Article Figures & Data
Figures
- Figure 1.
Phylogeny of the TEM and SHV β-lactamases. Branch lengths, in nucleotide substitutions, are adjacent to the branches. Except as indicated all clades have posterior probabilities of >75%. Clades indicated by a single dot have probabilities of 60–75%, and those with two dots have probabilities of 50–59%. Because TEM β-lactamases are named strictly according to differences in protein sequence(http://www.lahey.org/studies/webt.htm) variants that differ only by silent mutations are assigned names such as TEM-1a, TEM-1b, and so on. A complete list of accession numbers and references is available at http://www.rochester.edu/College/BIO/labs/HallLab/TEM_Phylo.html.
Tables
- TABLE 2
MICs of evolved TEM alleles
Isolate no. Druga Clinical MICb pACSE3 TEM1 1 2 3 4 5 6 7a 7b 8 9 AMC 32 2 >4096 >4096 4096 4096 4096 4096 >4096 >4096 4096 >4096 4096 PIP 128 2 >2048 2048 2048 2048 2048 2048 2048 4096 1024 2048 2048 TZP 128 1 256 16 16 64 32 128 32 64 32 32 32 TIC 128 4 >4096 >4096 >4096 >4096 >4096 >4096 >4096 >4096 >4096 2048 >4096 TIM 128 4 512 256 128 128 128 256 128 128 64 128 128 CEF 32 4 1024 512 512 1024 512 512 64 256 64 64 256 CXM 32 8 16 512 512 1024 1024 1024 32 128 64 32 512 (CRO) 64 0.063 0.25 512 128 64 128 64 32 32 16 32 64 (CTX) 64 0.125 0.125 512 256 512 256 512 32 32 16 32 32 (CAZ) 32 0.25 1 128 64 64 64 512 2048 2048 512 2048 2048 FEP 32 0.063 0.5 16 8 8 8 8 32 16 4 64 8 (ATM) 32 0.125 0.5 32 64 64 64 128 512 1024 128 1024 512 -
The MICs of the antibiotic in which the lines were first selected appear italic.
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↵a Abbreviations for (β-lactams are the following: AMC, ampicillin; PIP, pipericillin; TZP, pipericillin and tazobactam (8:1); TIC, ticarcillin; TIM, ticarcillin and clavulanate; CEF, cephalothin; CXM, cefuroxime; CRO, ceftriaxone; CTX, cefotaxime; CAZ, ceftazadime; FEP, cefepime; ATM, aztreonam. The “extended-spectrum” drugs used for selection are in parentheses.
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↵b The indicated MICs are the NCCLS breakpoints for resistance (National Committee for Clinical Laboratory Standards 1999).
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- TABLE 3
Mutations recovered from in vitro evolved TEM alleles
Amino acid substitutionb DNA sitea Mutation 1 2 3 4 5 6 7a 7b 8 9 11 A>G Q6R 45 G>A s 105 A>G s s 199 C>G A42G 220 C>T s 304 G>A (E104K) (E104K) (E104K) (E104K) (E104K) (E104K) (E104K) 484 C>A (R164S) (R164S) R164Nc (R164S) 485 G>A (R164H) R164Nc 496 G>A E168K 498 G>A s 511 A>G I173V I173V I173V 512 T>G I173T 539 T>C (M182T) (M182T) 546 A>G s 562 T>C s 571 C>T s 660 C>T s 697 T>A s 703 G>T A237S A237S 706 G>A (G238S) (G238S) (G238S) (G238S) (G238S) (G238S) 709 G>A (E240K) (E240K) (E240K) 748 G>C D254H 749 A>G D254G 756 G>A s 782 C>T (T265M) (T265M) 784 A>G T266A 787 G>A G267R 825 C>A s -
Substitutions that have arisen multiple times in nature are in parentheses. s, a silent mutation.
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↵a Position in the coding sequence.
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↵b Substitutions are given as the TEM-1 amino acid according to the IUPAC single-letter code, the position in the protein numbered according to Ambler et al. (1991), and the mutant amino acid. E104K means that the glutamate at position 104 of TEM-1 was replaced by lysine.
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↵c The R164N mutation is the result of two base substitutions.
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- TABLE 4
Amino acid substitutions in naturally occurring extended-spectrum TEM alleles
Amino acid position Enzyme 21 39 42 51 92 104 153 164 182 237 238 240 244 265 268 TEM-1 L Q A L G E H R M A G E R T S TEM-2a K K S TEM-3 K K S TEM-5 S T K TEM-6 K H TEM-8 K K S S TEM-9 F K S M TEM-10 S K TEM-11 K H TEM-12 S TEM-15 K S TEM-17 K TEM-20 T S TEM-21 K K R S TEM-22 K K G S TEM-24 K K S T K TEM-25 F S M TEM-26 K S TEM-27 H K M TEM-28 H K TEM-29 H TEM-42 K V S K M TEM-43 K H T TEM-47 S K M TEM-48 F S K M TEM-49 F S K M G TEM-53 F S TEM-54 L TEM-60 K P K S TEM-66 K D K S TEM-72 T S K No. of times the mutation has arisen 3 1 1 1 1 7 1 H5 S7 3 G1 T2 5 6 1 2 1 -
Data are from http://www.lahey.org/studies/webt.htm. The number of times each mutation has arisen independently is based on the phylogeny shown in Figure 1.
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↵a TEM-2 is not an extended-spectrum allele but is shown because the Q39K substitution that is found in nine extended-spectrum alleles arose in TEM-2.
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