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https://www.readbyqxmd.com/read/28412516/switching-between-nitrogen-and-glucose-limitation-unraveling-transcriptional-dynamics-in-escherichia-coli
#1
Michael Löffler, Joana Danica Simen, Jan Müller, Günter Jäger, Salaheddine Laghrami, Karin Schäferhoff, Andreas Freund, Ralf Takors, Ralf Takors
Transcriptional control under nitrogen and carbon-limitation conditions have been well analyzed for Escherichia coli. However, the transcriptional dynamics that underlie the shift in regulatory programs from nitrogen to carbon limitation is not well studied. In the present study, cells were cultivated at steady state under nitrogen (ammonia)-limited conditions then shifted to carbon (glucose) limitation to monitor changes in transcriptional dynamics. Nitrogen limitation was found to be dominated by sigma 54 (RpoN) and sigma 38 (RpoS), whereas the "housekeeping" sigma factor 70 (RpoD) and sigma 38 regulate cellular status under glucose limitation...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28341438/engineering-a-novel-porin-ompgf-via-strand-replacement-from-computational-analysis-of-sequence-motif
#2
Meishan Lin, Ge Zhang, Monifa Fahie, Leslie K Morgan, Min Chen, Timothy A Keiderling, Linda J Kenney, Jie Liang
β-Barrelmembrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. Computational engineering has the promise to generate βMPs with desired properties...
July 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28337196/salmonella-typhi-porins-ompc-and-ompf-are-potent-adjuvants-for-t-dependent-and-t-independent-antigens
#3
Marisol Pérez-Toledo, Nuriban Valero-Pacheco, Rodolfo Pastelin-Palacios, Cristina Gil-Cruz, Christian Perez-Shibayama, Mario A Moreno-Eutimio, Ingeborg Becker, Sonia Mayra Pérez-Tapia, Lourdes Arriaga-Pizano, Adam F Cunningham, Armando Isibasi, Laura C Bonifaz, Constantino López-Macías
Several microbial components, such as bacterial DNA and flagellin, have been used as experimental vaccine adjuvants because of their inherent capacity to efficiently activate innate immune responses. Likewise, our previous work has shown that the major Salmonella Typhi (S. Typhi) outer membrane proteins OmpC and OmpF (porins) are highly immunogenic protective antigens that efficiently stimulate innate and adaptive immune responses in the absence of exogenous adjuvants. Moreover, S. Typhi porins induce the expression of costimulatory molecules on antigen-presenting cells through toll-like receptor canonical signaling pathways...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28315387/functional-role-of-ompf-and-ompc-porins-in-pathogenesis-of-avian-pathogenic-escherichia-coli
#4
Hassan M A Hejair, Yinchu Zhu, Jiale Ma, Yue Zhang, Zihao Pan, Wei Zhang, Huochun Yao
Avian pathogenic Escherichia coli is an important pathogen causes systemic infections in avian species and large economic losses in poultry industry worldwide. The functional role of porins during the infection and their mechanisms of interaction with host tissues for adhesion to and invasion are poorly understood. However, whether porins play a role in infection remains unclear. In this study we evaluated the potential of ompF and ompC outer membrane porins in the pathogenesis of avian pathogenic E. coli (APEC) strain TW-XM...
March 14, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28264855/structural-alteration-of-ompr-as-a-source-of-ertapenem-resistance-in-a-ctx-m-15-producing-escherichia-coli-o25b-h4-sequence-type-131-clinical-isolate
#5
Hervé Dupont, Pascaline Choinier, David Roche, Sandine Adiba, Megan Sookdeb, Catherine Branger, Erick Denamur, Hedi Mammeri
In this study, an ertapenem-nonsusceptible Escherichia coli isolate was investigated to determine the genetic basis for its carbapenem resistance phenotype. This clinical strain was recovered from a patient that received, 1 year previously, ertapenem to treat a cholangitis due to a carbapenem-susceptible extended-spectrum-β-lactamase (ESBL)-producing E. coli isolate. Whole-genome sequencing of these strains was performed using Illumina and single-molecule real-time sequencing technologies. It revealed that they belonged to the ST131 clonal group, had the predicted O25b:H4 serotype, and produced the CTX-M-15 and TEM-1 β-lactamases...
May 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28245829/improving-escherichia-coli-membrane-integrity-and-fatty-acid-production-by-expression-tuning-of-fadl-and-ompf
#6
Zaigao Tan, William Black, Jong Moon Yoon, Jacqueline V Shanks, Laura R Jarboe
BACKGROUND: Construction of microbial biocatalysts for the production of biorenewables at economically viable yields and titers is frequently hampered by product toxicity. Membrane damage is often deemed as the principal mechanism of this toxicity, particularly in regards to decreased membrane integrity. Previous studies have attempted to engineer the membrane with the goal of increasing membrane integrity. However, most of these works focused on engineering of phospholipids and efforts to identify membrane proteins that can be targeted to improve fatty acid production have been unsuccessful...
February 28, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28240914/general-method-to-determine-the-flux-of-charged-molecules-through-nanopores-applied-to-%C3%AE-lactamase-inhibitors-and-ompf
#7
Ishan Ghai, Alessandro Pira, Mariano Andrea Scorciapino, Igor Bodrenko, Lorraine Benier, Matteo Ceccarelli, Mathias Winterhalter, Richard Wagner
A major challenge in the discovery of the new antibiotics against Gram-negative bacteria is to achieve sufficiently fast permeation in order to avoid high doses causing toxic side effects. So far, suitable assays for quantifying the uptake of charged antibiotics into bacteria are lacking. We apply an electrophysiological zero-current assay using concentration gradients of β-lactamase inhibitors combined with single-channel conductance to quantify their flux rates through OmpF. Molecular dynamic simulations provide in addition details on the interactions between the nanopore wall and the charged solutes...
March 6, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28094462/orientation-of-the-ompf-porin-in-planar-lipid-bilayers
#8
Sandra A Ionescu, Sejeong Lee, Nicholas G Housden, Renata Kaminska, Colin Kleanthous, Hagan Bayley
The outer-membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current-voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane-impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance...
January 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28076882/characterization-of-salmonella-typhi-ompc-and-ompf-porins-engineered-with-hiv-gp41-epitope-on-the-surface-loops
#9
Madhuranayaki Thulasingam, Subha Damodharan, Gopal Madhana Vigneshwari, Eswari P J Pandaranayaka, Luke Elizabeth Hanna, Ramakrishnan Usha, Sankaran Krishnaswamy
Porins form trimers in the outer membrane and help transport nutrients and waste products across the bacterial cell membrane. Porin loops are suitable candidates as display systems due to their high immunogenicity and presentation at the bacterial cell surface. In this study, Salmonella typhi porins (OmpC and OmpF) engineered with the Kennedy peptide from gp41 of HIV were characterised. The chimeric OmpC carrying the Kennedy peptide in loop7 did not trimerise, whereas the chimeric OmpF with the epitope in loop5 formed trimers and also was recognised by the antibodies in the HIV patient serum...
January 11, 2017: Proteins
https://www.readbyqxmd.com/read/28072422/the-fitness-costs-and-trade-off-shapes-associated-with-the-exclusion-of-nine-antibiotics-by-ompf-porin-channels
#10
Katherine Phan, Thomas Ferenci
The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28054667/yersinia-pestis-halotolerance-illuminates-plague-reservoirs
#11
Maliya Alia Malek, Idir Bitam, Anthony Levasseur, Jérôme Terras, Jean Gaudart, Said Azza, Christophe Flaudrops, Catherine Robert, Didier Raoult, Michel Drancourt
The plague agent Yersinia pestis persists for years in the soil. Two millennia after swiping over Europe and North Africa, plague established permanent foci in North Africa but not in neighboring Europe. Mapping human plague foci reported in North Africa for 70 years indicated a significant location at <3 kilometers from the Mediterranean seashore or the edge of salted lakes named chotts. In Algeria, culturing 352 environmental specimens naturally containing 0.5 to 70 g/L NaCl yielded one Y. pestis Orientalis biotype isolate in a 40 g/L NaCl chott soil specimen...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27965634/structural-elucidation-and-molecular-docking-of-a-novel-antibiotic-compound-from-cyanobacterium-nostoc-sp-mgl001
#12
Niveshika, Ekta Verma, Arun K Mishra, Angad K Singh, Vinay K Singh
Cyanobacteria are rich source of array of bioactive compounds. The present study reports a novel antibacterial bioactive compound purified from cyanobacterium Nostoc sp. MGL001 using various chromatographic techniques viz. thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). Further characterization was done using electrospray ionization mass spectroscopy (ESIMS) and nuclear magnetic resonance (NMR) and predicted structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy) -5, 8, 13, 16-tetraaza-hexacene - 2, 3 dicarboxylic acid (EMTAHDCA)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27915254/ompf-of-pectobacterium-carotovorum-subsp-carotovorum-pcc3-is-required-for-carocin-d-sensitivity
#13
Jeong-A Lim, Jisoo Hong, Jonguk Kim, Sunggi Heu, Eunjung Roh
Carocin D is a bacteriocin produced by Pectobacterium carotovorum subsp. carotovorum Pcc21. Carocin D inhibits the growth of P carotovorum subsp. carotovorum and closely related strains. Pectobacterium carotovorum subsp. carotovorum is a causative bacterium for soft rot disease and leads to severe economic losses. Bacteriocins recognize and interact with a specific membrane protein of target bacteria as a receptor. To identify the receptor responsible for carocin D recognition, mutants that underwent a phenotypic change from carocin D sensitivity to carocin D insensitivity were screened...
December 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27901137/energy-transduction-and-signal-averaging-of-fluctuating-electric-fields-by-a-single-protein-ion-channel
#14
C Verdia-Baguena, V Gomez, J Cervera, P Ramirez, S Mafe
We demonstrate the electrical rectification and signal averaging of fluctuating signals using a biological nanostructure in aqueous solution: a single protein ion channel inserted in the lipid bilayer characteristic of cell membranes. The conversion of oscillating, zero time-average potentials into directional currents permits charging of a load capacitor to significant steady-state voltages within a few minutes in the case of the outer membrane porin F (OmpF) protein, a bacterial channel of Escherichia coli...
December 21, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27884940/ecological-speciation-of-bacteriophage-lambda-in-allopatry-and-sympatry
#15
Justin R Meyer, Devin T Dobias, Sarah J Medina, Lisa Servilio, Animesh Gupta, Richard E Lenski
Understanding the conditions that allow speciation to occur is difficult because most research has focused on either long-lived organisms or asexual microorganisms. We propagated bacteriophage λ, a virus with rapid generations and frequent recombination, on two Escherichia coli host genotypes that expressed either the LamB or OmpF receptor. When supplied with either single host (allopatry), phage λ improved its binding to the available receptor while losing its ability to use the alternative. When evolving on both hosts together (sympatry), the viruses split into two lineages with divergent receptor preferences...
December 9, 2016: Science
https://www.readbyqxmd.com/read/27723824/cdia-effectors-from-uropathogenic-escherichia-coli-use-heterotrimeric-osmoporins-as-receptors-to-recognize-target-bacteria
#16
Christina M Beck, Julia L E Willett, David A Cunningham, Jeff J Kim, David A Low, Christopher S Hayes
Many Gram-negative bacterial pathogens express contact-dependent growth inhibition (CDI) systems that promote cell-cell interaction. CDI+ bacteria express surface CdiA effector proteins, which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors. CDI+ cells also produce immunity proteins that neutralize the toxin domains delivered from neighboring siblings. Here, we show that CdiAEC536 from uropathogenic Escherichia coli 536 (EC536) uses OmpC and OmpF as receptors to recognize target bacteria...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27716985/d-tyrosine-affects-aggregation-behavior-of-pantoea-agglomerans
#17
Jing Yang, Jiajia Yu, Jing Jiang, Chen Liang, Yongjun Feng
D-amino acids have been proved to disassemble biofilms by disassociating the matrix. Pantoea agglomerans is characterized by the formation of another kind of multicellular structure called symplasmata, which also remains the ability to form biofilms. In this study, a rice diazotrophic endophyte P. agglomerans YS19 was selected as a model strain to explore the effects of D-amino acids on these two kinds of cell aggregate structures. It was discovered that D-tyrosine disassociates biofilm, yet promotes symplasmata formation...
February 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/27693650/momp-from-campylobacter-jejuni-is-a-trimer-of-18-stranded-%C3%AE-barrel-monomers-with-a-ca-2-ion-bound-at-the-constriction-zone
#18
Luana G M Ferrara, Gregor D Wallat, Lucile Moynié, Naresh N Dhanasekar, Soumeya Aliouane, Silvia Acosta-Gutiérrez, Jean-Marie Pagès, Jean-Michel Bolla, Mathias Winterhalter, Matteo Ceccarelli, James H Naismith
The Gram-negative organism Campylobacter jejuni is the major cause of food poisoning. Unlike Escherichia coli, which has two major porins, OmpC and OmpF, C. jejuni has one, termed major outer membrane protein (MOMP) through which nutrients and antibiotics transit. We report the 2.1-Å crystal structure of C. jejuni MOMP expressed in E. coli and a lower resolution but otherwise identical structure purified directly from C. jejuni. The 2.1-Å resolution structure of recombinant MOMP showed that although the protein has timeric arrangement similar to OmpC, it is an 18-stranded, not 16-stranded, β-barrel...
September 30, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27683370/host-coevolution-alters-the-adaptive-landscape-of-a-virus
#19
Alita R Burmeister, Richard E Lenski, Justin R Meyer
The origin of new and complex structures and functions is fundamental for shaping the diversity of life. Such key innovations are rare because they require multiple interacting changes. We sought to understand how the adaptive landscape led to an innovation whereby bacteriophage λ evolved the new ability to exploit a receptor, OmpF, on Escherichia coli cells. Previous work showed that this ability evolved repeatedly, despite requiring four mutations in one virus gene. Here, we examine how this innovation evolved by studying six intermediate genotypes of λ isolated during independent transitions to exploit OmpF and comparing them to their ancestor...
September 28, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27645385/klebsiella-pneumoniae-major-porins-ompk35-and-ompk36-allow-more-efficient-diffusion-of-%C3%AE-lactams-than-their-escherichia-coli-homologs-ompf-and-ompc
#20
Etsuko Sugawara, Seiji Kojima, Hiroshi Nikaido
Klebsiella pneumoniae, one of the most important nosocomial pathogens, is becoming a major problem in health care because of its resistance to multiple antibiotics, including cephalosporins of the latest generation and, more recently, even carbapenems. This is largely due to the spread of plasmid-encoded extended-spectrum β-lactamases. However, antimicrobial agents must first penetrate the outer membrane barrier in order to reach their targets, and hydrophilic and charged β-lactams presumably diffuse through the porin channels...
December 1, 2016: Journal of Bacteriology
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