scholarly journals Identifying Small Molecules That Promote Quasipalindrome-Associated Template-Switch Mutations in Escherichia coli

2020 ◽  
Vol 10 (5) ◽  
pp. 1809-1815 ◽  
Author(s):  
Julie A. Klaric ◽  
Eli L. Perr ◽  
Susan T. Lovett
Keyword(s):  
Escherichia Coli ◽  
Small Molecules ◽  
Mutational Event ◽  
Template Strand ◽  
Dna Repeat ◽  
Mutational Hotspots ◽  
Small Molecule Libraries ◽  
Disk Diffusion Assay ◽  
Switch Mechanism ◽  
Template Switch

DNA can assemble into non-B form structures that stall replication and cause genomic instability. One such secondary structure results from an inverted DNA repeat that can assemble into hairpin and cruciform structures during DNA replication. Quasipalindromes (QP), imperfect inverted repeats, are sites of mutational hotspots. Quasipalindrome-associated mutations (QPMs) occur through a template-switch mechanism in which the replicative polymerase stalls at a QP site and uses the nascent strand as a template instead of the correct template strand. This mutational event causes the QP to become a perfect or more perfect inverted repeat. Since it is not fully understood how template-switch events are stimulated or repressed, we designed a high-throughput screen to discover drugs that affect these events. QP reporters were engineered in the Escherichia coli lacZ gene to allow us to study template-switch events specifically. We tested 700 compounds from the NIH Clinical Collection through a disk diffusion assay and identified 11 positive hits. One of the hits was azidothymidine (zidovudine, AZT), a thymidine analog and DNA chain terminator. The other ten were found to be fluoroquinolone antibiotics, which induce DNA-protein crosslinks. This work shows that our screen is useful in identifying small molecules that affect quasipalindrome-associated template-switch mutations. We are currently assessing more small molecule libraries and applying this method to study other types of mutations.

scholarly journals Structure of the master regulator Rns reveals an inhibitor of enterotoxigenic Escherichia coli virulence regulons

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Charles R. Midgett ◽  
Kacey Marie Talbot ◽  
Jessica L. Day ◽  
George P. Munson ◽  
F. Jon Kull
Keyword(s):  
Escherichia Coli ◽  
Small Molecules ◽  
Family Member ◽  
Shigella Flexneri ◽  
Decanoic Acid ◽  
Enterotoxigenic Escherichia Coli ◽  
Gram Negative Bacteria ◽  
Enteric Infections ◽  
First Time ◽  
Arac Family

AbstractEnteric infections caused by the gram-negative bacteria enterotoxigenic Escherichia coli (ETEC), Vibrio cholerae, Shigella flexneri, and Salmonella enterica are among the most common and affect billions of people each year. These bacteria control expression of virulence factors using a network of transcriptional regulators, some of which are modulated by small molecules as has been shown for ToxT, an AraC family member from V. cholerae. In ETEC the expression of many types of adhesive pili is dependent upon the AraC family member Rns. We present here the 3 Å crystal structure of Rns and show it closely resembles ToxT. Rns crystallized as a dimer via an interface similar to that observed in other dimeric AraC’s. Furthermore, the structure of Rns revealed the presence of a ligand, decanoic acid, that inhibits its activity in a manner similar to the fatty acid mediated inhibition observed for ToxT and the S. enterica homologue HilD. Together, these results support our hypothesis that fatty acids regulate virulence controlling AraC family members in a common manner across a number of enteric pathogens. Furthermore, for the first time this work identifies a small molecule capable of inhibiting the ETEC Rns regulon, providing a basis for development of therapeutics against this deadly human pathogen.

scholarly journals Molecular Characterization of Plasmid-Mediated Non-O157 Verotoxigenic Escherichia coli Isolated from Infants and Children with Diarrhea

2020 ◽  
Vol 17 (3) ◽  
pp. 0710
Author(s):  
Md Fazlul Karim Khan ◽  
Shah Samiur Rashid
Keyword(s):  
Escherichia Coli ◽  
Virulence Gene ◽  
Multidrug Resistant ◽  
Plasmid Curing ◽  
Health Issues ◽  
E Coli ◽  
Disk Diffusion Assay ◽  
Microbiological Techniques ◽  
Polymerase Chain

A significant increase in the incidence of non-O157 verotoxigenic Escherichia coli (VTEC) infections have become a serious health issues, and this situation is worsening due to the dissemination of plasmid mediated multidrug-resistant microorganisms worldwide. This study aims to investigate the presence of plasmid-mediated verotoxin gene in non-O157 E. coli. Standard microbiological techniques identified a total of 137 E. coli isolates. The plasmid was detected by Perfectprep Plasmid Mini preparation kit. These isolates were subjected to disk diffusion assay, and plasmid curing with ethidium bromide treatment. The plasmid containing isolates were subjected to a polymerase chain reaction (PCR) for investigating the presence of plasmid mediated verotoxin gene (VT1 and VT2) in non-O157 E. coli. Among the 137 E. coli isolates, 49 isolates were non-O157 E. coli while 29 (59.1%) isolates were verotoxin producing non-O157 serotypes and 26 non-O157 VTEC isolates possessed plasmids. Certain isolates harboured single sized plasmid while others had multiple plasmids with different size varied from 1.8kb to 7.6kb. A plasmid containing all (100%) the isolates was multidrug-resistant. Eight isolates changed their susceptibility patterns while three isolates were found to lose plasmid after post plasmid curing treatment and the rest of the isolates (15) remained constant. Different PCR sets characterized 3 plasmid-mediated verotoxins producing non-O157 E. coli. This current study demonstrated the occurrence of plasmid mediated verotoxin gene in non-O157 E. coli. To the best of our knowledge, this is the first report in the global literature on plasmid-mediated verotoxin gene in non-O157 E. coli. Timely diagnosis and surveillance of VTEC infections should prioritize to stop or slow down the virulence gene for dissemination by plasmid-mediated gene transfer amongst the same bacteria or other species.

scholarly journals Development of a Simple Assay Protocol for High-Throughput Screening of Mycobacterium tuberculosis Glutamine Synthetase for the Identification of Novel Inhibitors

2005 ◽  
Vol 10 (7) ◽  
pp. 725-729 ◽  
Author(s):  
Upasana Singh ◽  
Vinita Panchanadikar ◽  
Dhiman Sarkar
Keyword(s):  
Escherichia Coli ◽  
Mycobacterium Tuberculosis ◽  
Glutamine Synthetase ◽  
Small Molecules ◽  
High Throughput ◽  
High Throughput Screening ◽  
Coli Strain ◽  
Compound Library ◽  
Essential Enzyme ◽  
Assay Protocol

Mycobacterium tuberculosis glutamine synthetase (GS) is an essential enzyme involved in the pathogenicity of the organism. The screening of a compound library using a robust high-throughput screening (HTS) assay is currently thought to be the most efficient way of getting lead molecules, which are potent inhibitors for this enzyme. The authors have purified the enzyme to a >90% level from the recombinant Escherichia coli strain YMC21E, and it was used for partial characterization as well as standardization experiments. The results indicated that the Kmof the enzyme for L-glutamine and hydroxylamine were 60 mM and 8.3 mM, respectively. The Km for ADP, arsenate, and Mn2+ were 2 [.proportional]M, 5 [.proportional]M, and 25 [.proportional]M, respectively. When the components were adjusted according to their Km values, the activity remained constant for at least 3 h at both 25° C and 37° C. The Z′ factor determined in microplate format indicated robustness of the assay. When the signal/noise ratios were determined for different assay volumes, it was observed that the 200-[.proportional]l volume was found to be optimum. The DMSO tolerance of the enzyme was checked up to 10%, with minimal inhibition. The IC50 value determined for L-methionine S-sulfoximine on the enzyme activity was 3 mM. Approximately 18,000 small molecules could be screened per day using this protocol by a Beckman Coulter HTS setup.

scholarly journals The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants

2004 ◽  
Vol 383 (2) ◽  
pp. 371-382 ◽  
Author(s):  
Benoit THOUVENOT ◽  
Bruno CHARPENTIER ◽  
Christiane BRANLANT
Keyword(s):  
Escherichia Coli ◽  
Growth Conditions ◽  
Site Directed Mutagenesis ◽  
Dna Interactions ◽  
Template Strand ◽  
Chemical Probing ◽  
Upstream Promoter ◽  
Promoter Dna ◽  
High Level ◽  
Protein Pocket

The Escherichia coli multi-promoter region of the gapA gene ensures a high level of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) production under various growth conditions. In the exponential phase of growth, gapA mRNAs are mainly initiated at the highly efficient gapA P1 promoter. In the present study, by using site-directed mutagenesis and chemical probing of the RPo (open complex) formed by Eσ70 (holoenzyme associated with σ70) RNAP (RNA polymerase) at promoter gapA P1, we show that this promoter is an extended −10 promoter that needs a −35 sequence for activity. The −35 sequence compensates for the presence of a suboptimal −10 hexamer. A tract of thymine residues in the spacer region, which is responsible for a DNA distortion, is also required for efficient activity. We present the first chemical probing of an RPo formed at a promoter needing both a −10 extension and a −35 sequence. It reveals a complex array of RNAP–DNA interactions. In agreement with the fact that residue A-11 in the non-template strand is flipped out in a protein pocket in previously studied RPos, the corresponding A residue in gapA P1 promoter is protected in RPo and is essential for activity. However, in contrast with some of the previous findings on RPos formed at other promoters, the −12 A:T pair is opened. Strong contacts with RNAP occur both with the −35 sequence and the TG extension, so that the σ4 and σ2 domains may simultaneously contact the promoter DNA. RNAP–DNA interactions were also detected immediately downstream of the −35 hexamer and in a more distal upstream segment, reflecting a wrapping of RNAP by the core and upstream promoter DNA. Altogether, the data reveal that promoter gapA P1 is a very efficient promoter sharing common properties with both extended −10 and non-extended −10 promoters.

scholarly journals Methylation Dependent Functional Switch Mechanism of the Escherichia coli Ada Protein.

1995 ◽  
Vol 71 (6) ◽  
pp. 198-201 ◽  
Author(s):  
Hitoshi SAKASHITA ◽  
Takahiko SAKUMA ◽  
Yoshiko AKITOMO ◽  
Tadayasu OHKUBO ◽  
Masatsune KAINOSHO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Switch Mechanism ◽  
Ada Protein

scholarly journals Aryl Rhodanines Specifically Inhibit Staphylococcal and Enterococcal Biofilm Formation

2009 ◽  
Vol 53 (10) ◽  
pp. 4357-4367 ◽  
Author(s):  
Timothy J. Opperman ◽  
Steven M. Kwasny ◽  
John D. Williams ◽  
Atiyya R. Khan ◽  
Norton P. Peet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Molecules ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Antibiofilm Activity ◽  
Bacterial Strains ◽  
Gram Negative ◽  
Artificial Surfaces ◽  
Causative Agents ◽  
Biofilm Development

ABSTRACT Staphylococcus epidermidis and Staphylococcus aureus are the leading causative agents of indwelling medical device infections because of their ability to form biofilms on artificial surfaces. Here we describe the antibiofilm activity of a class of small molecules, the aryl rhodanines, which specifically inhibit biofilm formation of S. aureus, S. epidermidis, Enterococcus faecalis, E. faecium, and E. gallinarum but not the gram-negative species Pseudomonas aeruginosa or Escherichia coli. The aryl rhodanines do not exhibit antibacterial activity against any of the bacterial strains tested and are not cytotoxic against HeLa cells. Preliminary mechanism-of-action studies revealed that the aryl rhodanines specifically inhibit the early stages of biofilm development by preventing attachment of the bacteria to surfaces.

scholarly journals Bacterial protein translocation requires only one copy of the SecY complex in vivo

2012 ◽  
Vol 198 (5) ◽  
pp. 881-893 ◽  
Author(s):  
Eunyong Park ◽  
Tom A. Rapoport
Keyword(s):  
Escherichia Coli ◽  
Small Molecules ◽  
Protein Translocation ◽  
Cross Linking ◽  
Bacterial Protein ◽  
Oligomeric State ◽  
E Coli ◽  
Cotranslational Translocation ◽  
Escherichia Coli Cells

The transport of proteins across the plasma membrane in bacteria requires a channel formed from the SecY complex, which cooperates with either a translating ribosome in cotranslational translocation or the SecA ATPase in post-translational translocation. Whether translocation requires oligomers of the SecY complex is an important but controversial issue: it determines channel size, how the permeation of small molecules is prevented, and how the channel interacts with the ribosome and SecA. Here, we probe in vivo the oligomeric state of SecY by cross-linking, using defined co- and post-translational translocation intermediates in intact Escherichia coli cells. We show that nontranslocating SecY associated transiently through different interaction surfaces with other SecY molecules inside the membrane. These interactions were significantly reduced when a translocating polypeptide inserted into the SecY channel co- or post-translationally. Mutations that abolish the interaction between SecY molecules still supported viability of E. coli. These results show that a single SecY molecule is sufficient for protein translocation.

scholarly journals The First Small-Molecule Inhibitors of Members of the Ribonuclease E Family

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Louise Kime ◽  
Helen A. Vincent ◽  
Deena M. A. Gendoo ◽  
Stefanie S. Jourdan ◽  
Colin W. G. Fishwick ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Molecules ◽  
Small Molecule ◽  
High Throughput Screening ◽  
Small Molecule Inhibitors ◽  
Rnase E ◽  
Ribonuclease E ◽  
New Antibiotics ◽  
Drug Leads ◽  
Number Of Bacteria

Abstract The Escherichia coli endoribonuclease RNase E is central to the processing and degradation of all types of RNA and as such is a pleotropic regulator of gene expression. It is essential for growth and was one of the first examples of an endonuclease that can recognise the 5′-monophosphorylated ends of RNA thereby increasing the efficiency of many cleavages. Homologues of RNase E can be found in many bacterial families including important pathogens, but no homologues have been identified in humans or animals. RNase E represents a potential target for the development of new antibiotics to combat the growing number of bacteria that are resistant to antibiotics in use currently. Potent small molecule inhibitors that bind the active site of essential enzymes are proving to be a source of potential drug leads and tools to dissect function through chemical genetics. Here we report the use of virtual high-throughput screening to obtain small molecules predicted to bind at sites in the N-terminal catalytic half of RNase E. We show that these compounds are able to bind with specificity and inhibit catalysis of Escherichia coli and Mycobacterium tuberculosis RNase E and also inhibit the activity of RNase G, a paralogue of RNase E.

scholarly journals Physicochemical and Structural Parameters Contributing to the Antibacterial Activity and Efflux Susceptibility of Small Molecule Inhibitors of Escherichia coli

2021 ◽  
Author(s):  
Sara S. El Zahed ◽  
Shawn French ◽  
Maya A. Farha ◽  
Garima Kumar ◽  
Eric D. Brown
Keyword(s):  
Machine Learning ◽  
Escherichia Coli ◽  
Antibacterial Activity ◽  
Small Molecules ◽  
Small Molecule ◽  
In Silico ◽  
Molecular Descriptors ◽  
Structural Parameters ◽  
Side Chain ◽  
Gram Negative

Discovering new Gram-negative antibiotics has been a challenge for decades. This has been largely attributed to a limited understanding of the molecular descriptors governing Gram-negative permeation and efflux evasion. Herein, we address the contribution of efflux using a novel approach that applies multivariate analysis, machine learning, and structure-based clustering to some 4,500 actives from a small molecule screen in efflux-compromised Escherichia coli. We employed principal-component analysis and trained two decision tree-based machine learning models to investigate descriptors contributing to the antibacterial activity and efflux susceptibility of these actives. This approach revealed that the Gram-negative activity of hydrophobic and planar small molecules with low molecular stability is limited to efflux-compromised E. coli. Further, molecules with reduced branching and compactness showed increased susceptibility to efflux. Given these distinct properties that govern efflux, we developed the first machine learning model, called Susceptibility to Efflux Random Forest (SERF), as a tool to analyze the molecular descriptors of small molecules and predict those that could be susceptible to efflux pumps in silico. Here, SERF demonstrated high accuracy in identifying such molecules. Further, we clustered all 4,500 actives based on their core structures and identified distinct clusters highlighting side chain moieties that cause marked changes in efflux susceptibility. In all, our work reveals a role for physicochemical and structural parameters in governing efflux, presents a machine learning tool for rapid in silico analysis of efflux susceptibility, and provides a proof of principle for the potential of exploiting side chain modification to design novel antimicrobials evading efflux pumps.

Post Glycosylation Diversification (PGD): An Approach for Assembling Collections of Glycosylated Small Molecules

2018 ◽  
Author(s):  
Zachary Cannone ◽  
Ala Shaqra ◽  
Chris Lorenc ◽  
Liza Henowitz ◽  
Santosh Keshipeddy ◽  
...  
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
T Cell Activation ◽  
Cell Activation ◽  
De Novo ◽  
Protein Translation ◽  
Compound Libraries ◽  
Activation Assay ◽  
Small Molecule Libraries ◽  
New Compounds

Many small molecule natural products with are adorned with a carbohydrate as part of their molecular structure that acts to mediate key interactions with the target, attenuate physicochemical properties, or both. Facile incorporation of a carbohydrate group on de novo small molecules would enable these valuable properties to be leveraged in the evaluation of focused compound libraries. Here we report a new approach for the synthesis of glycosylated small molecule libraries that puts the glycosylation early in the synthesis of library compounds. Functionalized aglycones subsequently participate in chemoselective diversification reactions distal to the carbohydrate. A number of desosaminyl glycosides were prepared from only a few starting glycosides, using click cycloadditions, acylations, and Suzuki couplings as diversification reactions. New compounds were characterized for their inhibition of bacterial protein translation, bacterial growth, and in a T-cell activation assay.

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