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Previous Article | Next Article 
Antimicrobial Agents and Chemotherapy, November 2000, p. 3224-3228, Vol. 44, No. 11
0066-4804/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Genetic Characterization of vanG, a
Novel Vancomycin Resistance Locus of Enterococcus
faecalis
Stuart J.
McKessar,1
Anne M.
Berry,1
Jan M.
Bell,2
John D.
Turnidge,2 and
James
C.
Paton1,*
Molecular Microbiology
Unit1 and Department of Infectious
Diseases,2 Women's and Children's
Hospital, North Adelaide, South Australia 5006, Australia
Received 20 March 2000/Returned for modification 9 June
2000/Accepted 21 August 2000
 |
ABSTRACT |
Enterococcus faecalis strain WCH9 displays a moderate
level of resistance to vancomycin (MIC = 16 µg/ml) and full
susceptibility to teicoplanin but is negative by PCR analysis using
primers specific for all known enterococcal vancomycin
resistance genotypes (vanA, vanB,
vanC, vanD, and vanE). We have
isolated and sequenced a novel putative vancomycin resistance
locus (designated vanG), which contains seven open
reading frames, from this strain. These are organized
differently from those of all the other enterococcal van
loci, and, furthermore, the individual vanG gene
products exhibit less than 50% amino acid sequence identity to other
van gene products.
| |
TEXT |
Glycopeptides inhibit cell wall
synthesis through the interaction of their N termini with the
D-alanyl-D-alanine termini of peptidoglycan precursors (25). The resulting complexes
prevent the transglycosylases from incorporating
disaccharide pentapeptide subunits into the growing peptidoglycan
chain, thereby inhibiting cell wall synthesis (4). In
enterococci, both intrinsic and acquired resistance to glycopeptides
occurs via a common mechanism involving modification of the
peptidoglycan biosynthetic pathway (7). Six enterococcal
vancomycin resistance genotypes have been described and
characterized. Four of these (vanA, vanB,
vanD, and vanE) are acquired mechanisms and the
other two (vanC1 and vanC2/C3 specific to
Enterococcus gallinarum and Enterococcus casseliflavus/Enterococcus flavescens, respectively [the
vanC2 and vanC3 genotypes are closely
related, with the loci containing minor sequence differences, and are
therefore jointly referred to herein as vanC2/C3;
likewise, there is debate over whether E. casseliflavus and
E. flavescens are actually separate species, and they are
jointly referred to herein as E. casseliflavus/E. flavescens]) are intrinsic properties (15, 18, 21).
The genes for the VanA vancomycin resistance phenotype are located on
the 10.8-kb transposable element Tn1546, which encodes 7 polypeptides involved in resistance. These polypeptides function together to confer high-level resistance to vancomycin and
teicoplanin (6, 7), as well as variable levels of
resistance to all other glycopeptides (18). The VanB
resistance phenotype confers variable levels of resistance to
vancomycin but leaves the organism susceptible to teicoplanin
(8, 13). VanD is characterized by resistance to
moderate levels of vancomycin and to low levels of teicoplanin
(21), while the VanE resistance phenotype exhibits low-level
resistance to vancomycin but full susceptibility to teicoplanin
(15).
Enterococci of the VanA, VanB, and VanD phenotypes produce a suite of
functionally homologous proteins, including ligases (VanA, VanB, and
VanD) resulting in the formation of peptidoglycan precursors
terminating in D-Ala-D-Lac (18, 21),
dehydrogenases (VanH, VanHB, and VanHD)
which reduce pyruvate to D-lactate (7, 10,
11), dipeptidases (VanX, VanXB, and
VanXD) which hydrolyze the glycopeptide-susceptible cell
wall precursors ending in D-Ala-D-Ala (7,
11, 24), and carboxypeptidases (VanY, VanYB, and
VanYD) (5, 11, 14) which cleave the C-terminal
D-Ala residue of late peptidoglycan precursors
(22). VanE ligase synthesizes the formation of peptides
terminating in D-Ala-D-Ser, and serine racemase
activity has also been detected in VanE strains (15).
VanC1 and VanC2/C3 are intrinsic enterococcal resistance
phenotypes characterized by low-level resistance to
vancomycin but susceptibility to teicoplanin (7).
Three protein products of the vanC1 operon
have been characterized: VanC1, VanXYc, and VanT. VanC1 is a ligase that catalyzes the synthesis of cell wall precursors terminating in D-Ala-D-Ser (19).
VanXYc has both D,D-dipeptidase and
D,D-carboxypeptidase activities (23), while VanT
is a membrane-associated serine racemase which converts
L-Ser to D-Ser (3). Genes encoding a
putative two-component regulator (VanRc-VanSc)
are located downstream of the vanC1 locus (2).
Recently, we have investigated the genotype of Australian
isolates of vancomycin-resistant enterococci (VRE)
(9). Among the strains examined were four
Enterococcus faecalis isolates which exhibited
moderate resistance to vancomycin (MIC range, 12 to 16 µg/ml), but
full susceptibility to teicoplanin (MIC = 0.5 µg/ml), a
phenotype similar to that of VanB and VanE strains. The
four isolates were indistinguishable by
pulsed-field gel electrophoresis and were isolated from
inpatients at the same hospital in Brisbane, Queensland, Australia, in
1997. However, these strains were negative by PCR using primers
specific for all enterococcal vancomycin resistance genotypes known at
the time (vanA, vanB, vanC1,
vanC2/C3, and vanD) (9) and have since
tested negative by PCR using primers specific for the recently
described vanE genotype (15). In the present
study, we isolated and characterized the putative vancomycin resistance
locus from one of these isolates (WCH9).
Isolation of putative vancomycin resistance locus from E. faecalis WCH9.
In order to isolate a fragment of the
vancomycin resistance locus, E. faecalis WCH9 DNA was
extracted using the Wizard genomic DNA purification kit (Promega,
Madison, Wis.), and subjected to PCR amplification using the degenerate
primers V1 and V2 previously described by Perichon et al.
(21). These primers were designed to direct
amplification of an internal fragment from genes encoding glycopeptide resistance-associated ligases from a number of
gram-positive species. The resultant 1.63-kb PCR product was much
larger than expected and was purified using the BRESAspin PCR
purification kit (Bresatec Ltd., Adelaide, Australia) and cloned into
pGEMT-easy (Promega), generating plasmid pJCP1101. The
enterococcal DNA insert of this plasmid was then sequenced using dye
terminator chemistry on an ABI model 373A automated DNA sequencer.
Interestingly, analysis of the sequence revealed that
amplification of the 1.63-kb fragment was a consequence of
priming with only one of the degenerate primers (V1), presumably due to
the presence of an inverted repeat of the target sequence.
Nevertheless, BLASTX analysis (1) indicated that
the fragment encoded a putative protein with similarities to the
enterococcal VanB and VanA ligases (approximately 50 and 48% amino
acid sequence identity, respectively), and another with approximately
50% identity to the VanY D,D-carboxypeptidase of the
vanA locus.
In order to confirm that the isolated sequences were specific for
non-vanABCDE strains such as WCH9, a variety of VRE and sensitive enterococci were subjected to PCR using primers VANG1 (5'-CGGTTGTGCCGTACTTGGC-3') and VANG2
(5'-GGGTAAAGCCATAGTCTGGGGC-3'). These primers direct
amplification of an 810-bp fragment from the portion of the pJCP1101
insert encoding the ligase homologue. The PCR amplification conditions
used were the same as those previously described by Bell et al.
(9) for detection of the vanA, vanB, vanC1, and vanC2/C3 genotypes. The only strains
that yielded 810-bp PCR products were WCH9 and the three other related
non-vanABCDE VRE isolates. No PCR products were obtained
when DNA extracts from vancomycin-sensitive Enterococcus
faecium, E. faecalis vanA, E. faecalis vanB,
E. gallinarum vanC1, or vanC2/C3 E. casseliflavus/E. flavescens strains were tested (result not shown).
In order to isolate the remainder of the apparently novel
van locus, DNA from WCH9 was subjected to PCR using primers
on the basis of preliminary sequence analysis of inverse PCR fragments. Primers SM5 (5'-GTTGACGAATTCATATTCCCAGATAAA-3') and SM6
(5'-CGAAAGGAATTCTGGCATTGATTATTTTAG-3') directed
amplification of a 1,999-bp PCR product, which was cloned into
the EcoRI site of pBluescript KS (Stratagene, La Jolla,
Calif.) to generate plasmid pJCP1102. Plasmid pJCP1103 was constructed by cloning the 5,004-bp PCR product obtained using primers VANG2 and
SM7 (5'-CGGGACAAATAATTGGATGTC-3') into pGEMT-easy (see
Fig. 1).
DNA sequence analysis.
The sequence of the complete putative
vancomycin resistance locus was then determined by analysis of
the recombinant plasmids, and nested deletion derivatives thereof,
constructed according to the method of Henikoff (16).
Sequence data in the 5' direction of the region cloned in
pJCP1103 were also obtained by direct sequence analysis of an
additional inverse PCR product using primers SM30
(5'-CGATTGGAAAATCTGATCAATG-3') and SM31
(5'-CGTAACCTCCCGATATGAGCC-3') on
NdeI-digested, recircularized DNA. Although existing
enterococcal vancomycin resistance loci have been named vanA
through vanE, we designated this novel locus
vanG, because the name vanF was recently used for
a vanA-like locus in Paenibacillus popillae (20). Examination of the compiled sequence indicated that
the vanG locus was 7,652 nucleotides long and contained
seven complete open reading frames (ORFs), arranged as shown in Fig.
1. BLASTX analyses were performed to
identify the putative functions of the proteins, and the results are
summarized in Table 1. The 5' end of the
locus contains genes designated vanRG and
vanSG, encoding a putative two-component
regulatory system. The vanSG gene was
immediately followed by a stem-loop structure (
G = 
28.5 kcal/mol), suggesting that these two genes may be transcribed separately from the remainder of the locus, which encodes two putative
D,D-peptidases (VanYG1 and VanYG2),
the ligase (VanG), a racemase (VanTG), and a protein with
unknown function (VanWG). Interestingly, no obvious
promoter region could be found upstream of
vanYG1, and the nearest site with similarity to
consensus Escherichia coli promoter sequences is located
near the 3' end of vanWG. Thus, the ORFs
designated vanYG1 and
vanWG may or may not be transcribed. Each of the
genes in the vanG cluster is preceded by a potential ribosome binding site, although that for vanYG2
is very close to the initiation codon, which may result in a low
translation efficiency. An additional stem-loop structure
(G = 23.0 kcal/mol) is located approximately 20 nucleotides downstream of the vanTG termination
codon. BLASTX analysis of sequences downstream of this indicated a low
degree of similarity to a protein of unknown function (ORF9) from the
3' end of the E. faecalis conjugative transposon
Tn916 (GenBank accession number U09422).
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FIG. 1.
Map of region of E. faecalis WCH9 chromosome
containing the vanG locus, showing the location of the
various subclones used to determine the DNA sequence. The locations and
direction of transcription of the various ORFs are shown as solid
pointed boxes. The locations of two putative transcription terminators
are also indicated.
|
|
Similarities to other enterococcal van loci and gene
products.
The comparative genetic organization for the five VRE
van loci that have been fully sequenced to date is shown in
Fig. 2. Although except in the case of
vanC1 response regulator (R) and sensor protein
kinase (S) genes are located at the 5' end of the loci, the
organization of subsequent genes differs widely between van
types, suggesting diverse origins. Marked differences also occur at the
deduced amino acid sequence level. The alignment of the putative ligase
VanG with the respective ligases VanA, VanB, VanC1, and VanD is shown
in Fig. 3, and the percent amino acid
identity between each ligase is shown in Table
2. This shows that the degree of
similarity between VanG and the other ligases (39 to 47%) is no
greater than between any of the other proteins (values observed range
from 38% identity between VanC1 and VanD to 76% identity between VanA
and VanB). Thus, VanG is clearly not a minor variant of one of the
other enterococcal proteins and represents a distinct class of ligases.
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FIG. 2.
Genetic organization of the vanG locus,
compared with that of other enterococcal vancomycin resistance loci,
based on published sequence data for the vanA,
vanB, vanC1, and vanD loci (2, 6,
7, 11). ORFs encoding putative ligases and two-component
regulatory systems are shown in black and grey, respectively.
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FIG. 3.
Comparison of VanG with other enterococcal ligases. The
deduced amino acid sequence of VanG was aligned with those for VanA
(6), VanB (14), VanC1 (12), and VanD
(11) using CLUSTAL (17). Amino acid position
numbers are shown at the left of the sequences. Identical residues are
shaded black; residues with similar properties are shaded grey. Gaps
(dashes) have been introduced by the program to optimize the
alignment.
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|
View this table:
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TABLE 2.
Sequence identity between the deduced amino acid sequence
of VanG and those of other enterococcal ligases
|
|
The putative regulatory proteins VanRG and
VanSG had greatest identity with VanRD and
VanSD (54 and 57%, respectively). In addition,
VanRG also has 46% identity with VanR (over 236 amino acids [aa]) and 28% identity with VanRB (over 169 aa),
while VanSG has 42% identity with VanS (over 365 aa) and
20% identity with VanSB (over 274 aa). VanRG
has similar degrees of amino acid identity between both the N- and
C-terminal portions, which are the phosphorylation site and DNA-binding
regions, respectively. VanSG has a percent amino acid
identity in the C-terminal two-thirds, which include the histidine
kinase activity motif, greater than that in the N-terminal third, which
is involved in ligand binding.
The putative peptidase VanYG1, which may or may not be
transcribed, has a deduced amino acid sequence with 46% identity with that of VanYB (over 214 aa) and 27% identity with the
putative protein VanYG2 (over 177 aa). In addition, the
putative peptidase VanYG2 has 32% identity (over 247 aa)
and 33% identity (over 184 aa) with the VanY and VanYB
proteins, respectively. VanYG2 is approximately 49 and 14 amino acids shorter than its VanY and VanYB counterparts,
respectively. The vanG locus lacks a putative VanX
dipeptidase, indicating that the putative VanYG proteins may be similar to VanXYc of the vanC1 locus and
display both carboxypeptidase and dipeptidase activities.
Attempted transfer of vancomycin resistance.
Transfer of
vancomycin resistance from E. faecalis WCH9 to E. faecium ATCC 19434 was attempted by filter mating (26),
with selection on phenol red agar containing phenol red broth base (1.6% [wt/vol]), Bacto agar (1% [wt/vol]),
L-arabinose (1% [wt/vol]), and vancomycin (5 µg/ml).
However, although transmission of vancomycin resistance occurred when
vanB E. faecalis ATCC 51299 was mated with the sensitive
Enterococcus faecium recipient, transmission was not
demonstrated when the vanG strain was used as donor. Fines et al. (15) were similarly unable to demonstrate
transmission of the VanE phenotype. Transfer of vancomycin resistance
from E. faecalis WCH9 to another E. faecalis
strain was not attempted due to the lack of a selective marker capable
of distinguishing donor and recipient strains.
Conclusions.
In this study, we have isolated and characterized
a novel vancomycin resistance locus, designated vanG, from
E. faecalis strain WCH9, which locus displays a moderate
level of resistance to vancomycin and full susceptibility to
teicoplanin. The vanG locus contains seven ORFs, but
these are organized differently from all the other enterococcal
van loci characterized to date. Moreover, the
individual vanG gene products exhibit less than 50%
amino acid sequence identity to their respective homologues from the
other enterococcal van loci, suggesting diverse
evolutionary origins of vancomycin resistance in this genus. VanG
VRE appear to be rare, at least in Australia. The four
original strains were isolated from patients in a single institution over a relatively short period of time, consistent with
nosocomial spread. With the exception of reisolation from one of the
four original VanG VRE-carrying patients 12 months later, no further
strains belonging to this genotype have been detected.
However, its prevalence in other parts of the world remains to
be investigated.
Nucleotide sequence accession number.
The DNA sequence of the
vanG locus described here has been deposited with GenBank
under accession number AF253562.
| |
ACKNOWLEDGMENTS |
We are grateful to Graeme Nimmo for referring VRE isolates for characterization.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Molecular
Microbiology Unit, Women's and Children's Hospital, North Adelaide,
S.A. 5006, Australia. Phone: 61-8-8204 6302. Fax: 61-8-8204 6051. E-mail: patonj{at}wch.sa.gov.au.
| |
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Antimicrobial Agents and Chemotherapy, November 2000, p. 3224-3228, Vol. 44, No. 11
0066-4804/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
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