scholarly journals A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants

2020 ◽  
Author(s):  
Ruben Monarrez ◽  
Iruka Okeke
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genetic Basis ◽  
Mobile Element ◽  
Enteric Bacteria ◽  
Selective Advantage ◽  
Open Reading Frames ◽  
Bacterial Strains ◽  
Element Bearing ◽  
Reading Frames

Abstract Objective: Plasmids are key to antimicrobial resistance transmission among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper-autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid. Results: The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper-autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.

scholarly journals A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Rubén Monárrez ◽  
Iruka N. Okeke
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genetic Basis ◽  
Mobile Element ◽  
Enteric Bacteria ◽  
Selective Advantage ◽  
Open Reading Frames ◽  
Bacterial Strains ◽  
Element Bearing ◽  
Reading Frames

Abstract Objective Plasmids are key to antimicrobial resistance transmission among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper-autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid. Results The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper-autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.

scholarly journals A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants

2020 ◽  
Author(s):  
Ruben Monarrez ◽  
Iruka Okeke
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genetic Basis ◽  
Mobile Element ◽  
Enteric Bacteria ◽  
Selective Advantage ◽  
Open Reading Frames ◽  
Bacterial Strains ◽  
Element Bearing ◽  
Reading Frames

Abstract Objective: Plasmids are key to antimicrobial resistance transmission among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper-autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid. Results: The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper-autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.

scholarly journals A plasmid-encoded papB paralogue modulates autoaggregation of Escherichia coli transconjugants

2020 ◽  
Author(s):  
Ruben Monarrez ◽  
Iruka Okeke
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genetic Basis ◽  
Mobile Element ◽  
Enteric Bacteria ◽  
Selective Advantage ◽  
Open Reading Frames ◽  
Bacterial Strains ◽  
Element Bearing ◽  
Reading Frames

Abstract Objective: Plasmids are key to the transmission of antimicrobial resistance among enteric bacteria. It is becoming increasingly clear that resistance genes alone do not account for the selective advantage of plasmids and bacterial strains that harbor them. Deletion of a 32 Kb fitness-conferring region of pMB2, a conjugative resistance plasmid, produced a hyper­autoaggregation phenotype in laboratory Escherichia coli. This study sought to determine the genetic basis for hyper-autoaggregation conferred by the pMB2-derived mini-plasmid.Results: The 32 Kb fragment deleted from pMB2 included previously characterized nutrient acquisition genes as well as putative transposase and integrase genes, a 272 bp papB/ pefB-like gene, and several open-reading frames of unknown function. We cloned the papB/ pefB paralogue and found it sufficient to temper the hyper-autoaggregation phenotype. Hyper­autoaggregation conferred by the mini-plasmid did not occur in a fim-negative background. This study has identified and characterized a gene capable of down-regulating host adhesins and has shown that trans-acting papB/pefB paralogues can occur outside the context of an adhesin cluster. This plasmid-mediated modification of a bacterial host’s colonization program may optimize horizontal transfer of the mobile element bearing the genes.

scholarly journals Analysis of the Gene Cluster Encoding Toluene/o-Xylene Monooxygenase from Pseudomonas stutzeri OX1

1998 ◽  
Vol 64 (10) ◽  
pp. 3626-3632 ◽  
Author(s):  
Giovanni Bertoni ◽  
Manuela Martino ◽  
Enrica Galli ◽  
Paola Barbieri
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Dimethyl Sulfide ◽  
Pseudomonas Stutzeri ◽  
Open Reading Frames ◽  
Enzymatic System ◽  
Wild Type Allele ◽  
Wild Type ◽  
Bacterial Strains ◽  
Reading Frames

ABSTRACT The toluene/o-xylene monooxygenase cloned fromPseudomonas stutzeri OX1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. The nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. The sequence analysis revealed the presence of six open reading frames (ORFs) homologous to other genes clustered in operons coding for multicomponent monooxygenases found in benzene- and toluene-degradative pathways cloned from Pseudomonas strains. Significant similarities were also found with multicomponent monooxygenase systems for phenol, methane, alkene, and dimethyl sulfide cloned from different bacterial strains. The knockout of each ORF and complementation with the wild-type allele indicated that all six ORFs are essential for the full activity of the toluene/o-xylene monooxygenase inEscherichia coli. This analysis also shows that despite its activity on both hydrocarbons and phenols, toluene/ o-xylene monooxygenase belongs to a toluene multicomponent monooxygenase subfamily rather than to the monooxygenases active on phenols.

scholarly journals Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames.

1990 ◽  
Vol 172 (4) ◽  
pp. 1969-1977 ◽  
Author(s):  
N K Menon ◽  
J Robbins ◽  
H D Peck ◽  
C Y Chatelus ◽  
E S Choi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frames ◽  
Cloning And Sequencing ◽  
Reading Frames

scholarly journals A Novel DNA Polymerase Family Found inArchaea

1998 ◽  
Vol 180 (8) ◽  
pp. 2232-2236 ◽  
Author(s):  
Yoshizumi Ishino ◽  
Kayoko Komori ◽  
Isaac K. O. Cann ◽  
Yosuke Koga
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Pyrococcus Furiosus ◽  
Dna Polymerases ◽  
Open Reading Frames ◽  
Gene Products ◽  
Polymerase Gene ◽  
Hyperthermophilic Archaeon ◽  
Dna Polymerase Ii ◽  
Reading Frames

ABSTRACT One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical α-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeonPyrococcus furiosus, which has also at least one α-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499–512, 1997). The genes in M. jannaschiiencoding the proteins that are homologous to the DNA polymerase II ofP. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia colihad both DNA polymerizing and 3′→5′ exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.

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

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.

scholarly journals A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Adi Oron-Gottesman ◽  
Martina Sauert ◽  
Isabella Moll ◽  
Hanna Engelberg-Kulka
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Genetic Code ◽  
Open Reading Frames ◽  
Translation Machinery ◽  
E Coli ◽  
Universal Characteristic ◽  
Living Organisms ◽  
Reading Frames

ABSTRACT Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. IMPORTANCE The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in E. coli , under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.

scholarly journals Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map

1998 ◽  
Vol 62 (3) ◽  
pp. 985-1019 ◽  
Author(s):  
Kenneth E. Rudd
Keyword(s):  
Escherichia Coli ◽  
Physical Map ◽  
Restriction Enzymes ◽  
Open Reading Frames ◽  
Sequence Elements ◽  
Systematic Nomenclature ◽  
Repetitive Extragenic Palindrome ◽  
Complete Set ◽  
K 12 ◽  
Reading Frames

SUMMARY A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.

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