Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

Reddy, Bhaskara L.; Saier, Milton H.

doi:10.1371/journal.pone.0152733

Cited by 24 publications

(32 citation statements)

References 128 publications

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“…TC subclass 1.B includes β-barrel porins that are located in the outer membranes of these Gram-negative bacteria [25]. Similar to the distribution of TC subclass 1.A, the probiotic and pathogenic strains of E. coli contain more of these types of proteins than E. coli K-12 and the Salmonella strains.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains

Zafar

Saier

2017

Microbial Pathogenesis

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Escherichia coli is a genetically diverse species that can be pathogenic, probiotic, commensal, or a harmless laboratory strain. Pathogenic strains of E. coli cause urinary tract infections, diarrhea, hemorrhagic colitis, and pyelonephritis, while the two known probiotic E. coli strains combat inflammatory bowel disease and play a role in immunomodulation. Salmonella enterica, a close relative of E. coli, includes two important pathogenic serovars, Typhi and Typhimurium, causing typhoid fever and enterocolitis in humans, respectively, with the latter strain also causing a lethal typhoid fever-like disease in mice. In this study, we identify the transport systems and their substrates within seven E. coli strains: two probiotic strains, two extracellular pathogens, two intracellular pathogens, and K-12, as well as the two intracellular pathogenic S. enterica strains noted above. Transport systems characteristic of each probiotic or pathogenic species were thus identified, and the tabulated results obtained with all of these strains were compared. We found that the probiotic and pathogenic strains generally contain more iron-siderophore and sugar transporters than E. coli K-12. Pathogens have increased numbers of pore-forming toxins, protein secretion systems, decarboxylation-driven Na+ exporters, electron flow-driven monovalent cation exporters, and putative transporters of unknown function compared to the probiotic strains. Both pathogens and probiotic strains encode metabolite transporters that reflect their intracellular versus extracellular environments. The results indicate that the probiotic strains live extracellularly. It seems that relatively few virulence factors can convert a beneficial or commensal microorganism into a pathogen. Taken together, the results reveal the distinguishing features of these strains and provide a starting point for future engineering of beneficial enteric bacteria.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains

Zafar

Saier

2017

Microbial Pathogenesis

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“…The transmembrane portions of these proteins usually consist exclusively of β-strands which form a β-barrel [Reddy and Saier, 2016]. …”

Section: Resultsmentioning

confidence: 99%

Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS

Tajabadi

Medrano-Soto²,

Ahmadzadeh³

et al. 2017

Microb Physiol

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Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and B. exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm of the prey cell, Bex grows externally. We have analyzed and compared the transport proteins of these 2 organisms based on the current contents of the Transporter Classification Database (TCDB; www.tcdb.org). Bba has 103 transporters more than Bex, 50% more secondary carriers, and 3 times as many MFS carriers. Bba has far more metabolite transporters than Bex as expected from its larger genome, but there are 2 times more carbohydrate uptake and drug efflux systems, and 3 times more lipid transporters. Bba also has polyamine and carboxylate transporters lacking in Bex. Bba has more than twice as many members of the Mot-Exb family of energizers, but both may have energizers for gliding motility. They use entirely different types of systems for iron acquisition. Both contain unexpectedly large numbers of pseudogenes and incomplete systems, suggesting that they are undergoing genome size reduction. Interestingly, all 5 outer-membrane receptors in Bba are lacking in Bex. The 2 organisms have similar numbers and types of peptide and amino acid uptake systems as well as protein and carbohydrate secretion systems. The differences observed correlate with and may account, in part, for the different lifestyles of these 2 bacterial predators.

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“…To establish homology of OMBBs, previous studies created large databases of sequence similar proteins and then culled those sequences to increase the likelihood of true OMBBs (Remmert et al, 2010), (Reddy and Saier, 2016). Creating these large databases of sequences is extremely useful for teasing out evolutionary relationships within proteins that are related.…”

Section: Introductionmentioning

confidence: 99%

Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

Franklin

Nepomnyachiy

Feehan

et al. 2018

Preprint

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There are around 100 types of integral outer membrane proteins in each Gram negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels other than lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally-solved outer membrane β-barrels (OMBBs) by sequence we find evidence that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that efflux pumps have evolutionarily converged on the barrel. Finally, we find a possible ancestor for the OMBB efflux pumps as they are related to periplasmic components of the same pumps.

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Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

Cited by 24 publications

References 128 publications

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains

Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains

Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS

Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

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