scholarly journals Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

2021 ◽  
Author(s):  
Adam J Hockenberry ◽  
David C Weaver ◽  
Claus O Wilke
Keyword(s):  
Host Cell ◽  
Translational Regulation ◽  
Recombinant Expression ◽  
Bacterial Species ◽  
Start Codon ◽  
Sequence Motif ◽  
E Coli ◽  
Shine Dalgarno Sequence ◽  
Host Genes ◽  
New Strategies

Bacteriophages rely almost exclusively on host-cell machinery to produce their proteins, and their mRNAs must therefore compete with host mRNAs for valuable translational resources. In many bacterial species, highly translated mRNAs are characterized by the presence of a Shine-Dalgarno sequence motif upstream of the start codon and weak secondary structure within the start codon region. However, the general constraints and principles underlying the translation of phage mRNAs are largely unknown. Here, we show that phage mRNAs are highly enriched in strong Shine-Dalgarno sequences and have comparatively weaker secondary structures in the start codon region than host-cell mRNAs. Phage mRNAs appear statistically similar to the most highly expressed host genes in E. coli according to both features, strongly suggesting that they initiate translation at particularly high rates. Interestingly, we find that these observations are driven largely by virulent phages and that temperate phages encode mRNAs with similar start codon features to their host genes. These findings apply broadly across a wide-diversity of host-species and phage genomes. Further study of phage translational regulation — with a particular emphasis on virulent phages — may provide new strategies for engineering phage genomes and recombinant expression systems more generally.

scholarly journals Actin Cytoskeleton Manipulation by Effector Proteins Secreted by DiarrheagenicEscherichia coliPathotypes

2013 ◽  
Vol 2013 ◽  
pp. 1-22 ◽  
Author(s):  
Fernando Navarro-Garcia ◽  
Antonio Serapio-Palacios ◽  
Paul Ugalde-Silva ◽  
Gabriela Tapia-Pastrana ◽  
Lucia Chavez-Dueñas
Keyword(s):  
Actin Cytoskeleton ◽  
Host Cell ◽  
Virulence Factors ◽  
Cell Biology ◽  
Bacterial Species ◽  
Effector Proteins ◽  
Actin Binding ◽  
E Coli ◽  
Tissue Organization ◽  
Epithelial Barriers

The actin cytoskeleton is a dynamic structure necessary for cell and tissue organization, including the maintenance of epithelial barriers. Disruption of the epithelial barrier coincides with alterations of the actin cytoskeleton in several disease states. These disruptions primarily affect the paracellular space, which is normally regulated by tight junctions. Thereby, the actin cytoskeleton is a common and recurring target of bacterial virulence factors. In order to manipulate the actin cytoskeleton, bacteria secrete and inject toxins and effectors to hijack the host cell machinery, which interferes with host-cell pathways and with a number of actin binding proteins. An interesting model to study actin manipulation by bacterial effectors isEscherichia colisince due to its genome plasticity it has acquired diverse genetic mobile elements, which allow having differentE. colivarieties in one bacterial species. TheseE. colipathotypes, including intracellular and extracellular bacteria, interact with epithelial cells, and their interactions depend on a specific combination of virulence factors. In this paper we focus onE. colieffectors that mimic host cell proteins to manipulate the actin cytoskeleton. The study of bacterial effector-cytoskeleton interaction will contribute not only to the comprehension of the molecular causes of infectious diseases but also to increase our knowledge of cell biology.

Isolation and Characterization of Levoglucosan Metabolizing Bacteria

2021 ◽  
Author(s):  
Ajay S. Arya ◽  
Minh T. H. Hang ◽  
Mark A. Eiteman
Keyword(s):  
Recombinant Expression ◽  
Bacterial Species ◽  
Soluble Carbohydrate ◽  
Rrna Gene ◽  
Gene Products ◽  
16S Rrna Gene Sequences ◽  
E Coli ◽  
Isolation And Characterization ◽  
Charred Wood

Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented diverse genera of Microbacterium, Paenibacillus , Shinella , and Klebsiella . Genomic sequencing of the isolates verified that two isolates represented novel species, Paenibacillus athensensis MEC069 T and Shinella sumterensis MEC087 T , while the remaining isolates were closely related to either Microbacterium lacusdiani or Klebsiella pneumoniae . The genetic sequence of LGDH, lgdA , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the P. phenanthrenivorans LGDH was experimentally verified following recombinant expression in E. coli . Comparison of the putative genes surrounding lgdA in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Importance Levoglucosan is the most prevalent soluble carbohydrate remaining after high temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae . A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species which degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria which metabolize levoglucosan.

scholarly journals Characterization of Two New Aminopeptidases in Escherichia coli

2005 ◽  
Vol 187 (11) ◽  
pp. 3671-3677 ◽  
Author(s):  
Yu Zheng ◽  
Richard J. Roberts ◽  
Simon Kasif ◽  
Chudi Guan
Keyword(s):  
Escherichia Coli ◽  
Stop Codon ◽  
Bacterial Species ◽  
Start Codon ◽  
Aminopeptidase Activity ◽  
Peptide Substrates ◽  
E Coli ◽  
Terminal Domain ◽  
Methionyl Aminopeptidase

ABSTRACT Two genes in the Escherichia coli genome, ypdE and ypdF, have been cloned and expressed, and their products have been purified. YpdF is shown to be a metalloenzyme with Xaa-Pro aminopeptidase activity and limited methionine aminopeptidase activity. Genes homologous to ypdF are widely distributed in bacterial species. The unique feature in the sequences of the products of these genes is a conserved C-terminal domain and a variable N-terminal domain. Full or partial deletion of the N terminus in YpdF leads to the loss of enzymatic activity. The conserved C-terminal domain is homologous to that of the methionyl aminopeptidase (encoded by map) in E. coli. However, YpdF and Map differ in their preference for the amino acid next to the initial methionine in the peptide substrates. The implication of this difference is discussed. ypdE is the immediate downstream gene of ypdF, and its start codon overlaps with the stop codon of ypdF by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity.

scholarly journals Investigation of the regulation of expression of E. Coli Common Pilus subunit, ECPA, of enterohaemorrhagic E. Coli 0157:H7 under acid stress

2021 ◽  
Author(s):  
Hannah Tollman
Keyword(s):  
Translational Regulation ◽  
Bacterial Species ◽  
Acid Stress ◽  
Regulation Of Expression ◽  
Western Blots ◽  
E Coli ◽  
Severe Diarrhea ◽  
Regulatory Systems ◽  
Uremic Syndrome ◽  
Isogenic Mutants

Escherichia coli (EHEC) 0157:H7 is a pathogenic bacterial species that is most commonly linked to severe diarrhea, but is also the leading cause of the potentially fatal hemolytic-uremic syndrome (HUS). In order to establish infection in the colon, EHEC must endure different stresses encountered in the gastrointestinal (GI) tract, such as acid stress in the stomach, bile salt stress in the small intestine, and short-chain fatty acid (SCFA) stress in the colon. These bacteria are likely able to use GI stresses as indicators of their location, impacting gene expression of adhesion, motility, and virulence factors. The E. coli Common Pilus (ECP) has been shown to be an important factor for EHEC adhesion to epithelial cells, which is increased after either acid or SCFA stress. It has also been demonstrated via microarray that genes of this operon are upregulated after acid stress. The aim of this study is to determine how expression of the main subunit of this structure, EcpA, is regulated upon exposure of EHEC 0157:H7 to acid or SCFA-stress. Both transcriptional and translational regulation are hypothesized to be involved. Isogenic mutants have been constructed that lacked key regulators suspected to be important for each system. Two approaches are used to determine if the predicted regulatory systems are playing a role in response to stress: observing EcpA protein expression analysis through Western blotting with anti-EcpA antibodies, and examining differences in ecp operon promoter activity in regulatory mutants. In this study Western blots reconfirmed H-NS does not modulate ecpA expression in direct response to acute acid stress. This suggests an alternate regulatory response in EHEC 0157:H7 to acute acid stress resulting in the upregulation of ecpA expression previously observed with microarray analysis.

scholarly journals Investigation of the regulation of expression of E. Coli Common Pilus subunit, ECPA, of enterohaemorrhagic E. Coli 0157:H7 under acid stress

2021 ◽  
Author(s):  
Hannah Tollman
Keyword(s):  
Translational Regulation ◽  
Bacterial Species ◽  
Acid Stress ◽  
Regulation Of Expression ◽  
Western Blots ◽  
E Coli ◽  
Severe Diarrhea ◽  
Regulatory Systems ◽  
Uremic Syndrome ◽  
Isogenic Mutants

Escherichia coli (EHEC) 0157:H7 is a pathogenic bacterial species that is most commonly linked to severe diarrhea, but is also the leading cause of the potentially fatal hemolytic-uremic syndrome (HUS). In order to establish infection in the colon, EHEC must endure different stresses encountered in the gastrointestinal (GI) tract, such as acid stress in the stomach, bile salt stress in the small intestine, and short-chain fatty acid (SCFA) stress in the colon. These bacteria are likely able to use GI stresses as indicators of their location, impacting gene expression of adhesion, motility, and virulence factors. The E. coli Common Pilus (ECP) has been shown to be an important factor for EHEC adhesion to epithelial cells, which is increased after either acid or SCFA stress. It has also been demonstrated via microarray that genes of this operon are upregulated after acid stress. The aim of this study is to determine how expression of the main subunit of this structure, EcpA, is regulated upon exposure of EHEC 0157:H7 to acid or SCFA-stress. Both transcriptional and translational regulation are hypothesized to be involved. Isogenic mutants have been constructed that lacked key regulators suspected to be important for each system. Two approaches are used to determine if the predicted regulatory systems are playing a role in response to stress: observing EcpA protein expression analysis through Western blotting with anti-EcpA antibodies, and examining differences in ecp operon promoter activity in regulatory mutants. In this study Western blots reconfirmed H-NS does not modulate ecpA expression in direct response to acute acid stress. This suggests an alternate regulatory response in EHEC 0157:H7 to acute acid stress resulting in the upregulation of ecpA expression previously observed with microarray analysis.

scholarly journals Escherichia coli HS and Enterotoxigenic Escherichia coli Hinder Stress Granule Assembly

2020 ◽  
Vol 9 (1) ◽  
pp. 17
Author(s):  
Felipe Velásquez ◽  
Josefina Marín-Rojas ◽  
Ricardo Soto-Rifo ◽  
Alexia Torres ◽  
Felipe Del Canto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Host Cell ◽  
Stress Responses ◽  
Bacterial Species ◽  
Coli Strain ◽  
Stress Granule ◽  
Enterotoxigenic Escherichia Coli ◽  
E Coli ◽  
Eif2α Phosphorylation ◽  
Successful Infection

Escherichia coli, one of the most abundant bacterial species in the human gut microbiota, has developed a mutualistic relationship with its host, regulating immunological responses. In contrast, enterotoxigenic E. coli (ETEC), one of the main etiologic agents of diarrheal morbidity and mortality in children under the age of five in developing countries, has developed mechanisms to reduce the immune-activator effect to carry out a successful infection. Following infection, the host cell initiates the shutting-off of protein synthesis and stress granule (SG) assembly. This is mostly mediated by the phosphorylation of translation initiator factor 2α (eIF2α). We therefore evaluated the ability of a non-pathogenic E. coli strain (E. coli HS) and an ETEC strain (ETEC 1766a) to induce stress granule assembly, even in response to exogenous stresses. In this work, we found that infection with E. coli HS or ETEC 1766a prevents SG assembly in Caco-2 cells treated with sodium arsenite (Ars) after infection. We also show that this effect occurs through an eIF2α phosphorylation (eIF2α-P)-dependent mechanism. Understanding how bacteria counters host stress responses will lay the groundwork for new therapeutic strategies to bolster host cell immune defenses against these pathogens.

Efficacy of Silver Nanoparticles Synthesized from Hymenocallis species (Spider Lilly) Leaf Extract as Antimicrobial Agents

2019 ◽  
Vol 12 (5) ◽  
pp. 4644-4647
Author(s):  
K.K. Gupta ◽  
Neha Kumari ◽  
Neha Sinha ◽  
Akruti Gupta
Keyword(s):  
Silver Nanoparticles ◽  
Leaf Extract ◽  
Antimicrobial Agents ◽  
Color Change ◽  
Bacterial Species ◽  
Antimicrobial Property ◽  
Biogenic Synthesis ◽  
E Coli ◽  
Light Yellow ◽  
Antibiotic Property

Biogenic synthesis of silver nanoparticles synthesized from Hymenocallis species (Spider Lilly) leaf extract was subjected for investigation of its antimicrobial property against four bacterial species (E. coli, Salmonella sp., Streptococcus sp. & Staphylococcus sp.). The results revealed that synthesized nanoparticles solution very much justify the color change property from initial light yellow to final reddish brown during the synthesis producing a characteristics absorption peak in the range of 434-466 nm. As antimicrobial agents, their efficacy was evaluated by analysis of variance in between the species and among the different concentration of AgNPs solution, which clearly showed that there was significant variation in the antibiotic property between the four different concentrations of AgNPs solution and also among four different species of bacteria taken under studies. However, silver nanoparticles solution of 1: 9 and 1:4 were proved comparatively more efficient as antimicrobial agents against four species of bacteria.

Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

2020 ◽  
Vol 20 (29) ◽  
pp. 2681-2691
Author(s):  
Athina Geronikaki ◽  
Victor Kartsev ◽  
Phaedra Eleftheriou ◽  
Anthi Petrou ◽  
Jasmina Glamočlija ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Drug Targets ◽  
Bacterial Species ◽  
Pharmaceutical Research ◽  
Docking Studies ◽  
Fungal Species ◽  
Docking Analysis ◽  
E Coli ◽  
Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

scholarly journals Evolution of Chi motifs in Proteobacteria

2021 ◽  
Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Large Dataset ◽  
High Sequence Similarity ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Motif ◽  
And Staphylococcus Aureus

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

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