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Journal of Bioenergetics and... Dec 2022Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented...
Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented due to the production of several carotenoids and their derivatives. Two of these pigment molecules, salinixanthin and retinal, are reported to be essential cofactors of the xanthorhodopsin, a light-driven proton pump unique to this bacterium. Here, we isolate and characterize an outer membrane porin-like protein that retains salinixanthin. The characterization by mass spectrometry identified an unknown protein whose structure, predicted by AlphaFold, consists of a 8 strands beta-barrel transmembrane organization typical of porins. The protein is found to be part of a functional network clearly involved in the outer membrane trafficking. Cryo-EM micrographs showed the shape and dimensions of a particle comparable with the ones of the predicted structure. Functional implications, with respect to the high representativity of this protein in the outer membrane fraction, are discussed considering its possible role in primary functions such as the nutrients uptake and the homeostatic balance. Finally, also a possible involvement in balancing the charge perturbation associated with the xanthorhodopsin and ATP synthase activities is considered.
Topics: Porins; Bacteroidetes; Carotenoids
PubMed: 36229623
DOI: 10.1007/s10863-022-09950-7 -
Molecules (Basel, Switzerland) Jun 2021Here, we investigated general porin regulation in 488, the causative agent of Far Eastern scarlet-like fever, in response to sublethal concentrations of antibiotics. We...
Here, we investigated general porin regulation in 488, the causative agent of Far Eastern scarlet-like fever, in response to sublethal concentrations of antibiotics. We chose four antibiotics of different classes and measured gene expression using qRT-PCR and GFP reporter systems. Our data showed temporal regulation of the general porin genes and caused by antibiotic stress. The porin transcription initially decreased, providing early defensive response of the bacterium, while it returned to that of the untreated cells on prolonged antibiotic exposure. Unlike the major porin genes, the transcription of the alternative porin genes and was increased. Moreover, a short-term - and -mediated porin regulation was observed. The main finding was a phenotypic heterogeneity of population manifested in variable porin gene expression under carbenicillin exposure. This may offer adaptive fitness advantages for a particular bacterial subpopulation.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Carbenicillin; Gene Expression Regulation, Bacterial; Porins; Stress, Physiological; Yersinia pseudotuberculosis
PubMed: 34203552
DOI: 10.3390/molecules26133956 -
Frontiers in Immunology 2019infections remain a challenging health issue, causing significant morbidity and mortality worldwide. Current vaccines against typhoid fever display moderate efficacy...
infections remain a challenging health issue, causing significant morbidity and mortality worldwide. Current vaccines against typhoid fever display moderate efficacy whilst no licensed vaccines are available for paratyphoid fever or invasive non-typhoidal salmonellosis. Therefore, there is an urgent need to develop high efficacy broad-spectrum vaccines that can protect against typhoidal and non-typhoidal . The outer membrane porins OmpC and OmpF, have been shown to be highly immunogenic antigens, efficiently eliciting protective antibody, and cellular immunity. Furthermore, enterobacterial porins, particularly the OmpC, have a high degree of homology in terms of sequence and structure, thus making them a suitable vaccine candidate. However, the degree of the amino acid conservation of OmpC among typhoidal and non-typhoidal serovars is currently unknown. Here we used a bioinformatical analysis to classify the typhoidal and non-typhoidal OmpC amino acid sequences into different clades independently of their serological classification. Further, our analysis determined that the porin OmpC contains various amino acid sequences that are highly conserved among both typhoidal and non-typhoidal serovars. Critically, some of these highly conserved sequences were located in the transmembrane β-sheet within the porin β-barrel and have immunogenic potential for binding to MHC-II molecules, making them suitable candidates for a broad-spectrum vaccine. Collectively, these findings suggest that these highly conserved sequences may be used for the rational design of an effective broad-spectrum vaccine against .
Topics: Amino Acid Sequence; Bacterial Proteins; Conserved Sequence; Humans; Phylogeny; Porins; Protein Conformation, alpha-Helical; Salmonella; Salmonella Infections; Salmonella typhi; Sequence Alignment; Typhoid Fever
PubMed: 31998292
DOI: 10.3389/fimmu.2019.02966 -
Applied and Environmental Microbiology Apr 2022Bacterial porin-encoding genes are often found under positive selection. Local recombination has also been identified in a few of them to facilitate bacterial rapid...
Bacterial porin-encoding genes are often found under positive selection. Local recombination has also been identified in a few of them to facilitate bacterial rapid adaptation, although it remains unknown whether it is a common evolutionary mechanism for the porins or outer membrane proteins in Gram-negative bacteria. In this study, we investigated the beta-barrel (β-barrel) porin-encoding genes in Escherichia coli that were reported under positive Darwinian selection. Besides that was found with ingenic local recombination previously, we identified four other genes, i.e., , , , and , all showing the similar mosaic evolution patterns. Comparative analysis of the protein sequences disclosed a list of highly variable regions in each family, which are mostly located in the convex of extracellular loops and coinciding with the binding sites of bacteriophages. For each of the porin families, mosaic recombination leads to unique combinations of the variable regions with different sequence patterns, generating diverse protein groups. Structural modeling indicated a conserved global topology among the different porins, with the extracellular surface varying a lot due to individual or combinatorial variable regions. The conservation of global tertiary structure would ensure the channel activity, while the wide diversity of variable regions may represent selection to avoid the invasion of phages, antibiotics or immune surveillance factors. Our study identified multiple bacterial porin genes with mosaic evolution. We hypothesize that this could be generalized strategy for outer membrane proteins to both maintain normal life processes and evade the attack of unfavored factors rapidly. Microevolution studies can disclose more elaborate evolutionary mechanisms of genes, appearing especially important for genes with multifaceted function such as those encoding outer membrane proteins. However, in most cases, the gene is considered as a whole unit, and the evolutionary patterns are disclosed. Here, we report that multiple bacterial porin proteins follow mosaic evolution, with local ingenic recombination combined with spontaneous mutations based on positive Darwinian selection, and conservation for most structural regions. This could represent a common mechanism for bacterial outer membrane proteins. The variable regions within each porin family showed large coincidence with the binding sites of bacteriophages, antibiotics, and immune factors and therefore would represent effective targets for the development of new antibacterial agents or vaccines.
Topics: Animals; Anti-Bacterial Agents; Bacterial Outer Membrane Proteins; Bacterial Proteins; Escherichia coli; Humans; Porins; Sheep
PubMed: 35285711
DOI: 10.1128/aem.00060-22 -
Biochimica Et Biophysica Acta.... Mar 2022The misuse and overuse of fluoroquinolones in recent years have triggered alarming levels of resistance to these antibiotics. Porin channels are crucial for the...
Exploring the permeation of fluoroquinolone metalloantibiotics across outer membrane porins by combining molecular dynamics simulations and a porin-mimetic in vitro model.
The misuse and overuse of fluoroquinolones in recent years have triggered alarming levels of resistance to these antibiotics. Porin channels are crucial for the permeation of fluoroquinolones across the outer membrane of Gram-negative bacteria and modifications in porin expression are an important mechanism of bacterial resistance. One possible strategy to overcome this problem is the development of ternary copper complexes with fluoroquinolones. Compared to fluoroquinolones, these metalloantibiotics present a larger partition to the lipid bilayer and a more favorable permeation, by passive diffusion, across bacteriomimetic phospholipid-based model membranes. To rule out the porin-dependent pathway for the metalloantibiotics, we explored the permeation through OmpF (one of the most abundant porins present in the outer membrane of Gram-negative bacteria) using a multi-component approach. X-ray studies of OmpF porin crystals soaked with a ciprofloxacin ternary copper complex did not show a well-defined binding site for the compound. Molecular dynamics simulations showed that the translocation of the metalloantibiotic through this porin is less favorable than that of free fluoroquinolone, as it presented a much larger free energy barrier to cross the narrow constriction region of the pore. Lastly, permeability studies of different fluoroquinolones and their respective copper complexes using a porin-mimetic in vitro model corroborated the lower rate of permeation for the metalloantibiotics relative to the free antibiotics. Our results support a porin-independent mechanism for the influx of the metalloantibiotics into the bacterial cell. This finding brings additional support to the potential application of these metalloantibiotics in the fight against resistant infections and as an alternative to fluoroquinolones.
Topics: Anti-Bacterial Agents; Ciprofloxacin; Coordination Complexes; Copper; Crystallography, X-Ray; Escherichia coli; Fluoroquinolones; Lipid Bilayers; Molecular Dynamics Simulation; Porins
PubMed: 34896074
DOI: 10.1016/j.bbamem.2021.183838 -
International Journal of Molecular... Jul 2023The outer membrane of Gram-negative bacteria contains a variety of pore-forming structures collectively referred to as porins. Some of these are voltage dependent, but...
The outer membrane of Gram-negative bacteria contains a variety of pore-forming structures collectively referred to as porins. Some of these are voltage dependent, but weakly so, closing at high voltages. Triplin, a novel bacterial pore-former, is a three-pore structure, highly voltage dependent, with a complex gating process. The three pores close sequentially: pore 1 at positive potentials, 2 at negative and 3 at positive. A positive domain containing 14 positive charges (the voltage sensor) translocates through the membrane during the closing process, and the translocation is proposed to take place by the domain entering the pore and thus blocking it, resulting in the closed conformation. This mechanism of pore closure is supported by kinetic measurements that show that in the closing process the voltage sensor travels through most of the transmembrane voltage before reaching the energy barrier. Voltage-dependent blockage of the pores by polyarginine, but not by a 500-fold higher concentrations of polylysine, is consistent with the model of pore closure, with the sensor consisting mainly of arginine residues, and with the presence, in each pore, of a complementary surface that serves as a binding site for the sensor.
Topics: Humans; Ion Channel Gating; Porins; Thiourea; Translocation, Genetic
PubMed: 37511231
DOI: 10.3390/ijms241411473 -
The FEBS Journal Mar 2012OprF is the major porin of Pseudomonas aeruginosa and allows very slow, nonspecific, diffusion of solutes. The low permeability of this porin channel is a major factor... (Review)
Review
OprF is the major porin of Pseudomonas aeruginosa and allows very slow, nonspecific, diffusion of solutes. The low permeability of this porin channel is a major factor that enhances other types of resistance mechanisms and often creates strong multidrug resistance in this nosocomial pathogen. We have previously shown that the low permeability is caused by the folding of OprF into two conformers: a majority, two-domain closed-channel conformer containing the N-terminal transmembrane β-barrel and the C-terminal periplasmic, globular domain; and a minority, one-domain open-channel conformer comprising < 5% of the protein population. Our analysis of the bifurcate folding pathway using site-directed mutagenesis showed that slowing down the folding of the two-domain conformer increases the fraction of the open, one-domain conformer. Use of outer membrane protein assembly machinery mutants showed that the absence of the Skp chaperone led to an increased proportion of open conformers. As many environmental pathogens causing nosocomial infections appear to have outer membrane protein (OmpA)/OprF homologs as the major porin, efforts to understand the low permeability of these 'slow porins' are important in our fight against these organisms.
Topics: Bacterial Proteins; Molecular Chaperones; Mutagenesis, Site-Directed; Porins; Protein Conformation; Protein Folding; Pseudomonas aeruginosa
PubMed: 22240095
DOI: 10.1111/j.1742-4658.2012.08481.x -
The Lancet. Microbe Dec 2021Bartonella bacilliformis is the aetiological agent of Carrión's disease, a biphasic and highly lethal illness formerly restricted to the South American Andes that is...
BACKGROUND
Bartonella bacilliformis is the aetiological agent of Carrión's disease, a biphasic and highly lethal illness formerly restricted to the South American Andes that is now spreading to adjacent areas. Reliable serodiagnostic approaches and vaccines are urgently needed. In this study, we aimed to identify immunodominant proteins of B bacilliformis and to establish novel and reliable serodiagnostic tools.
METHODS
We used a reverse vaccinology approach in combination with an analysis of heterologous genomic expression libraries to identify immunodominant proteins, on the basis of the genome sequences of B bacilliformis strains KC583 and KC584. Antigens were screened with serum samples collected from Peruvian patients with B bacilliformis infections and from German healthy blood donors without history of travel to South America. We further analysed immunoreactive proteins of B bacilliformis with immunoblotting and line blots. We used selected target proteins to develop a diagnostic ELISA. To assess the performance of this ELISA, we did receiver operating characteristic analyses to assess the area under the curve, cutoff values, sensitivities, and specificities with 95% CIs.
FINDINGS
We used serum samples obtained between Dec 23, 1990, and May 5, 2018, from 26 Peruvian patients with B bacilliformis infections and serum samples taken between Aug 28 and Aug 31, 2020, from 96 healthy German blood donors. 21 potentially immunodominant proteins were identified and recombinantly expressed, and their reactivity was assessed with immunoblotting and line blots. Of these 21 antigens, 14 were found to be immunoreactive. By using serum samples of Peruvian patients with Carrión's disease and of healthy German blood donors, we identified three antigens (porin B, autotransporter E, and hypothetical protein B) as suitable immunodominant antigens, and we applied them in a diagnostic ELISA using two different antigen combinations (porin B plus autotransporter E and porin B plus autotransporter E plus hypothetical protein B). For the combination of porin B and autotransporter E, with optical density measured at 450 nm (OD) cutoff value of 0·29, sensitivity was 80·8% (95% CI 60·7-93·5) and specificity was 94·8% (88·3-98·3) for all Peruvian patient samples. For a combination of porin B, autotransporter E, and hypothetical protein B, with an OD cutoff of 0·34, sensitivity was 76·9% (56·4-91·0) and specificity was 93·8% (86·9-97·7) for all Peruvian patient samples.
INTERPRETATION
This novel ELISA could represent a useful serodiagnostic tool for future epidemiological studies of B bacilliformis in endemic areas. Additionally, the immunodominant antigens we have identified could provide a first basis for future vaccine development to prevent the highly lethal Carrión's disease.
FUNDING
DRUID (Novel Drug Targets against Poverty-Related and Neglected Tropical Infectious Diseases) Initiative and Robert Koch Institute.
TRANSLATIONS
For the Spanish and Quechua translations of the abstract see Supplementary Materials section.
Topics: Bartonella Infections; Bartonella bacilliformis; Humans; Immunodominant Epitopes; Porins; Type V Secretion Systems
PubMed: 35544109
DOI: 10.1016/S2666-5247(21)00184-1 -
Viruses Oct 2015
Topics: Animals; DNA Viruses; Humans; Porins; Protein Conformation; RNA Viruses; Viral Proteins
PubMed: 26702461
DOI: 10.3390/v7102866 -
Methods (San Diego, Calif.) Aug 2016Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual... (Review)
Review
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual enzymatic motions along DNA as small as 40pm can be resolved on sub-millisecond time scales. Additionally, SPRNT reveals an enzyme's exact location with respect to a DNA strand's nucleotide sequence, enabling identification of sequence-specific behaviors. SPRNT is enabled by a mutant version of the biological nanopore formed by Mycobacterium smegmatis porin A (MspA). SPRNT is strongly rooted in nanopore sequencing and therefore requires a solid understanding of basic principles of nanopore sequencing. Furthermore, SPRNT shares tools developed for nanopore sequencing and extends them to analysis of single-molecule kinetics. As such, this review begins with a brief history of our work developing the nanopore MspA for nanopore sequencing. We then describe the underlying principles of SPRNT, how it works in detail, and propose some potential future uses. We close with a comparison of SPRNT to other techniques and we present the methods that will enable others to use SPRNT.
Topics: Kinetics; Mycobacterium smegmatis; Nanopores; Nucleic Acids; Optical Tweezers; Porins; Single Molecule Imaging
PubMed: 27045943
DOI: 10.1016/j.ymeth.2016.03.026