37/661 (2), Fort P.O.
Recent Res. Devel. Antimicrob. Agents & Chemother., 7 (2013): 1-21 ISBN: 978-81-308-0465-1
1. Bacterial antimicrobial efflux pumps
of the MFS and MATE transporter
families: A review
Sanath Kumar1, Jared T. Floyd3, Guixin He2 and Manuel F. Varela3
1QC Laboratory, Harvest and Post Harvest Technology Division, Central Institute of Fisheries
Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061 India; 2University of
Massachusetts, Lowell, Department of Clinical Laboratory and Nutritional Sciences, Lowell, MA
01854, USA; 3Eastern New Mexico University, Department of Biology, Portales, NM 88130, USA
Abstract. Bacteria are causative agents of human infectious
disease and are a serious public health concern due to drug and
multi-drug resistance determinants that reduce the clinical efficacy
of antimicrobial agents. Among the variety of antimicrobial
resistance mechanisms, drug and multi-drug efflux pumps
represent a significant cause of chemotherapeutic failure in the
treatment efforts of bacterial infectious disease. This chapter deals
mainly with bacterial drug and multi-drug efflux pump systems of
the major facilitator superfamily (MFS) and multi-drug and toxic
compound extrusion (MATE) family. Studies of these bacterial
anti-bacterial drug efflux systems will help our understanding of
their molecular mechanisms and may help reduce the conditions
that foster multi-drug resistance.
Importance of bacterial antimicrobial resistance
In human clinical medicine, infectious disease caused by pathogenic and
opportunistic bacteria are often treated with chemotherapeutic antimicrobial
Correspondence/Reprint request: Dr. Manuel F. Varela, Eastern New Mexico University, Department of Biology
Portales, NM 88130, USA. E-mail: Manuel.Varela@enmu.edu
Sanath Kumar et al.
agents (51). In many cases, however, disease-causing bacteria circumvent the
antimicrobial natures of such therapeutic drugs (41, 95, 96). Therefore, drug
and multi-drug resistant mechanisms in bacteria that are causative agents of
infectious disease may reduce the efficacy of antimicrobial agents (42, 43).
In particular, infectious diseases involving multi-drug resistant bacteria may
be recalcitrant to chemotherapeutic efforts, thus confounding patient recovery
and increasing morbidity and mortality rates (7, 27). Hence, infectious
diseases caused by multi-drug resistant bacteria represent a serious public
health concern. Thus, it is important to have an understanding of such
bacterial drug and multi-drug resistance mechanisms to find the means to
circumvent bacterial drug resistances and thereby restore clinical efficacy of
Overview of bacterial resistance mechanisms
Bacteria may be intrinsically resistant to various drugs, or after exposure
to antimicrobial agents, bacterial variants may develop drug resistance
mechanisms. These resistance determinants reduce the antimicrobial activities
of the drugs. There are 4 major molecular mechanisms of bacterial drug
resistance. (i) Enzymatic drug inactivation involves the metabolic degradation
of the antimicrobial agent to a form that is deactivated and, thus, no longer
effective in killing or inhibiting the growth of the bacterium (101). (ii) Drug
target alteration involves the variation of the drug cellular target. A drug that is
no longer able to effectively bind its target will be unable to work against the
bacterium. Altered bacterial targets include, for instance, the ribosome, nucleic
acid replication machinery, the bacterial cell wall, and a biosynthetic metabolite
pathway (24, 37, 98). (iii) Reduced drug permeability involves the inability of
the drug to gain entry into the cytoplasm of the bacterial cell. Such a drug
resistant bacterium might have opted to reduce the expression of a putative
drug transport system in the membrane thus reducing cellular drug entry (12).
(iv) Antimicrobial agent efflux pump systems operate by extruding drugs from
the bacterial cell thereby reducing the effective cellular drug concentrations
(35). As will be described below, drug efflux pumps are embedded in the
biological membrane and may be energized passively or actively.
Antimicrobial efflux mechanisms
Currently, classes of antimicrobial efflux proteins can be separated into 5
major families based on the functional properties of efflux, such as energy
source utilized, substrate(s) transported, the number of membrane spanning
helices, and the binding domain(s) present.
Bacterial drug efflux pumps
ATP-binding cassette superfamily
Members of the ATP-binding cassette (ABC) superfamily of transporters
function as efflux and import systems in both eukaryotic and prokaryotic
systems (11, 49). These ABC proteins are the only group of solute
transporters that utilize energy via ATP-dependent hydrolysis to move
substances such as amino acids, sugars, drugs, and proteins, across the
membrane against their solute concentration gradients (33, 48). In bacteria
these ABC permeases arrange into 6 transmembrane α-helical segments that
associate as covalently linked homo-dimers or hetero-dimers, accompanied
by two nucleotide binding domains for ATP hydrolysis (11, 33, 48).
Resistance nodulation cell division superfamily
The resistance-nodulation-cell-division (RND) superfamily of solute
transporters consists of a large periplasmic domain that assembles with
periplasmic fusion proteins and an outer membrane pore to form a complete
tripartite channel from the inner cytoplasm past the outer membrane in
Gram-negative bacteria (48, 61). This family of membrane proteins is an
efficient mechanism for membrane transport via proton antiport because this
system completely extrudes harmful substances from the bacterial cell (61).
The most well known RND efflux pump is the AcrAB-TolC system of
Small multi-drug resistance family
The small multi-drug resistance (SMR) group of drug/proton antiporters
are composed of 4 transmembrane spanning α-helical segments that function
arguably as a tetramer or dimer (1, 9). Members of this family are capable of
transporting substrates such as aminoglycosides, and lipophillic cations
(1, 9). The well characterized SMR pumps include Smr of S. aureus and
EmrE of E.coli (9).
Multi-drug and toxic compound extrusion family
Although originally thought to be a member of the MFS group of
membrane proteins, NorM from Vibrio parahemolyticus was placed into a
new family, the multi-drug and toxic compound extrusion (MATE) family of
Na+/drug antiporters due to sequence dissimilarity (36). The MATE family of
transporters consists of 12 hydrophobic transmembrane domains. Members of
this family are capable of extruding compounds such as fluoroquinolones,
Sanath Kumar et al.
ethidium bromide, benzalkonium chloride, and acriflavine (36). Homologues
of MATE transporters have been described in the human liver and kidneys
(36). Since their discovery, two MATE family transporters (PmpM of
P.aeroginosa and AbeM of A. baumannii) have been described that can
utilize a proton gradient as the primary mechanism for drug antiport (36).
Major facilitator superfamily
The major facilitator superfamily (MFS) is the largest family of
secondary active solute transporters (73). The MFS members are ubiquitous
throughout all domains of life. Transporters of the MFS consist of 12 or 14
α-helical segments that typically function as a monomer within the
inner-membrane (38, 53, 54, 66, 67, 77, 78). The MFS group of drug
transporters consists of two domains that center around a central pore with
two domains that switch conformations from the cytoplasmic side of the
membrane to the periplasmic as a result of a gradient of Na+ or H+ ions (73).
Early and recent MFS single drug efflux pumps
The first drug efflux pump was discovered by Stuart Levy and colleagues
in which the efflux of the clinically-used antimicrobial agent tetracycline was
measured physiologically (44, 45). Denoted as TetA, these efflux pumps
represented the first known active antimicrobial agent extrusion systems and
that were powered by a proton gradient that in turn would be generated by
bacterial respiration following glycolysis and the Kreb’s cycle (58). TetR
proteins function to regulate gene expression (21, 29, 100). The TetA pumps
were found to be single-drug / H+ antiporters in which the proton gradient
caused the translocation of an H+ down its concentration gradient into the cell
and the concomitant transport of a tetracycline to the outside of the cell, thus
resulting in an active tetracycline efflux property (39, 40). Later, it was found
that the TetA pumps could be categorized into various classes, and early
determinants were denoted Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G),
Tet(H), Tet(J), Tet(31), from Gram-negative bacteria, Tet(K), Tet(L), Tet(Z),
Tet(33), from Gram-positive bacteria, and plasmid-encoded Tet(Y) (46).
Seminal work by Henderson and Griffith established that the TetA efflux
pumps shared a common evolutionary origin, similar amino acid sequences
and homology with drug antiporters (efflux pumps) for structurally-distinct
drug substrates, plus symporters and uniporters with structurally distinct
substrates, such as, e.g., sugars, amino acids, antimicrobial agents, Krebs
cycle intermediates, and ions (15, 19, 20, 52). These transporters constituted
members of a so-called major facilitator superfamily (MFS) of related
Bacterial drug efflux pumps
transporters (54, 67, 77). The MFS currently harbors thousands of closely-
and distantly-related solute transporters. Molecular, biochemical and
computational analyses showed that the TetA efflux pumps were integral
membrane proteins that traversed the biological membrane 12 or 14 times by
forming α-helices across the membrane, possessed a large central loop
composed of hydrophilic amino acid residues, and in which the N- and
C-termini resided in the cytoplasmic side of the membrane (74, 82). The best-
studied TetA efflux pump is the class B tetracycline-H+ encoded on the Tn10
transposon that had been isolated from Escherichia coli. Tet(B) was the
first tetracycline efflux pump to be purified to homogeneity (87). Multiple
sequence analysis revealed that TetA and members of the MFS shared
several categories of highly conserved amino acid sequence motifs (15).
The first category of sequence motifs is found in all or most of the MFS
members (77, 78, 106, 108). The second category of motifs is found only
within certain highly-related sub-families of the MFS (15). The third motif
category is found in groups of functionally-related transporters of the MFS
(76, 93, 94). Because these transporters of diverse substrates nonetheless
share similar sequences, and structures, it is thought that the members of
the MFS share a common evolutionary origin and, thus, a common
molecular mechanism of solute transport across the membrane, independent
of the nature of the solute structure. Interestingly, the TetA single-drug
efflux pumps share homology with multi-drug efflux pumps of the MFS.
Structure-function analyses of TetA efflux pumps demonstrated the
functional importance of a variety of amino acid residues for binding and
transporting the substrate and the energizing cation, H+, or for mediating
conformational changes that occur during the transport cycle (40). In
particular, certain charged amino acid residues were found to be important
for the activity of Tn10 class B tetracycline efflux pump (28, 105). Several
residues of a highly conserved amino acid sequence motif that is found
in the cytoplasmic loop between transmembrane domains 2 and 3 of
symporters and efflux pumps have been shown to be necessary for substrate
binding and transport (14, 107, 108).
Tet(40), a 12-TMS tetracycline efflux pump identified in Clostridium
saccharolyticum has 42% and 43% amino acid identity with TetA(P) and
TetA408(P) respectively, of C. perfringens (31). tet(40) genes were found
to be abundant in a human colon meta-genomic library. Another
tetracycline efflux pump which is phylogenetically distinct from the known
TetA efflux pumps is Tet(42) which has 30% sequence similarity with
TetA(Z), and has been reported from a deep subsurface bacteria (6). This
efflux pump is predicted to have 10-TMS unlike 12- or 14-TMS generally
found among TetA efflux pumps.
Sanath Kumar et al.
Current MFS multi-drug efflux pumps
MFS proteins constitute a major portion of the drug efflux pumps in
bacteria. For example, nearly half of the 37 efflux proteins in the E. coli
genome belong to the MFS of transporters (62). The availability of the whole
genome sequences of many pathogenic bacteria has enabled the identification
of putative efflux pumps of MFS family and study their substrate profiles.
Consequently, a number of efflux pumps have been described among diverse
groups of bacteria in the last decade. Many of these efflux pumps do not
confer clinical levels of resistance to the antibiotics. Nevertheless, the efflux
activity might result in the emergence of other mechanisms of resistance due
to the prolonged exposure to sub-lethal amounts of antibiotics. However, two
fundamental questions elude the efflux pump biologists; i) do the compounds
identified as efflux substrates represent the bonafide substrates of those efflux
pumps and ii) what physiological roles do efflux pumps have apart from the
observed efflux activity? In the following section, some of the recently
described efflux proteins in various Gram-negative and –positive bacteria
(Table 1) and their relevance in conferring antibiotic resistance have been
In Gram-negative bacteria, the
chloramphenicol and florfenicol is mediated by CmlA and Flo efflux pumps
encoded by genes of chromosomal or plasmid origin and share about 57%
sequence similarity at amino acid level (4). While Flo confers resistance to
both chloramphenicol and florfenicol, CmlA confers resistance only to
chloramphenicol. Kadlec et al (30) discovered CmlB1 from Bordetella
bronchiseptica, the transporter of which has about 75% similarity with
known CmlA proteins. CmlB1 is encoded on a plasmid and is responsible for
chloramphenicol resistance. This efflux pump remains to be studied with
respect to the energization of the efflux, its structure-function relationships,
and the distribution among other Gram-negative bacteria.
MdtM is a recently described chloramphenicol efflux pump from E. coli
(22). By site-directed mutagenesis, the role of Asp-22 and Arg-108 in TMS1
and TMS IV, respectively, in proton recognition has been demonstrated.
Interestingly, MdtM, with 41% sequence identity with the chloramphenicol
efflux pump MdfA, could reverse the effect of MdfA deletion suggesting that
these two efflux pumps are functionally redundant and dispensable with each
other (22, 23). Acinetobacter baumannii has a 12-TMS pump CraA that
effluxes chloramphenicol and with an amino acid similarity of about 61%
with MdfA of E. coli (75). The existence of homologous chloramphenicol
efflux pumps among the diverse Gram-negative bacteria suggests that
these pumps have retained some level of substrate specificity and may have
non-enzymatic resistance to
Bacterial drug efflux pumps
Table 1. Recently discovered bacterial efflux pumps of the Major Facilitator
Superfamily (MFS) and their preferred substrates.
pump of amino
Number Prominent substrates References
(6) Tet42 429
lincomycin, fusidic acid,
(55, 69, 81)
LmrS 480 (13)
EmrD-3 379 linezolid, rifampin,
evolved to perform other, yet to be determined, physiological functions
leading to variations in their primary structure.
The efflux pumps of other Enterobacteriaceae members share sequence
homology. KmrA of K. pneumoniae closely resembles Smv of the
Salmonella enterica serotypes Typhi and Typhimurium in amino acid
Sanath Kumar et al.
sequence, and both confer high methyl viologen resistance (64). In addition,
KmrA extrudes ethidium bromide, acriflavin, methylene blue and quinacrine.
KmrA-like efflux pumps have been identified in many Gram-positive
and -negative bacteria (64). Serratia marcescens has an efflux pump SmfY
which has more than 70% amino acid similarity with KmrA, SmvA of
S. Typhimurium, LfrA of Mycobacterium smegmatis, SgcB of Streptomyces
globisporus, VarS of Streptomyces virginiae and QacA of Staphylococcus
aureus. SmfY confers elevated resistance to several antimicrobials such as
acriflavine, DAPI, norfloxacin and benzalkonium chloride (83). Homologues
of some efflux pumps, which were originally believed to be confined to
Gram-positive bacteria only, have been discovered in Gram-negative
bacteria. One such example is Mef(B) of E. coli which is located on a non-
conjugative plasmid in some strains of porcine E. coli. Mef(B) effluxes
erythromycin and azithromycin and has about 35% amino acid similarity
with the macrolide efflux pump of Gram positive bacteria, Mef(A) (50). The
gene encoding Mef(B) is located upstream of the sulphonamide resistance
gene sul3. Based on its plasmid origin and the presence of flanking insertion
sequences (IS26), mef(B) is predicated to have been acquired by E. coli via
horizontal gene transfer (50). Similarly, the plasmid-borne QepA efflux pump
mediates fluoroquinolone resistance in E. coli (109). The qepA gene with a
high G+C content (72%) is present on a transposable element, and the QepA
protein shows sequence homology with the MFS proteins of Streptomyces
spp. and Nocardia spp., but less relatedness with the bacterial efflux proteins.
In the recent years, a rise in the level of antibiotic resistance in the global
pathogen V. cholerae has been noticed (110). A prominent drug efflux pump
EmrD-3 has been recently reported in our laboratory from an O1 serovar of
V. cholerae (84). This efflux pump of MFS family with 12 transmembrane
segments (TMS) shares homology with putative efflux pumps of many
Gram-positive and -negative bacteria. EmrD-3 resembles the Bcr/CflA
subfamily of membrane proteins such as Bcr (bicyclomycin resistance
protein) of E. coli, Flor (chloramphenicol and florfenicol resistance) protein
of S. enterica serotype Typhimurium DT104 and CmlA (chloramphenicol
resistance) of Pseudomonas. The antibiotic substrates of EmrD-3 include
linezolid, rifampin, trimethorprim, erythromycin, and chloramphenicol.
Though linezolid is not a drug of choice against V. cholerae, EmrD-3 very
efficiently extrudes this hydrophilic drug. It will be interesting to study at the
molecular level, how EmrD-3 is able to transport a range of both hydrophobic
and hydrophilic substances, a feature that may require conformational
changes by EmrD-3 within the membrane.
Some of the early efflux pumps such as NorA, QacA/B were discovered
in S. aureus and have been well characterized (88, 92). The genome of
Bacterial drug efflux pumps
S. aureus contains more than 20 efflux pumps, majority of which are of the
MFS type. NorA, NorB and NorC are the multi-drug efflux pumps while
Tet38 is a tetracycline-specific efflux pump in S. aureus, all negatively
regulated by a global regulator of gene expression MgrA (91). NorC, similar
to NorA and NorB, provides resistance to fluoroquinolones and has 61%
amino acid similarity with NorB (90, 91). SdrM, a 447 amino acid efflux
protein of S. aureus has a high efflux activity of acriflavine against a H+
gradient and in addition, effluxes norfloxacin (103). SdrM has 68% and 65%
amino acid similarity with NorB and Qac proteins. Some of the Gram-
positive efflux pumps are not active in an E. coli background or may exhibit
differential efflux activity as seen in the case of MdeA. The mdeA gene
cloned from a clinical strain of S. aureus N315 resulted in elevated resistance
to Hoechst 33342, ethidium bromide, rhodamine 6G and antibiotics
such as doxorubicin, daunorubicin, tetraphenylphosphonium chloride in
S. aureus RN4220, whereas in E. coli the resistance was conferred to
tetraphenylphosphonium chloride, Hoechst 33342 and norfloxacin (104).
Recently, a new MdeA transporter was cloned from S. mutans (32).
Though many of the efflux pumps are known to increase the
antimicrobial resistance of the host strain marginally, often to clinically
insignificant levels, some others confer high levels of resistance to clinically
important antibiotics. LmrS, a chromosomally-encoded multi-drug efflux
pump first discovered in a methicillin-resistant S. aureus strain (MRSA),
confers high levels of resistance to lincomycin, kanamycin, fusidic acid, and
linezolid (13). In addition, LmrS extrudes ethidium bromide, TPCL and SDS,
trimethoprim, florfenicol, chloramphenicol, erythromycin and streptomycin.
Several Gram-positive bacteria such as Enterococcus, Bacillus, Lactobacillus
and Listeria contain proteins that are homologous to LmrS. The highest
amino acid similarity (62%) of LmrS is with the lincomycin resistance
protein LmrB of Bacillus subtilis (13). The extrusion of linezolid and fusidic
acid resulting in clinically relevant resistance is of serious concern since these
two drugs offer last line of treatment to MRSA. However, the presence of
lmrS in methicillin sensitive strains of S. aureus suggests that the expression
of this gene is controlled by a yet unknown mechanism of gene regulation.
In some bacteria, the physiological roles of efflux pumps could be
predicted based on their substrate specificity as in the case of BetA (bile
efflux transporter) of the probiotic bacterium Bifidobacterium longum. BetA
is 683 amino acids long with the N-terminal 471 residues forming the permease
part of the protein while the remaining C-terminal residues fold into a large
loop containing a cystathionine-β-synthase (CBS) domain with a predicted
regulatory role (16). The homologues of BetA are widely distributed among
bifidobacteria and its bile efflux activity presumably facilitates their
Sanath Kumar et al.
colonization in the gastrointestinal tract. The exact mechanism of bile efflux
by BetA and its potentiators have not yet been elucidated.
A constitutively expressed efflux pump EfmA in Enterococcus faecium
has been found to be responsible for fluoroquinolone and macrolide
resistance and is homologous with efflux proteins of other Gram-positive
bacteria such as the Mdt(A) of Lactococcus lactis (86% similarity), MefE of
Streptococcus pneumoniae (78% similarity) and MefA of Streptococcus
pyogenes (76% similarity) and is predicted to be a 12-TMS protein (63).
Drug/H+ antiport activity has been demonstrated in this efflux protein.
Interestingly, the expression of efmA did not change when the bacterium was
grown in the presence of several antibiotics including the substrates of this
efflux pump (63). This observation supports the hypothesis that the actual
substrates of such efflux pumps may not be the ones identified in the
laboratory experiments or alternatively, protecting the host bacterium against
the antimicrobial compounds is not their primary physiological role.
Though it has been believed that efflux pumps may have important roles
in the virulence of pathogenic bacteria apart from unidentified physiological
functions, this has not been convincingly demonstrated in a bacterial system.
However, a recent work by Crimmins et al. (10) has identified the role of
two efflux pumps, MdrM and MdrT, in promoting the virulence of
L. monocytogenes due to their interaction with the host innate immune
system resulting in the secretion of beta interferon (IFN-β) and several other
cytokines (70). MdrM and MdrT have about 64% amino acid similarity
between them and are homologous with the QacA efflux pump of S. aureus.
These efflux pumps are used by the bacterium to induce host secretion of
small nucleic acid secondary messenger molecules called cyclic-di-AMP
(c-di-AMP) into the cytosol, which trigger the cytosolic immune response
cascade (99). This mechanism of interacting with the host cytosolic system is
crucial for the survival of the intracellular cytosolic pathogens such as
Both Lactococcus lactis and L. garvieae harbor a multiple drug
transporter Mdt(A) with some unusual structural features (68, 97). The 418
amino acids of Mdt(A) fold into 12 TMS and has two antiporter motifs (motif
C), on TMS5 and TMS9, and a putative ATP-binding site which are unique
to this protein. The gene encoding Mdt(A) is plasmid-borne in L. lactis but is
located on the chromosome in L. garvieae. In L. lactis, Mdt(A) effluxes
14-, 15- and 16-membered macrolides, lincosamides, streptogramins and
tetracyclines (68). Interestingly enough, though the addition of glucose
resulted in efflux, protonophores such as CCCP did not inhibit the efflux
activity (68). Mdt(A) found in L. garvieae has mutations (Val-154→Phe and
Ile-296→Val in TMS5 and TMS9 respectively), in the two antiporter motifs
Bacterial drug efflux pumps
(motif C); and this mutated protein did not confer elevated resistance to
erythromycin or tetracycline (97).
One of the well studied efflux pumps of the Gram-positive bacteria is the
LmrP protein of L. lactis responsible for the extrusion of structurally different
antibiotics such as tetracycline, streptogramin, lincosamide, and 14- and
15-membered macrolides (5, 69). This 408 amino acid pump of 12-TMS has
been subjected to extensive structure-function studies in order to understand
the molecular bases of drug efflux. Mazurkiewicz et al (55-57) performed
cysteine scanning analysis of LmrP by replacing Cys-270 (the only cysteine
in LmrP) with alanine followed by replacement of 19 acidic residues with
cysteine. The mutant proteins individually expressed were challenged with
fluorescein maleimide which showed that three residues, Asp-142, Glu-327,
and Glu-388, are embedded in the membrane suggesting important roles for
these residues since LmrP transports a range of hydrophobic drugs which
requires interactions with negatively charged amino acids (55). Amino acid
substitutions in these positions with cysteine, alanine, lysine, glutamate, or
aspartate individually suggested that negative charges in positions 142 (TMS-V)
and 327 (TMS-X) were critical for the recognition of cationic efflux
substrates by LmrP (55). This study also demonstrated conformational
changes in LmrP with cysteines at positions 142 and 327 upon binding with
cationic substrates ethidium bromide and Hoechst 33342 which resulted in
the exposure of these residues to the aqueous phase. Also, the differential
binding of these two substrates with individual cysteine mutants at positions
142 or 327 suggests that the LmrP has multiple drug binding sites (55, 81).
Some of the recently characterized MFS efflux pumps of Mycobacterium
tuberculosis include Stp (spectinomycin and tetracycline resistance protein)
which is present in all members of the M. tuberculosis complex (71). Another
drug/H+ antiporter P55 found in strains of M. tuberculosis complex is
responsible for decreased susceptibility to rifampin, clofazimine and several
other antimicrobial compounds (72). The structure-function relationships of
these efflux pumps are yet to be understood at the molecular level.
The MATE family of multi-drug efflux pumps
The drug efflux pumps of the MATE family represent an important
bacterial antimicrobial agent resistance mechanism (36). The first multi-drug
efflux pump of this family, NorM, was discovered in 1998 in the laboratory
of Tsuchiya, who cloned the norM gene from the Gram-negative bacterium
V. parahaemolyticus and found the pump to be energized by Na+ instead of
H+ (60). The Tsuchiya laboratory was also the first to construct an E. coli
bacterial host strain, KAM3, that was suitable for the cloning of new drug
Sanath Kumar et al.
efflux pump systems because it was made devoid of the known AcrAB efflux
pump system and contained a restriction endonuclease cloning system (60).
Later, the gene encoding YdhE, another MATE efflux pump, was removed
from the E. coli KAM3, and the resulting strain was called KAM32 (8).
These strains were later used to characterize the efflux pump activities of not
only MATE transporters, but of many others (36). Using these new
E. coli strains the range of substrates for NorM was found to include agents
such as ciprofloxacin, norfloxacin, kanamycin, streptomycin, trimethoprim,
daunomycin, doxorubicin, DAPI, acriflavine, and ethidium bromide (26, 59,
60, 102). The4 Tsuchiya laboratory was able to discover and physiologically
study many more multi-drug transporters of the MATE family, such as AbeM
from the Gram-negative pathogen Acinetobacter baumannii (86), HmrM
from Haemophilus influenzae (102), PmpM from P. aeruginosa (17), VcmA
from V. cholerae (26), VcrM from V. cholerae (25), VcmB from V. cholerae
(2), VcmD from V. cholerae (2), VcmH from V. cholerae (2), VcmM from
V. cholerae (2), and VmrA from V. parahaemolyticus (8). Additional
laboratories have cloned other MATE family drug efflux pumps, the work of
which is summarized in the review of Kuroda and Tsuchiya (36).
Recently, the gene encoding a MATE transporter, emmdR (previously
ECL_03329) from the chromosome of E. cloacae ATCC13047, was cloned
in the laboratory of He (18). This new MATE transporter, EmmdR, was
demonstrated to translocate ciprofloxacin and norfloxacin across the
membrane in a proton-dependent manner (18). Furthermore, EmmdR confers
reduced susceptibility in drug-hypersensitive E. coli KAM32 host cells to a
variety of structurally distinct antimicrobial agents, such as benzalkonium
chloride, levofloxacin, ethidium bromide, acriflavine, rhodamine6G, and
trimethoprim (18). This new efflux pump represents an emerging and
promising new avenue as a molecular target for putative efflux pump
inhibitors for the treatment of infectious disease caused by multi-drug
resistant E. cloacae (80).
Bacterial pathogens that harbor multi-drug efflux pump mechanisms
confound the clinical efficacy of anti-bacterial chemotherapy. Due to the
inability of anti-bacterial agents to work properly in such multi-drug resistant
pathogens, infectious disease caused by such pathogens may persist not only
in the clinical setting, but also in the community setting. Furthermore, genetic
transfer of drug and multi-drug resistance determinants between bacterial
species in the gut and other environments, such as in agriculture, may foster
widespread dissemination (79, 85). Promising work may be advanced in the
Bacterial drug efflux pumps
field of efflux pump inhibitors and drug efflux modulation (3, 47). From a
biomedical science research standpoint, understanding the structure-function
relationships inherent in multi-drug efflux pumps would be advantageous in
identifying good targets for chemotherapeutic modulation (35). Towards this
avenue, understanding the precise molecular mechanism of drug translocation
across the biological membrane in terms of kinetics, biochemistry and of
molecular structure changes during drug and cation transport, would serve to
elucidate novel targets for inhibition. Determination of protein crystal
structures and a correlation to actual drug and cation translocation during
the mechanistic transport cycle would be important. Changes in medical
practices such that antimicrobial drug prescriptions are provided only
prudently and when properly indicated (e.g., not for viral infections) would
be optimal towards reducing conditions that foster both resistance and genetic
element transfer (89). Genomic analyses of pathogenic versus non-pathogenic
bacteria may indicate which determinants are required for pathogenesis (34).
Study of the evolutionary aspects of multi-drug efflux pumps would be
insightful in terms of understanding efficacious chemotherapy for outbreaks
of infectious diseases.
This publication was supported by a grant from the National Institute of
General Medical Sciences (P20GM103451) of the National Institutes of Health.
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