Efflux pump

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Protein TolC, the outer membrane component of a tripartite efflux pump in Escherichia coli. 1ek9.jpg
Protein TolC, the outer membrane component of a tripartite efflux pump in Escherichia coli.
AcrB, the other component of pump, Escherichia coli. 1iwg.jpg
AcrB, the other component of pump, Escherichia coli.

An efflux pump is an active transporter in cells that moves out unwanted material. Efflux pumps are an important component in bacteria in their ability to remove antibiotics. [1] The efflux could also be the movement of heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals, bacterial metabolites and neurotransmitters. All microorganisms, with a few exceptions, have highly conserved DNA sequences in their genome that encode efflux pumps. Efflux pumps actively move substances out of a microorganism, in a process known as active efflux, which is a vital part of xenobiotic metabolism. This active efflux mechanism is responsible for various types of resistance to bacterial pathogens within bacterial species - the most concerning being antibiotic resistance because microorganisms can have adapted efflux pumps to divert toxins out of the cytoplasm and into extracellular media. [2]

Contents

Efflux systems function via an energy-dependent mechanism (active transport) to pump out unwanted toxic substances through specific efflux pumps. Some efflux systems are drug-specific, whereas others may accommodate multiple drugs with small multidrug resistance (SMR) transporters. [3] [4]

Efflux pumps are proteinaceous transporters localized in the cytoplasmic membrane of all kinds of cells. They are active transporters, meaning that they require a source of chemical energy to perform their function. Some are primary active transporters utilizing adenosine triphosphate hydrolysis as a source of energy, whereas others are secondary active transporters (uniporters, symporters, or antiporters) in which transport is coupled to an electrochemical potential difference created by pumping hydrogen or sodium ions into the cell.

Bacterial

Bacterial efflux pumps are classified into five major superfamilies, based on their amino acid sequence and the energy source used to export their substrates:

  1. The major facilitator superfamily (MFS) [5]
  2. The ABC transporters [5]
  3. The small multidrug resistance family (SMR) [5]
  4. The resistance-nodulation-cell division superfamily (RND) [5]
  5. The multi antimicrobial extrusion protein family (MATE). [5]

Of these, only the ABC superfamily are primary transporters, the rest being secondary transporters utilizing proton or sodium gradient as a source of energy. Whereas MFS dominates in Gram positive bacteria, the RND family was once thought to be unique to Gram negative bacteria. They have since been found in all major kingdoms. [6]

Structure

Efflux pumps generally consist of an outer membrane protein, a middle periplasmic protein, an inner membrane protein, and a transmembrane duct. The transmembrane duct is located in the outer membrane of the cell. The duct is also bound to two other proteins: a periplasmic membrane protein and an integral membrane transporter. The periplasmic membrane protein and the inner membrane protein of the system are coupled to control the opening and closing of the duct (channel). When a toxin binds to this inner membrane protein, the inner membrane proteins gives rise to a biochemical cascade that transmits signals to the periplasmic membrane protein and outer membrane protein to open the channel and move the toxin out of the cell. This mechanism uses an energy-dependent, protein-protein interaction that is generated by the transfer of the toxin for an H+ ion by the inner membrane transporter. [7] The fully assembled in vitro and in vivo structures of AcrAB-TolC pump have been solved by cryoEM and cryoET. [8] [9]

Function

Although antibiotics are the most clinically important substrates of efflux systems, it is probable that most efflux pumps have other natural physiological functions. Examples include:

The ability of efflux systems to recognize a large number of compounds other than their natural substrates is probably because substrate recognition is based on physicochemical properties, such as hydrophobicity, aromaticity and ionizable character rather than on defined chemical properties, as in classical enzyme-substrate or ligand-receptor recognition. Because most antibiotics are amphiphilic molecules - possessing both hydrophilic and hydrophobic characters - they are easily recognized by many efflux pumps.[ citation needed ]

Impact on antimicrobial resistance

The impact of efflux mechanisms on antimicrobial resistance is large; this is usually attributed to the following:

Eukaryotic

In eukaryotic cells, the existence of efflux pumps has been known since the discovery of P-glycoprotein in 1976 by Juliano and Ling. [18] Efflux pumps are one of the major causes of anticancer drug resistance in eukaryotic cells. They include monocarboxylate transporters (MCTs), multiple drug resistance proteins (MDRs)- also referred as P-glycoprotein, multidrug resistance-associated proteins (MRPs), peptide transporters (PEPTs), and Na+ phosphate transporters (NPTs). These transporters are distributed along particular portions of the renal proximal tubule, intestine, liver, blood–brain barrier, and other portions of the brain.

Inhibitors

Several trials are currently being conducted to develop drugs that can be co-administered with antibiotics to act as inhibitors for the efflux-mediated extrusion of antibiotics. As yet, no efflux inhibitor has been approved for therapeutic use, but some are being used to determine the prevalence of efflux pumps in clinical isolates and in cell biology research. Verapamil, for example, is used to block P-glycoprotein-mediated efflux of DNA-binding fluorophores, thereby facilitating fluorescent cell sorting for DNA content. Various natural products have been shown to inhibit bacterial efflux pumps including the carotenoids capsanthin and capsorubin, [19] the flavonoids rotenone and chrysin, [19] and the alkaloid lysergol. [20] Some nanoparticles, for example zinc oxide, also inhibit bacterial efflux pumps. [21]

See also

Related Research Articles

<span class="mw-page-title-main">Transmembrane protein</span> Protein spanning across a biological membrane

A transmembrane protein is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.

<span class="mw-page-title-main">Drug resistance</span> Pathogen resistance to medications

Drug resistance is the reduction in effectiveness of a medication such as an antimicrobial or an antineoplastic in treating a disease or condition. The term is used in the context of resistance that pathogens or cancers have "acquired", that is, resistance has evolved. Antimicrobial resistance and antineoplastic resistance challenge clinical care and drive research. When an organism is resistant to more than one drug, it is said to be multidrug-resistant.

<span class="mw-page-title-main">ABC transporter</span> Gene family

The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.

<span class="mw-page-title-main">P-glycoprotein</span> Mammalian protein found in Homo sapiens

P-glycoprotein 1 also known as multidrug resistance protein 1 (MDR1) or ATP-binding cassette sub-family B member 1 (ABCB1) or cluster of differentiation 243 (CD243) is an important protein of the cell membrane that pumps many foreign substances out of cells. More formally, it is an ATP-dependent efflux pump with broad substrate specificity. It exists in animals, fungi, and bacteria, and it likely evolved as a defense mechanism against harmful substances.

<i>Acinetobacter baumannii</i> Species of bacterium

Acinetobacter baumannii is a typically short, almost round, rod-shaped (coccobacillus) Gram-negative bacterium. It is named after the bacteriologist Paul Baumann. It can be an opportunistic pathogen in humans, affecting people with compromised immune systems, and is becoming increasingly important as a hospital-derived (nosocomial) infection. While other species of the genus Acinetobacter are often found in soil samples, it is almost exclusively isolated from hospital environments. Although occasionally it has been found in environmental soil and water samples, its natural habitat is still not known.

<span class="mw-page-title-main">Cross-resistance</span> Chemicals stop working at the same time

Cross-resistance is when something develops resistance to several substances that have a similar mechanism of action. For example, if a certain type of bacteria develops resistance to one antibiotic, that bacteria will also have resistance to several other antibiotics that target the same protein or use the same route to get into the bacterium. A real example of cross-resistance occurred for nalidixic acid and ciprofloxacin, which are both quinolone antibiotics. When bacteria developed resistance to ciprofloxacin, they also developed resistance to nalidixic acid because both drugs inhibit topoisomerase, a key enzyme in DNA replication. Due to cross-resistance, antimicrobial treatments like phage therapy can quickly lose their efficacy against bacteria. This makes cross-resistance an important consideration in designing evolutionary therapies.

<span class="mw-page-title-main">Multidrug and toxin extrusion protein 1</span> Protein-coding gene in the species Homo sapiens

Multidrug and toxin extrusion protein 1 (MATE1), also known as solute carrier family 47 member 1, is a protein that in humans is encoded by the SLC47A1 gene. SLC47A1 belongs to the MATE family of transporters that are found in bacteria, archaea and eukaryotes.

<span class="mw-page-title-main">Multidrug and toxin extrusion protein 2</span> Protein-coding gene in the species Homo sapiens

Multidrug and toxin extrusion protein 2 is a protein which in humans is encoded by the SLC47A2 gene.

Multi-antimicrobial extrusion protein (MATE) also known as multidrug and toxin extrusion or multidrug and toxic compound extrusion is a family of proteins which function as drug/sodium or proton antiporters.

<span class="mw-page-title-main">Plasmid-mediated resistance</span> Antibiotic resistance caused by a plasmid

Plasmid-mediated resistance is the transfer of antibiotic resistance genes which are carried on plasmids. Plasmids possess mechanisms that ensure their independent replication as well as those that regulate their replication number and guarantee stable inheritance during cell division. By the conjugation process, they can stimulate lateral transfer between bacteria from various genera and kingdoms. Numerous plasmids contain addiction-inducing systems that are typically based on toxin-antitoxin factors and capable of killing daughter cells that don't inherit the plasmid during cell division. Plasmids often carry multiple antibiotic resistance genes, contributing to the spread of multidrug-resistance (MDR). Antibiotic resistance mediated by MDR plasmids severely limits the treatment options for the infections caused by Gram-negative bacteria, especially family Enterobacteriaceae. The global spread of MDR plasmids has been enhanced by selective pressure from antimicrobial medications used in medical facilities and when raising animals for food.

<span class="mw-page-title-main">Acriflavine resistance protein family</span>

The Escherichia coliAcriflavine resistance encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents.

<span class="mw-page-title-main">Antibiotic resistance in gonorrhea</span>

Neisseria gonorrhoeae, the bacterium that causes the sexually transmitted infection gonorrhea, has developed antibiotic resistance to many antibiotics. The bacteria was first identified in 1879.

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily is a group of integral membrane protein families. The MOP flippase superfamily includes twelve distantly related families, six for which functional data are available:

  1. One ubiquitous family (MATE) specific for drugs - (TC# 2.A.66.1) The Multi Antimicrobial Extrusion (MATE) Family
  2. One (PST) specific for polysaccharides and/or their lipid-linked precursors in prokaryotes - (TC# 2.A.66.2) The Polysaccharide Transport (PST) Family
  3. One (OLF) specific for lipid-linked oligosaccharide precursors of glycoproteins in eukaryotes - (TC# 2.A.66.3) The Oligosaccharidyl-lipid Flippase (OLF) Family
  4. One (MVF) lipid-peptidoglycan precursor flippase involved in cell wall biosynthesis - (TC# 2.A.66.4) The Mouse Virulence Factor (MVF) Family
  5. One (AgnG) which includes a single functionally characterized member that extrudes the antibiotic, Agrocin 84 - (TC# 2.A.66.5) The Agrocin 84 Antibiotic Exporter (AgnG) Family
  6. And finally, one (Ank) that shuttles inorganic pyrophosphate (PPi) - (TC# 2.A.66.9) The Progressive Ankylosis (Ank) Family

The p-aminobenzoyl-glutamate transporter(AbgT) family (TC# 2.A.68) is a family of transporter proteins belonging to the ion transporter (IT) superfamily. The AbgT family consists of the AbgT (YdaH; TC# 2.A.68.1.1) protein of E. coli and the MtrF drug exporter (TC# 2.A.68.1.2) of Neisseria gonorrhoeae. The former protein is apparently cryptic in wild-type cells, but when expressed on a high copy number plasmid, or when expressed at higher levels due to mutation, it appeared to allow uptake (Km = 123 nM; see Michaelis–Menten kinetics) and subsequent utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs. p-Aminobenzoate is a constituent of and a precursor for the biosynthesis of folic acid. MtrF was annotated as a putative drug efflux pump.

Arsenite resistance (Ars) efflux pumps of bacteria may consist of two proteins, ArsB and ArsA, or of one protein. ArsA proteins have two ATP binding domains and probably arose by a tandem gene duplication event. ArsB proteins all possess twelve transmembrane spanners and may also have arisen by a tandem gene duplication event. Structurally, the Ars pumps resemble ABC-type efflux pumps, but there is no significant sequence similarity between the Ars and ABC pumps. When only ArsB is present, the system operates by a pmf-dependent mechanism, and consequently belongs in TC subclass 2.A. When ArsA is also present, ATP hydrolysis drives efflux, and consequently the system belongs in TC subclass 3.A. ArsB therefore appears twice in the TC system but ArsA appears only once. These pumps actively expel both arsenite and antimonite.

The 6TMS Neutral Amino Acid Transporter (NAAT) Family is a family of transporters belonging to the Lysine Exporter (LysE) Superfamily. Homologues are found in numerous Gram-negative and Gram-positive bacteria including many human pathogens. Several archaea also encode MarC homologues. Some of these organisms have 2 or more paralogues. Most of these proteins are of about the same size although a few are larger. They exhibit 6 putative TMSs. A representative list of members belonging to the NAAT family can be found in the Transporter Classification Database.

Multidrug resistance pumps also known Multidrug efflux pumps are a type of efflux pump and P-glycoprotein. MDR pumps in the cell membrane extrudes many foreign substances out of the cells and some pumps can have a broad specificity. MDR pumps exist in animals, fungi, and bacteria and likely evolved as a defense mechanism against harmful substances. There are seven families of MDRs and are grouped by homology, energy source, and overall structure.

<span class="mw-page-title-main">Resistance-nodulation-cell division superfamily</span>

Resistance-nodulation-division (RND) family transporters are a category of bacterial efflux pumps, especially identified in Gram-negative bacteria and located in the cytoplasmic membrane, that actively transport substrates. The RND superfamily includes seven families: the heavy metal efflux (HME), the hydrophobe/amphiphile efflux-1, the nodulation factor exporter family (NFE), the SecDF protein-secretion accessory protein family, the hydrophobe/amphiphile efflux-2 family, the eukaryotic sterol homeostasis family, and the hydrophobe/amphiphile efflux-3 family. These RND systems are involved in maintaining homeostasis of the cell, removal of toxic compounds, and export of virulence determinants. They have a broad substrate spectrum and can lead to the diminished activity of unrelated drug classes if over-expressed. The first reports of drug resistant bacterial infections were reported in the 1940s after the first mass production of antibiotics. Most of the RND superfamily transport systems are made of large polypeptide chains. RND proteins exist primarily in gram-negative bacteria but can also be found in gram-positive bacteria, archaea, and eukaryotes.

<span class="mw-page-title-main">Colin Hughes (microbiologist)</span> British microbiologist

Colin Hughes PhD ScD FLSW is a British microbiologist who has worked in the areas of bacterial virulence, motility and antibiotic resistance. He is Emeritus Professor of Microbiology at the University of Cambridge, Fellow of Trinity College Cambridge, and Fellow of the Learned Society of Wales.

<span class="mw-page-title-main">Multidrug-resistant bacteria</span>

Multidrug-resistant bacteria are bacteria that are resistant to three or more classes of antimicrobial drugs. MDR bacteria have seen an increase in prevalence in recent years and pose serious risks to public health. MDR bacteria can be broken into 3 main categories: Gram-positive, Gram-negative, and other (acid-stain). These bacteria employ various adaptations to avoid or mitigate the damage done by antimicrobials. With increased access to modern medicine there has been a sharp increase in the amount of antibiotics consumed. Given the abundant use of antibiotics there has been a considerable increase in the evolution of antimicrobial resistance factors, now outpacing the development of new antibiotics.

References

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  2. 1 2 Blanco P, Hernando-Amado S, Reales-Calderon JA, Corona F, Lira F, Alcalde-Rico M, Bernardini A, Sanchez MB, Martinez JL (February 2016). "Bacterial Multidrug Efflux Pumps: Much More Than Antibiotic Resistance Determinants". Microorganisms. 4 (1): 14. doi: 10.3390/microorganisms4010014 . PMC   5029519 . PMID   27681908.
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  4. ↑ Sun J, Deng Z, Yan A (October 2014). "Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations". Biochemical and Biophysical Research Communications. 453 (2): 254–67. doi: 10.1016/j.bbrc.2014.05.090 . PMID   24878531.
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  6. ↑ Lubelski J, Konings WN, Driessen AJ (September 2007). "Distribution and physiology of ABC-type transporters contributing to multidrug resistance in bacteria". Microbiology and Molecular Biology Reviews. 71 (3): 463–76. doi:10.1128/MMBR.00001-07. PMC   2168643 . PMID   17804667.
  7. ↑ Ughachukwu P, Unekwe P (July 2012). "Efflux pump-mediated resistance in chemotherapy". Annals of Medical and Health Sciences Research. 2 (2): 191–8. doi: 10.4103/2141-9248.105671 . PMC   3573517 . PMID   23439914.
  8. ↑ Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D (29 March 2017). "An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump". eLife. 6. doi: 10.7554/eLife.24905 . PMC   5404916 . PMID   28355133.
  9. ↑ Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z (14 June 2019). "In situ structure and assembly of the multidrug efflux pump AcrAB-TolC". Nature Communications. 10 (1): 2635. Bibcode:2019NatCo..10.2635S. doi: 10.1038/s41467-019-10512-6 . PMC   6570770 . PMID   31201302.
  10. ↑ Okusu H, Ma D, Nikaido H (January 1996). "AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants". Journal of Bacteriology. 178 (1): 306–8. doi:10.1128/jb.178.1.306-308.1996. PMC   177656 . PMID   8550435.
  11. ↑ Vecchione JJ, Alexander B, Sello JK (November 2009). "Two distinct major facilitator superfamily drug efflux pumps mediate chloramphenicol resistance in Streptomyces coelicolor". Antimicrobial Agents and Chemotherapy. 53 (11): 4673–7. doi:10.1128/AAC.00853-09. PMC   2772354 . PMID   19687245.
  12. ↑ Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF (May 2014). "Structure of the AcrAB-TolC multidrug efflux pump". Nature. 509 (7501): 512–5. Bibcode:2014Natur.509..512D. doi:10.1038/nature13205. PMC   4361902 . PMID   24747401.
  13. ↑ Rouquette C, Harmon JB, Shafer WM (August 1999). "Induction of the mtrCDE-encoded efflux pump system of Neisseria gonorrhoeae requires MtrA, an AraC-like protein". Molecular Microbiology. 33 (3): 651–8. doi: 10.1046/j.1365-2958.1999.01517.x . PMID   10417654.
  14. ↑ Pletzer D, Weingart H (January 2014). "Characterization of AcrD, a resistance-nodulation-cell division-type multidrug efflux pump from the fire blight pathogen Erwinia amylovora". BMC Microbiology. 14: 13. doi: 10.1186/1471-2180-14-13 . PMC   3915751 . PMID   24443882.
  15. 1 2 Morita Y, Sobel ML, Poole K (March 2006). "Antibiotic inducibility of the MexXY multidrug efflux system of Pseudomonas aeruginosa: involvement of the antibiotic-inducible PA5471 gene product". Journal of Bacteriology. 188 (5): 1847–55. doi:10.1128/JB.188.5.1847-1855.2006. PMC   1426571 . PMID   16484195.
  16. ↑ Alav I, Sutton JM, Rahman KM (February 2018). "Role of bacterial efflux pumps in biofilm formation". Journal of Antimicrobial Chemotherapy. 73 (8): 2003–2020. doi: 10.1093/jac/dky042 . PMID   29506149.
  17. ↑ Li XZ, Plésiat P, Nikaido H (April 2015). "The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria". Clinical Microbiology Reviews. 28 (2): 337–418. doi:10.1128/CMR.00117-14. PMC   4402952 . PMID   25788514.
  18. ↑ Juliano RL, Ling V (November 1976). "A surface glycoprotein modulating drug permeability in Chinese hamster ovary cell mutants". Biochimica et Biophysica Acta (BBA) - Biomembranes. 455 (1): 152–62. doi:10.1016/0005-2736(76)90160-7. PMID   990323.
  19. 1 2 Molnár J, Engi H, Hohmann J, Molnár P, Deli J, Wesolowska O, Michalak K, Wang Q (2010). "Reversal of multidrug resistance by natural substances from plants". Current Topics in Medicinal Chemistry. 10 (17): 1757–68. doi:10.2174/156802610792928103. PMID   20645919.
  20. ↑ Cushnie TP, Cushnie B, Lamb AJ (November 2014). "Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities" (PDF). International Journal of Antimicrobial Agents. 44 (5): 377–86. doi:10.1016/j.ijantimicag.2014.06.001. PMID   25130096. S2CID   205171789.
  21. ↑ Banoee M, Seif S, Nazari ZE, Jafari-Fesharaki P, Shahverdi HR, Moballegh A, Moghaddam KM, Shahverdi AR (May 2010). "ZnO nanoparticles enhanced antibacterial activity of ciprofloxacin against Staphylococcus aureus and Escherichia coli" (PDF). Journal of Biomedical Materials Research Part B: Applied Biomaterials. 93 (2): 557–61. doi:10.1002/jbm.b.31615. PMID   20225250.
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