Characterization of the AggR Regulon in Enteroaggregative Escherichia coli

AggR is a transcriptional regulator of enteroaggregativeEscherichia coli(EAEC) and has been proposed as the defining factor for typical EAEC strains. Expression of multiple putative virulence factors, including the aggregative adherence fimbriae (AAF), dispersin, the dispersin translocator Aat, and the Aai type VI secretion system, have been found to be regulated by AggR. Here, we confirm the existence of at least 44 AggR-regulated genes using DNA microarray and real-time quantitative reverse transcription-PCR (qRT-PCR); these genes include chromosomal and plasmid-borne loci and 19 previously unsuspected genes. Two previously uncharacterized virulence plasmid-encoded open reading frames (ORFs) (designated ORF3 and ORF4) exhibit significant identity with isoprenoid biosynthesis genes ofBacteriaandArchaea. The predicted ORF4 product is closely related to isopentenyl isomerase (IDI) enzymes, whereas the predicted product of the adjacent ORF3 exhibits an aspartate-rich region that is common amongtrans-isoprenyl phosphate synthases. We show that mutations in these ORFs confer changes in bacterial surface properties. AggR coordinately controls expression of a large number of EAEC genes.

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Characterization of Two Virulent Phages of Lactobacillus plantarum

Applied and Environmental Microbiology ◽

10.1128/aem.02565-12 ◽

2012 ◽

Vol 78 (24) ◽

pp. 8719-8734 ◽

Cited By ~ 27

Author(s):

Mariángeles Briggiler Marcó ◽

Josiane E. Garneau ◽

Denise Tremblay ◽

Andrea Quiberoni ◽

Sylvain Moineau

Keyword(s):

Lactobacillus Plantarum ◽

Corn Silage ◽

Open Reading Frames ◽

High Identity ◽

Content Type ◽

Defense Systems ◽

Double Stranded Dna ◽

Type Phage ◽

Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

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Fur-Dam Regulatory Interplay at an Internal Promoter of the Enteroaggregative Escherichia coli Type VI Secretion sci1 Gene Cluster

Journal of Bacteriology ◽

10.1128/jb.00075-20 ◽

2020 ◽

Vol 202 (10) ◽

Cited By ~ 3

Author(s):

Yannick R. Brunet ◽

Christophe S. Bernard ◽

Eric Cascales

Keyword(s):

Escherichia Coli ◽

Gene Cluster ◽

Gene Clusters ◽

Secretion System ◽

Target Cells ◽

Type Vi Secretion System ◽

Content Type ◽

Internal Promoter ◽

E Coli ◽

Type Vi Secretion

ABSTRACT The type VI secretion system (T6SS) is a weapon for delivering effectors into target cells that is widespread in Gram-negative bacteria. The T6SS is a highly versatile machine, as it can target both eukaryotic and prokaryotic cells, and it has been proposed that T6SSs are adapted to the specific needs of each bacterium. The expression of T6SS gene clusters and the activation of the secretion apparatus are therefore tightly controlled. In enteroaggregative Escherichia coli (EAEC), the sci1 T6SS gene cluster is subject to a complex regulation involving both the ferric uptake regulator (Fur) and DNA adenine methylase (Dam)-dependent DNA methylation. In this study, an additional, internal, promoter was identified within the sci1 gene cluster using +1 transcriptional mapping. Further analyses demonstrated that this internal promoter is controlled by a mechanism strictly identical to that of the main promoter. The Fur binding box overlaps the −10 transcriptional element and a Dam methylation site, GATC-32. Hence, the expression of the distal sci1 genes is repressed and the GATC-32 site is protected from methylation in iron-rich conditions. The Fur-dependent protection of GATC-32 was confirmed by an in vitro methylation assay. In addition, the methylation of GATC-32 negatively impacted Fur binding. The expression of the sci1 internal promoter is therefore controlled by iron availability through Fur regulation, whereas Dam-dependent methylation maintains a stable ON expression in iron-limited conditions. IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Its expression and activation therefore need to be tightly regulated. Here, we identified an internal promoter within the sci1 T6SS gene cluster in enteroaggregative E. coli. We show that this internal promoter is controlled by Fur and Dam-dependent methylation. We further demonstrate that Fur and Dam compete at the −10 transcriptional element to finely tune the expression of T6SS genes. We propose that this elegant regulatory mechanism allows the optimum production of the T6SS in conditions where enteroaggregative E. coli encounters competing species.

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Genome Sequence of a T4-like Phage, Escherichia Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing Escherichia coli Strains

Microbiology Resource Announcements ◽

10.1128/mra.00804-19 ◽

2019 ◽

Vol 8 (32) ◽

Author(s):

Yen-Te Liao ◽

Yujie Zhang ◽

Alexandra Salvador ◽

Vivian C. H. Wu

Keyword(s):

Escherichia Coli ◽

Surface Water ◽

Genome Size ◽

Shiga Toxin ◽

Open Reading Frames ◽

Content Type ◽

E Coli ◽

Double Stranded Dna ◽

A Genome ◽

Reading Frames

Escherichia phage vB_EcoM-Sa45lw, a new member of the T4-like phages, was isolated from surface water in a produce-growing area. The phage, containing double-stranded DNA with a genome size of 167,353 bp and 282 predicted open reading frames (ORFs), is able to infect generic Escherichia coli and Shiga toxin-producing E. coli O45 and O157 strains.

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Characterization of the Enterobacter Phage vB_EclM_CIP9

Microbiology Resource Announcements ◽

10.1128/mra.01600-19 ◽

2020 ◽

Vol 9 (13) ◽

Author(s):

Klara Wang ◽

Marielou G. Tamayo ◽

Tiffany V. Penner ◽

Bradley W. M. Cook ◽

Deborah A. Court ◽

...

Keyword(s):

Enterobacter Cloacae ◽

Opportunistic Pathogen ◽

Multidrug Resistant ◽

Open Reading Frames ◽

Resistant Isolate ◽

Content Type ◽

Hospital Acquired Infections ◽

Hospital Acquired ◽

Reading Frames

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

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Complete Genome Sequence of Salmonella Bacteriophage SS3e

Journal of Virology ◽

10.1128/jvi.01550-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10253-10254 ◽

Cited By ~ 12

Author(s):

Sung-Hun Kim ◽

Jeong-Hyun Park ◽

Bok-Kwon Lee ◽

Hyuk-Joon Kwon ◽

Ji-Hyun Shin ◽

...

Keyword(s):

Escherichia Coli ◽

Sequence Analysis ◽

Genomic Sequence ◽

Enterobacter Cloacae ◽

Open Reading Frames ◽

Lytic Bacteriophage ◽

Content Type ◽

Double Stranded Dna ◽

Genomic Sequence Analysis ◽

Reading Frames

ASalmonellalytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only variousSalmonellaserovars but alsoEscherichia coli,Shigella sonnei,Enterobacter cloacae, andSerratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar toSalmonellaphages SETP13 and MB78.

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Genomewide Overexpression Screen for Fosfomycin Resistance in Escherichia coli: MurA Confers Clinical Resistance at Low Fitness Cost

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.06122-11 ◽

2012 ◽

Vol 56 (5) ◽

pp. 2767-2769 ◽

Cited By ~ 34

Author(s):

Alejandro Couce ◽

Alejandra Briales ◽

Alexandro Rodríguez-Rojas ◽

Coloma Costas ◽

Álvaro Pascual ◽

...

Keyword(s):

Escherichia Coli ◽

Fitness Cost ◽

Open Reading Frames ◽

Content Type ◽

Clinical Level ◽

Clinical Resistance ◽

Chromosomal Genes ◽

Complete Set ◽

Fosfomycin Resistance ◽

Reading Frames

ABSTRACTTo determine whether the overexpression of chromosomal genes can confer fosfomycin resistance, genomewide screening of a complete set of 5,272 plasmid-expressed open reading frames ofEscherichia coli(ASKA collection) was performed. Major results are that (i) no clinical level of resistance is achieved by overexpressing chromosomal genes, exceptmurA; (ii) this level is reached at a low fitness cost; and (iii) this cost is much lower than that imposed by other mutations conferring fosfomycin resistance.

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Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase

Applied and Environmental Microbiology ◽

10.1128/aem.68.11.5671-5684.2002 ◽

2002 ◽

Vol 68 (11) ◽

pp. 5671-5684 ◽

Cited By ~ 87

Author(s):

Hiroaki Iwaki ◽

Yoshie Hasegawa ◽

Shaozhao Wang ◽

Margaret M. Kayser ◽

Peter C. K. Lau

Keyword(s):

Escherichia Coli ◽

Regulatory Gene ◽

Regulatory Elements ◽

Open Reading Frames ◽

Chromosomal Locus ◽

New Genes ◽

Transcriptional Units ◽

Acid Catalyzed ◽

Reading Frames

ABSTRACT Cyclopentanone 1,2-monooxygenase, a flavoprotein produced by Pseudomonas sp. strain NCIMB 9872 upon induction by cyclopentanol or cyclopentanone (M. Griffin and P. W. Trudgill, Biochem. J. 129:595-603, 1972), has been utilized as a biocatalyst in Baeyer-Villiger oxidations. To further explore this biocatalytic potential and to discover new genes, we have cloned and sequenced a 16-kb chromosomal locus of strain 9872 that is herein reclassified as belonging to the genus Comamonas. Sequence analysis revealed a cluster of genes and six potential open reading frames designated and grouped in at least four possible transcriptional units as (orf11-orf10-orf9)-(cpnE-cpnD-orf6-cpnC)-(cpnR-cpnB-cpnA)-(orf3-orf4 [partial 3′ end]). The cpnABCDE genes encode enzymes for the five-step conversion of cyclopentanol to glutaric acid catalyzed by cyclopentanol dehydrogenase, cyclopentanone 1,2-monooxygenase, a ring-opening 5-valerolactone hydrolase, 5-hydroxyvalerate dehydrogenase, and 5-oxovalerate dehydrogenase, respectively. Inactivation of cpnB by using a lacZ-Kmr cassette resulted in a strain that was not capable of growth on cyclopentanol or cyclopentanone as a sole carbon and energy source. The presence of σ54-dependent regulatory elements in front of the divergently transcribed cpnB and cpnC genes supports the notion that cpnR is a regulatory gene of the NtrC type. Knowledge of the nucleotide sequence of the cpn genes was used to construct isopropyl-β-thio-d-galactoside-inducible clones of Escherichia coli cells that overproduce the five enzymes of the cpn pathway. The substrate specificities of CpnA and CpnB were studied in particular to evaluate the potential of these enzymes and establish the latter recombinant strain as a bioreagent for Baeyer-Villiger oxidations. Although frequently nonenantioselective, cyclopentanone 1,2-monooxygenase was found to exhibit a broader substrate range than the related cyclohexanone 1,2-monooxygenase from Acinetobacter sp. strain NCIMB 9871. However, in a few cases opposite enantioselectivity was observed between the two biocatalysts.

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Genetic Characterization of Plasmid-Borne blaOXA-58 in Distinct Acinetobacter Species

mSphere ◽

10.1128/msphere.00376-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 10

Author(s):

Adriana P. Matos ◽

Rodrigo Cayô ◽

Luiz G. P. Almeida ◽

Ana Paula Streling ◽

Carolina S. Nodari ◽

...

Keyword(s):

Open Reading Frames ◽

South American ◽

Acinetobacter Species ◽

Content Type ◽

Clinical Strains ◽

Carbapenem Resistant ◽

Encoding Genes ◽

Reading Frames ◽

Over Time

ABSTRACT We characterize by whole-plasmid-sequence (WPS) two-plasmid-borne blaOXA-58 obtained from Acinetobacter seifertii (Asp-1069) and A. baumannii (Acb-45063) clinical strains recovered 17 years apart from distinct Brazilian regions. Multilocus sequence type (MLST) analysis showed that the Asp-1069 and Acb-45063 strains belong to ST551 and ST15/CC15, respectively. WPS analysis demonstrated that blaOXA-58 was located in two distinct plasmids named pAs1069_a (24,672 bp/44 open reading frames [ORFs]) and pAb45063_b (19,808 bp/24 ORFs), which belong to the GR8/GR23 (repAci23) and GR4 (repAci4) incompatibility groups, respectively. The genetic environments surrounding blaOXA-58 revealed that it was flanked by two intact ISAba3 copies on pAb45063_b, which differed from pAs1069_a. In the latter, the upstream ISAba3 copy was truncated by insertion of ISAba825 element. Although Re27-specific recombination sites were found adjacent to ISAba3-blaOXA-58-ISAba3 arrangement on pAb45063_b, such structures were absent on pAs1069_a. The conserved ISAba125-araC1-lysE arrangement was disrupted by TnaphA6 harboring the aminoglycosides resistance gene aphA6 on pAs1069_a, while an IS26-blaTEM-1-aac(3)-IIa-IS26 genetic structure was found upstream from ISAba3-blaOXA-58-ISAba3 on pAb45063_b. Other two plasmids, pAb45063_a (183,767 bp/209 ORFs) and pAs1069_b (13,129 bp/14 ORFs), were also found in the OXA-58-producing Acinetobacter species strains, harboring the strA and strB genes and the sul2 gene, which confer resistance to streptomycin and sulfonamides, respectively. The plasmid-mediated virulence factors corresponding to genes tonB, spl, glmM, ppa, sulP, and map were found in both strains, as well distinct toxin-antitoxin system-encoding genes stbD and relE (pAs1069_a), brnT and brnA (pAb45063_b), and xreE (pAb45063_a). Although infrequently reported in Brazil, plasmid-borne blaOXA-58 showed a complex and diverse genetic backbone that confers stability in different Acinetobacter species that have been isolated from nosocomial settings over time. IMPORTANCE Although the blaOXA-58 gene has been infrequently described in Brazil, contrasting with other bordering South American countries, we verified the maintenance of this resistance determinant over time among carbapenem-resistant Acinetobacter species isolates, not only in nosocomial settings but also in the environment. In addition, to the best of our knowledge, this is the first study to have used WPS analysis to evaluate the genetic surroundings of blaOXA-58 in Brazil. Moreover, the A. seifertii and A. baumannii clinical strains evaluated in this study were recovered 17 years apart in hospitals located in distinct Brazilian geographic regions.

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Characterization of a Novel Panton-Valentine Leukocidin (PVL)-Encoding Staphylococcal Phage and Its Naturally PVL-Lacking Variant

Applied and Environmental Microbiology ◽

10.1128/aem.03852-12 ◽

2013 ◽

Vol 79 (8) ◽

pp. 2828-2832 ◽

Cited By ~ 11

Author(s):

Lynn El Haddad ◽

Sylvain Moineau

Keyword(s):

Raw Milk ◽

Open Reading Frames ◽

Direct Repeats ◽

Content Type ◽

Genes Encoding ◽

Tail Protein ◽

Reading Frames ◽

Panton Valentine Leukocidin ◽

Valentine Leukocidin

ABSTRACTA new siphophage (LH1) was isolated from raw milk using aStaphylococcus aureusST352 host. Its genome (46,048 bp, 57 open reading frames) includes the two genes encoding Panton-Valentine leukocidin (PVL), a virulence factor usually harbored byS. aureusprophages. Nine structural proteins were identified, including a tail protein generated through a +1 frameshift. A phage lytic mutant was isolated, and its analysis revealed the deletion of genes coding for the PVL and an integrase. The deletion likely occurred through recombination between direct repeats.

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

Journal of Bacteriology ◽

10.1128/jb.182.12.3467-3474.2000 ◽

2000 ◽

Vol 182 (12) ◽

pp. 3467-3474 ◽

Cited By ~ 264

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.

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