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Advances in Microbial Physiology 2016The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research... (Review)
Review
The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research over the last three decades. The process presents two challenges to the microorganism. Firstly, electrons have to be transported at the cell surface, which in Gram-negative bacteria presents an additional problem of electron transfer across the ~6nm of the outer membrane. Secondly, the electrons must be transferred to or from the terminal electron acceptors or donors. This review covers the known mechanisms that bacteria use to transport electrons across the cell envelope to external electron donors/acceptors. In Gram-negative bacteria, electron transfer across the outer membrane involves the use of an outer membrane β-barrel and cytochrome. These can be in the form of a porin-cytochrome protein, such as Cyc2 of Acidithiobacillus ferrooxidans, or a multiprotein porin-cytochrome complex like MtrCAB of Shewanella oneidensis MR-1. For mineral-respiring organisms, there is the additional challenge of transferring the electrons from the cell to mineral surface. For the strict anaerobe Geobacter sulfurreducens this requires electron transfer through conductive pili to associated cytochrome OmcS that directly reduces Fe(III)oxides, while the facultative anaerobe S. oneidensis MR-1 accomplishes mineral reduction through direct membrane contact, contact through filamentous extensions and soluble flavin shuttles, all of which require the outer membrane cytochromes MtrC and OmcA in addition to secreted flavin.
Topics: Bacterial Outer Membrane Proteins; Cytochrome c Group; Electron Transport; Ferric Compounds; Gallionellaceae; Geobacter; Iron; Minerals; Oxidation-Reduction; Porins; Shewanella
PubMed: 27134022
DOI: 10.1016/bs.ampbs.2016.02.002 -
Virulence Dec 2023subspecies ( ) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres' respiratory outbreaks. We...
BACKGROUND
subspecies ( ) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres' respiratory outbreaks. We characterized genomic and phenotypic changes in 15 serial isolates from two CF patients (1S and 2B) with chronic pulmonary M. massiliense infection leading to death, as well as four isolates from a CF centre outbreak in which patient 2B was the index case.
RESULTS
Comparative genomic analysis revealed the mutations affecting growth rate, metabolism, transport, lipids (loss of glycopeptidolipids), antibiotic susceptibility (macrolides and aminoglycosides resistance), and virulence factors. Mutations in 23S rRNA, 4, porin locus and R genes occurred in isolates from both CF patients. Interestingly, we identified two different spontaneous mutation events at the mycobacterial porin locus: a fusion of two tandem porin paralogs in patient 1S and a partial deletion of the first porin paralog in patient 2B. These genomic changes correlated with reduced porin protein expression, diminished C-glucose uptake, slower bacterial growth rates, and enhanced TNF-α induction in mycobacteria-infected THP-1 human cells. Porin gene complementation of porin mutants partly restored C-glucose uptake, growth rate and TNF-α levels to those of intact porin strains.
CONCLUSIONS
We hypothesize that specific mutations accumulated and maintained over time in , including mutations shared among transmissible strains, collectively lead to more virulent, host adapted lineages in CF patients and other susceptible hosts.
Topics: Humans; Anti-Bacterial Agents; Cystic Fibrosis; Genomics; Glucose; Lung; Mutation; Mycobacterium; Mycobacterium abscessus; Tumor Necrosis Factor-alpha; Porins
PubMed: 37221835
DOI: 10.1080/21505594.2023.2215602 -
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 -
Advances in Protein Chemistry and... 2022The outer membrane of a gram-negative bacteria encapsulates the plasma membrane thereby protecting it from the harsh external environment. This membrane acts as a... (Review)
Review
The outer membrane of a gram-negative bacteria encapsulates the plasma membrane thereby protecting it from the harsh external environment. This membrane acts as a sieving barrier due to the presence of special membrane-spanning proteins called "porins." These porins are β-barrel channel proteins that allow the passive transport of hydrophilic molecules and are impermeable to large and charged molecules. Many porins form trimers in the outer membrane. They are abundantly present on the bacterial surface and therefore play various significant roles in the host-bacteria interactions. These include the roles of porins in the adhesion and virulence mechanisms necessary for the pathogenesis, along with providing resistance to the bacteria against the antimicrobial substances. They also act as the receptors for phage and complement proteins and are involved in modulating the host cellular responses. In addition, the potential use of porins as adjuvants, vaccine candidates, therapeutic targets, and biomarkers is now being exploited. In this review, we focus briefly on the structure of the porins along with their important functions and roles in the host-bacteria interactions.
Topics: Adjuvants, Vaccine; Anti-Bacterial Agents; Cell Membrane; Gram-Negative Bacteria; Porins
PubMed: 35034723
DOI: 10.1016/bs.apcsb.2021.09.004 -
Pathogens and Disease Mar 2016Emergent rational drug design techniques explore individual properties of target biomolecules, small and macromolecule drug candidates, and the physical forces governing... (Review)
Review
Emergent rational drug design techniques explore individual properties of target biomolecules, small and macromolecule drug candidates, and the physical forces governing their interactions. In this minireview, we focus on the single-molecule biophysical studies of channel-forming bacterial toxins that suggest new approaches for their inhibition. We discuss several examples of blockage of bacterial pore-forming and AB-type toxins by the tailor-made compounds. In the concluding remarks, the most effective rationally designed pore-blocking antitoxins are compared with the small-molecule inhibitors of ion-selective channels of neurophysiology.
Topics: Antitoxins; Bacterial Toxins; Drug Design; Drug Discovery; Inhibitory Concentration 50; Porins; Structure-Activity Relationship
PubMed: 26656888
DOI: 10.1093/femspd/ftv113 -
Sovremennye Tekhnologii V Meditsine 2021was to develop a new software tool for identifying gene mutations that determine the porin-mediated resistance to antibiotics in gram-negative bacteria and to...
UNLABELLED
was to develop a new software tool for identifying gene mutations that determine the porin-mediated resistance to antibiotics in gram-negative bacteria and to demonstrate the functionality of this program by detecting porin-mediated resistance to carbapenems in clinical isolates of .
MATERIALS AND METHODS
The proposed algorithm is based on searching for a correspondence between the reference and the studied genes. When the sought nucleotide sequence is found in the analyzed genome, it is compared with the reference one and analyzed. The genomic analysis is then verified by comparing between the amino acid sequences encoded by the reference and studied genes. The genes of the susceptible ATCC 27853 strain were used as the reference nucleotide sequences encoding for porins (OprD, OpdD, and OpdP) involved in the transport of carbapenems into the bacterial cell. The complete genomes of clinical isolates from the PATRIC database 3.6.9 and our own collection were used to test the functionality of the proposed program. The analyzed isolates were phenotypically characterized according to the CLSI standard. The search for carbapenemase genes in the studied genomes of was carried out using the ResFinder 4.1.
RESULTS
The developed program for detecting the genetic determinants of non-plasmid antibiotic resistance made it possible to identify mutations of various types and significance in the porin genes of clinical isolates. These mutations led to modifications of the peptide structure of porin proteins. Single amino acid substitutions prevailed in the OpdD and OpdP porins of carbapenem-susceptible and carbapenem-resistant isolates. In the carbapenem-resistant strains, the gene encoding for OprD porin was found heavily modified, including insertions and/or deletions, which led to premature termination of porin synthesis. In several isolates resistant to meropenem, no mutations were detected in the gene encoding for OprD, which might be associated with alternative mechanisms of resistance to carbapenems.
CONCLUSION
The proposed software product can become an effective tool for deciphering the molecular genetic mechanisms of bacterial chromosomal resistance to antibiotics. Testing the program revealed differences between the occurrences of mutations significant for carbapenem resistance in the , , and genes.
Topics: Drug Resistance, Bacterial; Microbial Sensitivity Tests; Porins; Pseudomonas aeruginosa; Software
PubMed: 35265355
DOI: 10.17691/stm2021.13.6.02 -
Nature Sep 2020Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in...
Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore-but not the 12-helix pore-enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.
Topics: Cell Line; Computer Simulation; Cryoelectron Microscopy; Crystallography, X-Ray; Electric Conductivity; Escherichia coli; Genes, Synthetic; Hydrazines; Ion Channels; Ion Transport; Liposomes; Models, Molecular; Patch-Clamp Techniques; Porins; Protein Engineering; Protein Structure, Secondary; Solubility; Synthetic Biology; Water
PubMed: 32848250
DOI: 10.1038/s41586-020-2646-5 -
Cells Sep 2021Autophagy is a cellular recycling program which efficiently reduces the cellular burden of ageing. Autophagy is characterised by nucleation of isolation membranes, which...
Autophagy is a cellular recycling program which efficiently reduces the cellular burden of ageing. Autophagy is characterised by nucleation of isolation membranes, which grow in size and further expand to form autophagosomes, engulfing cellular material to be degraded by fusion with lysosomes (vacuole in yeast). Autophagosomal membranes do not bud from a single cell organelle, but are generated de novo. Several lipid sources for autophagosomal membranes have been identified, but the whole process of their generation is complex and not entirely understood. In this study, we investigated how the mitochondrial outer membrane protein porin 1 (Por1), the yeast orthologue of mammalian voltage-dependent anion channel (VDAC), affects autophagy in yeast. We show that deficiency reduces the autophagic capacity and leads to changes in vacuole and lipid homeostasis. We further investigated whether limited phosphatidylethanolamine (PE) availability in ∆ was causative for reduced autophagy by overexpression of the PE-generating phosphatidylserine decarboxylase 1 (Psd1). Altogether, our results show that deficiency is associated with reduced autophagy, which can be circumvented by additional overexpression. This suggests a role for Por1 in Psd1-mediated autophagy regulation.
Topics: Autophagosomes; Autophagy; Carboxy-Lyases; Mitochondria; Mitochondrial Proteins; Phosphatidylethanolamines; Porins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 34572064
DOI: 10.3390/cells10092416 -
Nature Reviews. Microbiology Mar 2020Gram-negative bacteria and their complex cell envelope, which comprises an outer membrane and an inner membrane, are an important and attractive system for studying the... (Review)
Review
Gram-negative bacteria and their complex cell envelope, which comprises an outer membrane and an inner membrane, are an important and attractive system for studying the translocation of small molecules across biological membranes. In the outer membrane of Enterobacteriaceae, trimeric porins control the cellular uptake of small molecules, including nutrients and antibacterial agents. The relatively slow porin-mediated passive uptake across the outer membrane and active efflux via efflux pumps in the inner membrane creates a permeability barrier. The synergistic action of outer membrane permeability, efflux pump activities and enzymatic degradation efficiently reduces the intracellular concentrations of small molecules and contributes to the emergence of antibiotic resistance. In this Review, we discuss recent advances in our understanding of the molecular and functional roles of general porins in small-molecule translocation in Enterobacteriaceae and consider the crucial contribution of porins in antibiotic resistance.
Topics: Anti-Bacterial Agents; Bacterial Outer Membrane Proteins; Biological Transport; Cell Membrane; Drug Resistance, Bacterial; Enterobacteriaceae; Porins
PubMed: 31792365
DOI: 10.1038/s41579-019-0294-2 -
Trends in Microbiology Apr 2024Neisseria gonorrhoeae is a human-specific pathogen responsible for the sexually transmitted infection, gonorrhoea. N. gonorrhoeae promotes its survival by manipulating... (Review)
Review
Neisseria gonorrhoeae is a human-specific pathogen responsible for the sexually transmitted infection, gonorrhoea. N. gonorrhoeae promotes its survival by manipulating both innate and adaptive immune responses. The most abundant gonococcal outer-membrane protein is PorB, an essential porin that facilitates ion exchange. Importantly, gonococcal PorB has several immunomodulatory properties. To subvert the innate immune response, PorB suppresses killing mechanisms of macrophages and neutrophils, and recruits negative regulators of complement to the gonococcal cell surface. For manipulation of adaptive immune responses, gonococcal PorB suppresses the capability of dendritic cells to stimulate proliferation of T cells. As gonococcal PorB is highly abundant in outer-membrane vesicles, consideration of the immunomodulatory properties of this porin is critical when designing gonococcal vaccines.
Topics: Humans; Gonorrhea; Neisseria gonorrhoeae; Porins; Cell Membrane; Immunity
PubMed: 37891023
DOI: 10.1016/j.tim.2023.10.002