Capturing the mutational landscape of the beta-lactamase TEM-1


Abstract

Adaptation proceeds through the selection of mutations. The distribution of mutant fitness effect and the forces shaping this distribution are therefore keys to predict the evolutionary fate of organisms and their constituents such as enzymes. Here, by producing and sequencing a comprehensive collection of 10,000 mutants, we explore the mutational landscape of one enzyme involved in the spread of antibiotic resistance, the beta-lactamase TEM-1. We measured mutation impact on the enzyme activity through the estimation of amoxicillin minimum inhibitory concentration on a subset of 990 mutants carrying a unique missense mutation, representing 64% of possible amino acid changes in that protein reachable by point mutation. We established that mutation type, solvent accessibility of residues, and the predicted effect of mutations on protein stability primarily determined alone or in combination changes in minimum inhibitory concentration of mutants. Moreover, we were able to capture the drastic modification of the mutational landscape induced by a single stabilizing point mutation (M182T) by a simple model of protein stability. This work thereby provides an integrated framework to study mutation effects and a tool to understand/define better the epistatic interactions.

Submission Details

ID: LPbrW77i

Submitter: Connie Wang

Submission Date: July 31, 2017, 11:46 a.m.

Version: 1

Publication Details
Jacquier H;Birgy A;Le Nagard H;Mechulam Y;Schmitt E;Glodt J;Bercot B;Petit E;Poulain J;Barnaud G;Gros PA;Tenaillon O,Proc Natl Acad Sci U S A (2013) Capturing the mutational landscape of the beta-lactamase TEM-1. PMID:23878237
Additional Information

Study Summary

Number of data points 990
Proteins beta-lactamase TEM-1
Unique complexes 990
Assays/Quantities/Protocols Experimental Assay: Survival in Amoxicillin
Libraries Mutational landscape of beta-lactamase

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1AXB 1997-10-14T00:00:00+0000 2.0 TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI INHIBITED WITH AN ACYLATION TRANSITION STATE ANALOG
1BT5 1998-09-02T00:00:00+0000 1.8 CRYSTAL STRUCTURE OF THE IMIPENEM INHIBITED TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI
1BTL 1993-11-01T00:00:00+0000 1.8 CRYSTAL STRUCTURE OF ESCHERICHIA COLI TEM1 BETA-LACTAMASE AT 1.8 ANGSTROMS RESOLUTION
1CK3 1999-04-27T00:00:00+0000 2.28 N276D MUTANT OF ESCHERICHIA COLI TEM-1 BETA-LACTAMASE
1ERM 2000-04-06T00:00:00+0000 1.7 X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-1-ACETAMIDO-2-(3-CARBOXYPHENYL)ETHANE BORONIC ACID
1ERO 2000-04-06T00:00:00+0000 2.1 X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-2-PHENYLACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL BORONIC ACID
1ERQ 2000-04-06T00:00:00+0000 1.9 X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-1-ACETAMIDO-2-(3-CARBOXY-2-HYDROXYPHENYL)ETHYL BORONIC ACID
1ESU 2000-04-11T00:00:00+0000 2.0 S235A MUTANT OF TEM1 BETA-LACTAMASE
1FQG 2000-09-05T00:00:00+0000 1.7 MOLECULAR STRUCTURE OF THE ACYL-ENZYME INTERMEDIATE IN TEM-1 BETA-LACTAMASE
1JTD 2001-08-20T00:00:00+0000 2.3 Crystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
99.7 beta-lactamase TEM-1 Q48406 BLAT_KLEOX
100.0 beta-lactamase TEM-1 P62594 BLAT_SALTI
100.0 beta-lactamase TEM-1 P62593 BLAT_ECOLX