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. 1999 Feb;43(2):367–370. doi: 10.1128/aac.43.2.367

Updated Sequence Information for TEM β-Lactamase Genes

Sylvie Goussard 1,*, Patrice Courvalin 1
PMCID: PMC89080  PMID: 9925535

Abstract

The sequences of the promoter regions and of the structural genes for 13 penicillinase, extended-spectrum, and inhibitor-resistant TEM-type β-lactamases have been determined, and an updated blaTEM gene nomenclature is proposed.


In members of the family Enterobacteriaceae, the most prevalent mechanism of resistance to broad-spectrum β-lactams is detoxification of the drugs by plasmid-mediated enzymes that are variants of TEM and SHV penicillinases (4, 13). The TEM-derived extended-spectrum or inhibitor-resistant β-lactamases differ from the parental TEM-1 and TEM-2 penicillinases by various combinations of amino acid substitutions. The structural genes for TEM-1 penicillinases are designated blaTEM-1a and blaTEM-1b, and the structural gene for TEM-2 is designated blaTEM-2 (10). As an aid to the study of the mutational events which account for the sequence diversity of TEM-type β-lactamases and to the nomenclature of the numerous variants, we have determined and analyzed the sequences of the structural genes and of the promoters of various blaTEM genes. Amplification and direct sequencing of the PCR product were as described previously (15). The origins (Table 1) and the nucleotide changes in the blaTEM genes and the corresponding amino acid substitutions in the deduced sequence of the enzymes (Tables 2 and 3) are summarized.

TABLE 1.

Origins of the enzymes studied

Enzyme Alternate designation(s) Gene(s) Clinical isolate(s) Origin or reference
TEM-1 blaTEM-1c E. coli BM2729 This work
TEM-8 CAZ-2 blaTEM-8 K. pneumoniae HM12 14, 17
TEM-10 TEM-23, MGH-1 blaTEM-10b and blaTEM-23 E. coli F2 26
TEM-11 CAZ-lo blaTEM-11 E. coli 1724A 14, 27
TEM-12 TEM-101, YOU-2, CAZ-3 blaTEM-12c E. coli F1, E. coli MG32 26, 28
TEM-13 blaTEM-13 M. morganii BM2717 14
TEM-15 blaTEM-15a K. pneumoniae BM2730 14
TEM-15 TEM-17 blaTEM-15b K. pneumoniae BM2731 and BM2732 14
TEM-24 CAZ-6 blaTEM-24b E. aerogenes SLE48 This work
TEM-53 blaTEM-53 K. pneumoniae BM2733 This work
TEM-33 IRT-5 blaTEM-33b E. coli BM2725 This work
TEM-33 IRT-5 blaTEM-33c E. coli BM2724 This work
TEM-54 blaTEM-54 E. coli BM2728 This work

TABLE 2.

Substitutions in blaTEM genes and derived penicillinases and extended-spectrum β-lactamases

Region and nucleotide no.a (amino acid no.b) Nucleotide (amino acid) in the following gene (enzyme):
blaTEM-1a (TEM-1 [Tn3]) blaTEM-1b (TEM-1 [Tn2]) blaTEM-2 (TEM-2 [Tn1]) blaTEM-1c (TEM-1) blaTEM-8 (TEM-8) blaTEM-10b (TEM-10)
Promoter region P3 P3 Pa and Pb P3 Pa and Pb Pa and Pb
 32 C C T C T T
 147 T T T T A T
 162 G G G G G G
 175 A G A A A G
Coding region
 226d C (Phe) T C C C T
 263 (21) C (Leu)21 C C C C C
 317 (39) C (Gln)39 C (Gln)39 A (Lys)39 C (Gln)39 A (Lys)39 C (Gln)39
 346d A (Glu) A G A G A
 436d C (Gly) T T T T T
 512 (104) G (Glu)104 G G G A (Lys)104 G
 604d G (Ala) T G G G T
 682d T (Thr) T C T C T
 692 (164) C (Arg)164 C C C A (Ser)164 A (Ser)164
 693 (164) G (Arg)164 G G G G G
 911 (237) G (Ala)237 G G G G G
 914 (238) G (Gly)238 G G G A (Ser)238 G
 917 (240) G (Glu)240 G G G G A (Lys)240
 925d G (Gly) G A G A G
 990 (265) C (Thr)265 C C C C C
Nucleotide (amino acid) in the following gene (enzyme):
blaTEM-11 (TEM-11) blaTEM-12c (TEM-12) blaTEM-13 (TEM-13) blaTEM-15a (TEM-15) blaTEM-15b (TEM-15) blaTEM-24b (TEM-24) blaTEM-53 (TEM-53)
Pa and Pb Pa and Pb or P3 P3 P4 Pa and Pb Pa and Pb Pa and Pb
T T/Cc C C T T T
T T T T T A T
G G G T G G G
A G A A G A A
C T C C T C C
C C C C C C T (Phe)21
A (Lys)39 C (Gln)39 A (Lys)39 C (Gln)39 C (Gln)39 A (Lys)39 C (Gln)39
G A G A A G G
T T T C T T T
G G G A (Lys)104 A (Lys)104 A (Lys)104 G
G T G G T G G
C T C T T C C
C A (Ser)164 C C C A (Ser)164 A (Ser)164
A (His)164 G G G G G G
G G G G G A (Thr)237 G
G G G A (Ser)238 A (Ser)238 G G
G G G G G A (Lys)240 G
G G A G G G A
C C T (Met)265 C C C C
a

Numbering is according to Sutcliffe (25). 

b

Numbering is according to Ambler et al. (1). 

c

Position 32 is T for blaTEM-12c from E. coli F1 (26) and C for blaTEM-12c from E. coli MG32 (28). 

d

Position at which only silent mutations occur. 

TABLE 3.

Substitutions in blaTEM genes and derived inhibitor-resistant β-lactamases

Region and nucleotide no.a (amino acid no.b) Nucleotide (amino acid) in the following gene (enzyme):
blaTEM-1a (TEM-1 [Tn3]) blaTEM-1b (TEM-1 [Tn2]) blaTEM-2 (TEM-2 [Tn1]) blaTEM-33b (TEM-33) blaTEM-33c (TEM-33) blaTEM-54 (TEM-54)
Promoter region P3 P3 Pa and Pb Pa and Pb P4 Pa and Pb
 32 C C T T C T
 162 G G G G T G
 175 A G A G A A
Coding region
 226c C (Phe) T C T C C
 317 (39) C (Gln)39 C (Gln)39 A (Lys)39 C (Gln)39 C (Gln)39 C (Gln)39
 346c A (Glu) A G A G A
 407 (69) A (Met)69 A A C (Leu)69 C (Leu)69 A
 436c C (Gly) T T T T C
 604c G (Ala) T G T G G
 682c T (Thr) T C T C T
 925c G (Gly) G A G A G
 929 (244) C (Arg)244 C C C C C
 930 (244) G (Arg)244 G G G G T (Leu)244
 1022 (276) A (Asn)276 A A A A A
a

Numbering is according to Sutcliffe (25). 

b

Numbering is according to Ambler et al. (1). 

c

Positions at which only silent mutations occur. 

Two promoters for initiation of transcription of the blaTEM genes have been described: the weak P3 promoter for blaTEM-1 in Tn3 (20) and, following a C-to-T substitution at position 32, the two overlapping promoters (Pa and Pb) which lead to a ca. 10-fold increase in transcriptional levels (8).

Penicillinases. (i) blaTEM-1c.

Escherichia coli BM2729 was isolated in 1989 and has a phenotype of resistance to β-lactam antibiotics which corresponds to the synthesis of a penicillinase. The corresponding blaTEM-1c gene differs from blaTEM-1a by the nucleotide substitution C436→T, which is silent.

(ii) blaTEM-13.

Morganella morganii BM2717 (14) harbored a plasmid that carries both the blaTEM-2 and the blaTEM-13 genes (data not shown). The sequence of blaTEM-13 differs from that of blaTEM-2 by C990→T, resulting in Thr265→Met, as determined by oligotyping (14). Most interestingly, upstream from blaTEM-13 and blaTEM-2 we found the weak promoter P3 (C32) instead of the expected strong promoters Pa and Pb. The presence of the two genes on the same replicon could therefore result from gene duplication followed by a point mutation.

Extended-spectrum β-lactamases. (i) blaTEM-8.

The TEM-8 extended-spectrum β-lactamase, later designated CAZ-2 (6), was detected in Klebsiella pneumoniae HM12, which was isolated in 1987, and the structural gene for the enzyme was sequenced (6, 17). The promoter region has a thymine at position 32 (Table 2) which was not reported for the gene for CAZ-2. The blaTEM-8 gene derives from blaTEM-2 by three base pair changes and differs from blaTEM-3 at position 692, where a C-to-A substitution leads to Arg164→Ser.

(ii) blaTEM-11.

The gene for the extended-spectrum β-lactamase TEM-11 harbored by E. coli 1724A (27) was oligotyped (14), with a remaining ambiguity found at position 238, and was characterized by restriction fragment length polymorphism analysis, which revealed an adenine at position 925 (2). However, sequence determination indicated G925 (Table 2). Thus, the blaTEM-11 gene differs from blaTEM-2 at two positions, G693→A, resulting in Arg164→His, and A925→G, which is silent. The strong promoters Pa and Pb for that gene are identical to those for blaTEM-2. The blaTEM-11 gene could therefore result from a recombination event, in the vicinity of position 692, between blaTEM-2, which would have provided the 5′ portion of the gene, and blaTEM-6 (11), which would have contributed the 3′ part of the gene. Alternatively, the blaTEM-11 gene could be a point mutant from a yet uncharacterized TEM-2 progenitor with a G925 or a double mutant of blaTEM-2.

(iii) blaTEM-15a.

The gene for extended-spectrum β-lactamase TEM-15 from K. pneumoniae BM2730 was oligotyped (14) and was sequenced without the promoter (21). We have resequenced the entire region whose sequence differs from that of blaTEM-1a at three positions: G512→A (Glu104→Lys), G914→A (Gly238→Ser), and G162→T. The last change occurs at position 1 of the −10 consensus Pribnow box sequence of the P3 promoter and has been shown to be responsible for the hyperproduction of TEM-1 (22). We suggest the designation P4 for this new promoter. Since this structural gene was apparently derived from blaTEM-1a, we propose the nomenclature blaTEM-15a.

(iv) blaTEM-15b.

The deduced amino acid sequence of blaTEM-15b is identical to that of blaTEM-15a. The enzyme, formerly designated TEM-17 on the basis of oligotyping (14), was therefore redesignated TEM-15. The TEM-17 sequence that we originally proposed has subsequently been found in Capnocytophaga ochracea (EMBL accession no. Y14574). The sequence of blaTEM-15b differs from that of blaTEM-1b at two positions: G512→A, which leads to Glu104→Lys, and G914→A, which results in Gly238→Ser, whereas the strong Pa and Pb promoters are present upstream. We thus suggest the designation blaTEM-15b since this gene is likely to be derived from blaTEM-1b. The TEM-15 β-lactamase displays the same amino acid substitutions which enlarge the substrate range of TEM-3, except that TEM-15 has Gln39 instead of Lys.

(v) blaTEM-12c and blaTEM-10b.

blaTEM-12c and blaTEM-10b originate from two E. coli strains, F1 and F2, which were isolated from the same patient at a 24-h interval (26). The blaTEM-12c gene is identical to blaTEM-12, which encodes YOU-2 (19), and is located downstream from the Pa and Pb promoters. Since blaTEM-12a refers to the structural gene for TEM-101 (9) and blaTEM-12b is the designation for the gene described by Heritage et al. (12) and also the gene for CAZ-3 (7), we propose the nomenclature blaTEM-12c. We also found a blaTEM-12c gene in E. coli MG32 (28). This gene was chromosomally located and, in an unusual fashion, was preceded by the weak P3 promoter.

The sequence of blaTEM-10b differs from that of blaTEM-12c by a single base pair change, G917→A, which results in Glu240→Lys. The blaTEM-10b gene is identical to blaTEM-10 from plasmids pJPQ100 and pMG223 in K. pneumoniae and pCLL2302 in E. coli (18, 19). These genes could be designated blaTEM-10b since they are derived from blaTEM-1b; blaTEM-10a would then correspond to the gene carried by pCLL2301 from K. pneumoniae (18), which is derived from blaTEM-1a. The structural genes for TEM-10 and TEM-12 have previously been detected in the same clinical isolate (3).

(vi) blaTEM-24b.

The sequence of blaTEM-24 encoding TEM-24 (or CAZ-6) has been published with only part of the promoter region (6), and we suggest the designation blaTEM-24a. The sequence of blaTEM-24b differs by a silent mutation (T682→C) from that of blaTEM-24a and is under the control of the strong promoters Pa and Pb. It has been proposed that blaTEM-24a could result from recombination of blaTEM-3 and blaTEM-5 between positions 604 and 682 (6). Similarly, blaTEM-24b could originate from a recombination event between positions 693 and 911 of blaTEM-8 (6, 17) and blaTEM-5 (23). Whatever the authentic origin of the gene may be, our observation documents dissemination of TEM-24 in Enterobacter aerogenes.

(vii) blaTEM-53.

The sequence of the new mutant gene blaTEM-53 differs from that of blaTEM-2 at three loci, with each base pair change leading to an amino acid substitution: C263→T (Leu21→Phe), A317→C (Lys39→Gln), and C692→A (Arg164→Ser). The gene is expressed from the strong promoters Pa and Pb. It is worth noting that the corresponding mature protein is identical to TEM-12. This gene could be secondary to a recombination event, between positions 436 and 512, of blaTEM-4 (23) or blaTEM-9 (16), which would provide the 5′ third of the gene, and blaTEM-7 (9), which would correspond to the 3′ two-thirds.

Inhibitor-resistant β-lactamases. (i) blaTEM-33.

The sequence of blaTEM-33, which we propose be renamed blaTEM-33a, has been published (24). We report here the sequence of two genes, designated blaTEM-33b and blaTEM-33c, that have been detected in clinical isolates (Table 1).

(ii) blaTEM-33b.

The structural gene has the mutation A407→C relative to the sequence of blaTEM-1b, resulting in Met69→Leu, and is under the control of the Pa and Pb promoters.

(iii) blaTEM-33c.

blaTEM-33c is derived from blaTEM-2 following two changes: A317→C (Lys39→Gln) and A407→C (Met69→Leu). The promoter region has the G162→T mutation, which is commonly found upstream from the genes for inhibitor-resistant β-lactamases. Thus, the blaTEM-33c gene is derived from that for the “TEM-2 like” enzyme (5), which consists of TEM-2 with Lys39→Gln and the T32→C and G162→T mutations upstream from the gene.

(iv) blaTEM-54.

blaTEM-54 has not yet been described and originates from E. coli BM2728 (Table 1). It derives from blaTEM-1a following one mutation, G930→T, which leads to the amino acid change Arg244→Leu, whereas the promoter region corresponds to Pa and Pb.

In summary, we have determined the sequences of the structural genes and of the promoter regions specifying two TEM-derived penicillinases, eight extended-spectrum β-lactamases, and three inhibitor-resistant β-lactamases. The sequence variety found probably reflects the existence in nature of genes other than blaTEM-1a, blaTEM-1b, blaTEM-1c, blaTEM-2, and blaTEM-13 for penicillinases. With the exception of chromosomal blaTEM-12, the genes were located downstream from strong promoters such as Pa and Pb and the new promoter P4.

Nucleotide sequence accession numbers.

The nucleotide sequence data for blaTEM-53 and blaTEM-54 have been submitted to the GenBank nucleotide sequence data library under accession no. AF104441 and AF104442, respectively.

Acknowledgments

We thank G. Arlet, G. Aubert, R. Bismuth, V. Jarlier, T. Lambert, P. Legrand, D. Lesage, G. Vedel, G. Verschraegen, and D. A. Weber for gifts of strains.

This work was supported in part by a Bristol-Myers Squibb Unrestricted Biomedical Research Grant in Infectious Diseases.

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