Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes in
            <i>Escherichia coli</i>

Chen, Xiongbin; Cai, Xuxia; Chen, Zewei; Wu, Jinjin; Hao, Gaofeng; Luo, Qing; Liu, Shuhong; Zhang, Junya; Hu, Yueming; Zhu, Guoqiang; Koester, Wolfgang; White, Aaron P.; Cai, Yi; Wang, Yejun

doi:10.1128/aem.00060-22

“…There seems to be confusion about the ompC genes in the published E. coli genomes. The ompC gene seems to have undergone substantial mosaic evolution [85] and ompC of E. coli ATCC 8739 has been previously described to be disrupted by an IS1 insertion [86]. Surprisingly, neither o mpC ( EcolC_1435 ) of the E. coli ATCC 8739 reference genome (CP000946.1)[86] nor respective genes in other accessible ATCC 8739 genomes (CP022959.1; CP033020.1) had a truncated ompC and instead showed 91.17% similarity with 100% query coverage when BLASTed against full length ompC ( b2215 ) of the E. coli K-12 (U00096.3).…”

Section: Resultsmentioning

confidence: 99%

Experimental evolution ofEscherichia colion solid silver, copper, stainless steel, and glass surfaces

Rosenberg,

Park,

Umerov

et al. 2024

Preprint

1

0

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To study bacterial adaptation to antimicrobial metal surfaces in application-relevant semi-dry environmental conditions,Escherichia coliATCC 8739 was exposed to copper, silver, stainless steel, and glass surfaces for thirty consecutive cycles in exposure conditions designed to select for either survival or growth. Subsequent mutation analysis did not find changes in overall mutation frequency that could lead to enhanced adaptation potential nor mutations incop, cus, cue, sil, pcoor general efflux genes known to actively maintain copper/silver homeostasis in copper or silver exposed populations compared to populations evolved on steel and glass control surfaces. However, mutations insilSrapidly activated the crypticsilefflux locus during silver ion challenge in liquid assay with the evolved populations and caused collateral increase in ampicillin and ciprofloxacin tolerance, indicating that efflux might be specific to granting heavy metal tolerance in liquid but not surface exposure format. Instead, during cyclic surface exposure mutations in genes related to cellular barrier functions and sulfur metabolism were enriched on copper and silver surfaces. This increased metal surface tolerance but had less to no protective effect in subsequent conventional MBC and MIC tests indicating that reducing bioavailability and passively restricting uptake of the toxic metals rather than active efflux contributes to increased viability on copper and silver surfaces compared to liquid format. Our findings highlight the critical importance of appropriate exposure conditions not only in efficacy assessment but also risk assessment of antimicrobial surfaces rendering results acquired via liquid tests not applicable for dry-use surfaces.ImportanceThis study examines the evolutionary adaptations ofEscherichia coliunder sublethal exposure to copper and silver surfaces, revealing a moderate increase in surface tolerance but no heightened mutation frequency or enhanced metal ion tolerance in standard tests. Notably, enriched mutations indicate a shift toward more energy-passive mechanisms of metal tolerance. Additionally, while enhanced silver efflux—with a collateral increase in antibiotic tolerance—was rapidly selected in a single round of silver exposure in liquid tests and substantially increased copper and silver ion tolerance in conventional test formats, the causal mutations did not improve viability on silver and copper surfaces, underscoring the different fitness dynamics of tolerance mechanisms dependent on exposure conditions. These findings emphasize the need for appropriate exposure conditions in evaluating of both efficacy and the potential risks of using antimicrobial surfaces, as the results from conventional liquid-based tests may not apply in solid contexts.

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“…The study investigating structures of beta-barrel porins including Escherichia coli LamB, OmpA, OmpC, and OmpF shows that these porins have mosaic evolution patterns resulting in high variability in their external parts. Interestingly, these regions coincide with the binding sites of bacteriophages (Chen et al 2022 ) which emphasizes another function of the porins like rapid avoidance of the invasion of phages or antibiotics.…”

Section: Introductionmentioning

confidence: 84%

Microbial membrane transport proteins and their biotechnological applications

Özkan,

Yılmaz,

Ergenekon

et al. 2024

World J Microbiol Biotechnol

7

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Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.

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“…Previous studies in Escherichia coli and Yersinia spp. have found evidence of extensive intra- and interspecies recombination in the genes coding for the surface exposed regions of OmpF and other major porin proteins [43, 44]. Less is known about the extent of HGT in the Neisserial porins and their role in antigenic variation and AMR.…”

Section: Introductionmentioning

confidence: 99%

Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis

Manoharan-Basil

¹

,

Gestels

²

,

Abdellati

³

et al. 2023

Microbial Genomics

3

0

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The PorB porins are the major pore-forming proteins in the genus Neisseria . The trimeric PorB porins consist of 16 highly conserved transmembrane domains that form an amphipathic β-sheet connected by short periplasmic turns and eight extracellular hydrophilic loops. These loops are immunogenic and also play an important role in mediating antimicrobial influx. This study sought to (i) characterize the variations in Neisserial loop 3(355–438 bp) associated with intermediate resistance to penicillin/tetracycline and (ii) evaluate if there was evidence of horizontal gene transfer in any of the loops. We collated an integrated database consisting of 19 018 Neisseria spp. genomes – 17 882 Neisseria gonorrhoeae , 114 Neisseria meningitidis and 1022 commensal Neisseria spp. To identify the porB alleles, a gene-by-gene approach (chewBBACA) was employed. To evaluate the presence of recombination events, the Recombination Detection Programme (RDP4) was used. In total, 3885 porB alleles were detected. Paralogues were identified in 17 Neisseria isolates. Putative recombination was identified in loop regions. Intraspecies recombination among N. gonorrhoeae isolates and interspecies recombination between N. meningitidis and commensal Neisseria spp., and N. gonorrhoeae and N. lactamica were identified. Here, we present a large-scale study of 19 018 Neisseria isolates to describe recombination and variation in the porB gene. Importantly, we found putative recombination in loop regions between the pathogenic and non-pathogenic Neisseria spp. These findings suggest the need for pheno- and genotypic surveillance of antimicrobial susceptibility in commensal Neisseria spp. to prevent the emergence of AMR in the pathogenic Neisseria . This article contains data hosted by Microreact.

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Mosaic Evolution of Beta-Barrel-Porin-Encoding Genes in Escherichia coli

Cited by 7 publications

References 66 publications

Experimental evolution ofEscherichia colion solid silver, copper, stainless steel, and glass surfaces

Experimental evolution ofEscherichia colion solid silver, copper, stainless steel, and glass surfaces

Microbial membrane transport proteins and their biotechnological applications

Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis

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