◽  
K 12 ◽  
Reading Frames

ABSTRACT In an effort to efficiently discover genes in the diazotrophic endophyte of maize, Klebsiella pneumoniae 342, DNA from strain 342 was hybridized to a microarray containing 96% (n = 4,098) of the annotated open reading frames fromEscherichia coli K-12. Using a criterion of 55% identity or greater, 3,000 (70%) of the E. coli K-12 open reading frames were also found to be present in strain 342. Approximately 24% (n = 1,030) of the E. coli K-12 open reading frames are absent in strain 342. For 1.6% (n= 68) of the open reading frames, the signal was too low to make a determination regarding the presence or absence of the gene. Genes with high identity between the two organisms are those involved in energy metabolism, amino acid metabolism, fatty acid metabolism, cofactor synthesis, cell division, DNA replication, transcription, translation, transport, and regulatory proteins. Functions that were less highly conserved included carbon compound metabolism, membrane proteins, structural proteins, putative transport proteins, cell processes such as adaptation and protection, and central intermediary metabolism. Open reading frames of E. coli K-12 with little or no identity in strain 342 included putative regulatory proteins, putative chaperones, surface structure proteins, mobility proteins, putative enzymes, hypothetical proteins, and proteins of unknown function, as well as genes presumed to have been acquired by lateral transfer from sources such as phage, plasmids, or transposons. The results were in agreement with the physiological properties of the two strains. Whole genome comparisons by genomic interspecies microarray hybridization are shown to rapidly identify thousands of genes in a previously uncharacterized bacterial genome provided that the genome of a close relative has been fully sequenced. This approach will become increasingly more useful as more full genome sequences become available.

scholarly journals Identification and Characterization ofaarF, a Locus Required for Production of Ubiquinone inProvidencia stuartii and Escherichia coli and for Expression of 2′-N-Acetyltransferase inP. stuartii

1998 ◽  
Vol 180 (1) ◽  
pp. 128-135 ◽  
Author(s):  
David R. Macinga ◽  
Gregory M. Cook ◽  
Robert K. Poole ◽  
Philip N. Rather
Keyword(s):  
Escherichia Coli ◽  
Regulation Of Gene Expression ◽  
Open Reading Frames ◽  
Mrna Levels ◽  
E Coli ◽  
Providencia Stuartii ◽  
High Level ◽  
Identification And Characterization ◽  
Reading Frames ◽  
Level Resistance

ABSTRACT Providencia stuartii contains a chromosomal 2′-N-acetyltransferase [AAC(2′)-Ia] involved in the O acetylation of peptidoglycan. The AAC(2′)-Ia enzyme is also capable of acetylating and inactivating certain aminoglycosides and confers high-level resistance to these antibiotics when overexpressed. We report the identification of a locus in P. stuartii, designated aarF, that is required for the expression of AAC(2′)-Ia. Northern (RNA) analysis demonstrated thataac(2′)-Ia mRNA levels were dramatically decreased in aP. stuartii strain carrying anaarF::Cm disruption. TheaarF::Cm disruption also resulted in a deficiency in the respiratory cofactor ubiquinone. The aarF locus encoded a protein that had a predicted molecular mass of 62,559 Da and that exhibited extensive amino acid similarity to the products of two adjacent open reading frames of unknown function (YigQ and YigR), located at 86 min on the Escherichia coli chromosome. AnE. coli yigR::Kan mutant was also deficient in ubiquinone content. Complementation studies demonstrated that theaarF and the E. coli yigQR loci were functionally equivalent. The aarF or yigQRgenes were unable to complement ubiD and ubiEmutations that are also present at 86 min on the E. colichromosome. This result indicates that aarF(yigQR) represents a novel locus for ubiquinone production and reveals a previously unreported connection between ubiquinone biosynthesis and the regulation of gene expression.

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