In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

Vollan, Hilde Synnøve; Tannæs, Tone; Vriend, Gert; Bukholm, Geir

doi:10.3390/ijms17040599

Cited by 13 publications

(16 citation statements)

References 129 publications

(148 reference statements)

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“…TC subclass 1.B includes β-barrel porins. These proteins form transmembrane pores usually permitting the energy-independent passage of solutes across the outer membranes of Gram-negative bacteria [20, 21]. Among the strains, BT has the largest number of such proteins (108).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of transport proteins in seven Bacteroides species

Zafar

Saier

2018

PLoS ONE

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The communities of beneficial bacteria that live in our intestines, the gut microbiome, are important for the development and function of the immune system. Bacteroides species make up a significant fraction of the human gut microbiome, and can be probiotic and pathogenic, depending upon various genetic and environmental factors. These can cause disease conditions such as intra-abdominal sepsis, appendicitis, bacteremia, endocarditis, pericarditis, skin infections, brain abscesses and meningitis. In this study, we identify the transport systems and predict their substrates within seven Bacteroides species, all shown to be probiotic; however, four of them (B. thetaiotaomicron, B. vulgatus, B. ovatus, B. fragilis) can be pathogenic (probiotic and pathogenic; PAP), while B. cellulosilyticus, B. salanitronis and B. dorei are believed to play only probiotic roles (only probiotic; OP). The transport system characteristics of the four PAP and three OP strains were identified and tabulated, and results were compared among the seven strains, and with E. coli and Salmonella strains. The Bacteroides strains studied contain similarities and differences in the numbers and types of transport proteins tabulated, but both OP and PAP strains contain similar outer membrane carbohydrate receptors, pore-forming toxins and protein secretion systems, the similarities were noteworthy, but these Bacteroides strains showed striking differences with probiotic and pathogenic enteric bacteria, particularly with respect to their high affinity outer membrane receptors and auxiliary proteins involved in complex carbohydrate utilization. The results reveal striking similarities between the PAP and OP species of Bacteroides, and suggest that OP species may possess currently unrecognized pathogenic potential.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics of transport proteins in seven Bacteroides species

Zafar

Saier

2018

PLoS ONE

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“…In a second step, we calculated the secondary structure content of our model as well as phosphoporin and OmpF crystal structures, and we then compared to the Omp2a experimental circular dichroism (CD) data (Table 1) which reports a majority % of β-strands followed by a high % of coil in the extracellular loops for several bacterial porins (Vollan, Tannaes, Vriend, & Bukholm, 2016). In our model, the βstrands % are slightly smaller than in the other porins but the dimensions of the barrel are well retained: 3.5 nm in width for 4.5 nm in height (Zeth & Thein, 2010).…”

Section: Resultsmentioning

confidence: 99%

3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes

Lopes-Rodrigues

Zanuy

Alemán

et al. 2018

Journal of Biomolecular Structure and Dynamics

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Brucella melitensis is a pathogenic bacterium responsible for brucellosis in mammals and humans. Its outer membrane proteins control the diffusion of solutes through the cell, and they consequently have a crucial role in the design of new diagnostics and vaccines. In this work, we have investigated the structure and dynamics of the Brucella melitensis porin Omp2a, combining a threading method and all-atom molecular dynamics simulations in lipid bilayers. The model proposed for Omp2a shows structural characteristics similar to bacterial porins such as Phosphoporin and OmpF, enhancing the relevance of the predicted structure. Moreover, molecular dynamics simulations demonstrate the stability with time of both the barrel and its inner channel placed in an environment mimicking the natural membrane. It is shown that the structure is well retained in the three systems while the POPE membrane tends to reduce the size of the inner pore. The gathered information on structure will help to understand the Omp2a functions and promote the development of new nanotechnologies and vaccine applications.

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“…However, it has been proven that improper antimicrobial therapy can be decreased through using an empiric combination therapy. However, combination therapy is a useful method for obtaining a synergistic consequences and preventing the emergence of resistance (49,68,(70)(71)(72)(73)(74)(75)(76).…”

Section: Discussionmentioning

confidence: 99%

Overview Perspective of Bacterial Strategies of Resistance to Biocides and Antibiotics

Goudarzi

Navidinia

2019

Arch Clin Infect Dis

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Context: Considerable controversy surrounds the use of biocides in an ever-growing range of consumer products and the eventuality that their indiscriminate consumption might decrease biocide effectiveness and modify susceptibilities to antibiotics. Several line of evidence suggest that exposure to biocides may cause increased antibiotic resistance. Thus, we reviewed the common resistance strategies of bacteria against both biocides and antibiotics. Methods: Several publications have explained the cell target of biocides and the various mechanisms used by bacterial cells to escape biocides' toxic activity. Here, we briefly reviewed the commonly used resistance mechanisms of bacteria against both biocides and antibiotics. Results: Biocides could act on multiple sites in microorganisms and cause resistance by non-specific means. We mentioned several mechanisms such as efflux pumps, cell wall changes to the reduction of permeability, genetic linkage with both biocide resistance genes and antibiotic resistance genes, the penetration/uptake changes in envelope by passive diffusion, effect on the integrity and morphology of membrane, and effects on diverse key steps of bacterial metabolism. Along with this toxic effect and stress, bacterial cells express some similar defense strategies that can overlap the main functions conferring resistance versus structurally nonrelated molecules. Conclusions: It can be stated that healthcare-associated, community-acquired, and nosocomial infections should be surveyed annually. Since biocide-antibiotic cross-resistance can be conferred by a number of distinct mechanisms, it is important to evaluate the propensity of a bacterium to express these mechanisms. Advances in modern genetic methods and the development of an assay using specific chemosensitizers or markers might allow the development of routine tests to identify resistance mechanisms. Further studies are needed to establish a correlation between biocide exposure (s) and development of antibiotic resistance, but the number of studies in the clinical or environmental settings is limited.

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In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

Cited by 13 publications

References 129 publications

Comparative genomics of transport proteins in seven Bacteroides species

Comparative genomics of transport proteins in seven Bacteroides species

3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes

Overview Perspective of Bacterial Strategies of Resistance to Biocides and Antibiotics

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