Fig 1.
A schematic representation of the combined effect of porin deficiency and β-lactamase production.
Left panel. In the wild type, the effective passage through porins leads to a high periplasmic concentration of carbapenems (red spots). The weak carbapenemase activity of the bacterium’s β-lactamases (i.e., ESBLs or AmpC enzymes), symbolized here by scissors, is outweighed by the high antibiotic concentration; the carbapenems bind and inhibit the target penicillin-binding proteins (PBPs). Middle and right panels. In mutant strains, defects in porins (loss of porins or porin alteration) slow the passage of carbapenems into the periplasmic space. The resulting low amounts of carbapenem are hydrolyzed by the bacterium’s β-lactamases, and thus do not reach the target PBPs thus contributing to carbapenem resistance. Created with BioRender.com.
Fig 2.
Overall structure of the OmpF porin of Escherichia coli.
A. Cartoons of E. coli OmpF homotrimers viewed from the periplasmic space. B. Side view of E. coli OmpF monomer. Gray, β-strands; blue, extracellular loops and α-helice; magenta, pore-constricting loop L3 and α-helice; red, short periplasmic turns and periplasmic α-helice. These graphics are based on PDB file 2OMF and were drawn by using the program UCSF ChimeraX 1.8 (https://www.rbvi.ucsf.edu/chimerax) [22].
Fig 3.
Overall structure of the OmpC porin of Escherichia coli.
A. Cartoons of E. coli OmpC homotrimers viewed from the periplasmic space. B. Side view of E. coli OmpF monomer. Gray, β-strands; blue, extracellular loops and α-helices; magenta, pore-constricting loop L3 and α-helice; red, short periplasmic turns and periplasmic α-helice. These graphics are based on PDB file 2J1N and were drawn by using the program UCSF ChimeraX 1.8 (https://www.rbvi.ucsf.edu/chimerax) [22].
Fig 4.
Transcriptional regulation of genes encoding the two porins OmpF and OmpC in Escherichia coli.
Transcriptional regulation of ompC and ompF expression by the two component systems EnvZ/OmpR and CpxRA. The preferential expression of one of the two porins depends on the level of OmpR-P which depends on the level of phosphorylation of EnvZ. Under low osmolarity, a low level of OmpR is phosphorylated. It is sufficient to bind to the ompF promoter, prompting high levels of OmpF on the membrane, but insufficient to bind to a low-affinity binding sites of ompC promoter. In contrast, under high osmolarity more OmpR-P is formed, which eventually binds to all sites of the ompF promoter, including F4, creating a loop which represses ompF transcription. Meanwhile, OmpR-P also binds with all sites of the ompC promoter thus increasing the level of OmpC. Created with BioRender.com.
Fig 5.
Post-transcriptional regulation of ompF expression in Escherichia coli.
Post-transcriptional regulation of ompF by the formation of an RNA/RNA hybrid between the small regulatory RNA micF and ompF mRNA preventing the binding of the ribosome. Three positive regulators MarA, SoxS, and Rob, themselves activated by different environmental stimuli, activate transcription of micF.
Fig 6.
Overall structure of the OprD porin of Pseudomonas aeruginosa.
A. Side view of OprD monomer unit. B. View of the OprD monomer unit from the top. Gray, β-strands; turquoise, extracellular loops and extracellular α-helices; orange, short periplasmic turns and periplasmic α-helices; magenta, pore-constricting loop L3; gold, pore-constricting loop L7 with dotted lines representing the L7 segment not visible on the structure; red, residues composing the basic ladder: Lys 375, Arg 391, Arg 389, Arg 30, and Arg 39 (from left to right). These graphics are based on PDB file 3SY7 and were drawn by using the program UCSF ChimeraX 1.8 (https://www.rbvi.ucsf.edu/chimerax) [22].
Fig 7.
Overall structure of the OpdP porin of Pseudomonas aeruginosa.
A. Side view of OpdP monomer unit. B. View of the OpdP monomer unit from the top. Gray, β-strands; turquoise, extracellular loops and extracellular α-helices; orange, short periplasmic turns and periplasmic α-helices; magenta, pore-constricting loop L3; gold, pore-constricting loop L7; dotted lines representing segment not visible on the structure. These graphics are based on PDB file 3SYB and were drawn by using the program UCSF ChimeraX 1.8 (https://www.rbvi.ucsf.edu/chimerax) [22].
Fig 8.
Regulatory network of oprD expression in Pseudomonas aeruginosa.
The expression of oprD is positively regulated by basic amino acids such as arginine [72] and negatively regulated by the transcriptional regulator MexT and three two-component systems: ParRS, CopRS (induced by Copper) and CzcRS (induced by Zinc). In addition, MexT, activates the expression of MexEF-OprN, ParRS activates the expression MexXY-OprM, both leading to antimicrobial resistance and CopRS and CzcRS activate the expression of the CzcCBA efflux system, leading to metal resistance. Created with BioRender.com.
Fig 9.
A schematic representation of the change in the secondary structure of ompK36 mRNA caused by a 25c > t transition.
A. The usual conformation of ompK36WT mRNA. B. The 25c > t transition leads to an intra-mRNA interaction between the uracil at position 25 (the red arrow) and the first adenine of the ribosome binding site at position −14. This specific interaction induces the formation of a stem structure that prevents the binding of the ribosome to the ribosome binding site (highlighted in gray), and thus restricts translation initiation. The figure was adapted from Wong and colleagues [75].
Table 1.
Impact of porin deficiency and β-lactamase production on carbapenem MICs for laboratory strains of Klebsiella pneumoniae and E. coli.
Table 2.
Impact of porin deficiency and β-lactamase production on carbapenem MICs for laboratory strains of Pseudomonas aeruginosa.
Table 3.
Overview of the interplay between carbapenems resistance and fitness/virulence in porin-deficient: examples of Klebsiella pneumoniae and Pseudomonas aeruginosa strains.