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Radojković M, Ubbink M. Positive epistasis drives clavulanic acid resistance in double mutant libraries of BlaC β-lactamase. Commun Biol 2024; 7:197. [PMID: 38368480 PMCID: PMC10874438 DOI: 10.1038/s42003-024-05868-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/26/2024] [Indexed: 02/19/2024] Open
Abstract
Phenotypic effects of mutations are highly dependent on the genetic backgrounds in which they occur, due to epistatic effects. To test how easily the loss of enzyme activity can be compensated for, we screen mutant libraries of BlaC, a β-lactamase from Mycobacterium tuberculosis, for fitness in the presence of carbenicillin and the inhibitor clavulanic acid. Using a semi-rational approach and deep sequencing, we prepare four double-site saturation libraries and determine the relative fitness effect for 1534/1540 (99.6%) of the unique library members at two temperatures. Each library comprises variants of a residue known to be relevant for clavulanic acid resistance as well as residue 105, which regulates access to the active site. Variants with greatly improved fitness were identified within each library, demonstrating that compensatory mutations for loss of activity can be readily found. In most cases, the fittest variants are a result of positive epistasis, indicating strong synergistic effects between the chosen residue pairs. Our study sheds light on a role of epistasis in the evolution of functional residues and underlines the highly adaptive potential of BlaC.
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Affiliation(s)
- Marko Radojković
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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2
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Pines G, Pines A, Eckert CA. Highly Efficient Libraries Design for Saturation Mutagenesis. Synth Biol (Oxf) 2022; 7:ysac006. [PMID: 35734540 PMCID: PMC9205323 DOI: 10.1093/synbio/ysac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 11/30/2022] Open
Abstract
Saturation mutagenesis is a semi-rational approach for protein engineering where sites are saturated either entirely or partially to include amino acids of interest. We previously reported on a codon compression algorithm, where a set of minimal degenerate codons are selected according to user-defined parameters such as the target organism, type of saturation and usage levels. Here, we communicate an addition to our web tool that considers the distance between the wild-type codon and the library, depending on its purpose. These forms of restricted collections further reduce library size, lowering downstream screening efforts or, in turn, allowing more comprehensive saturation of multiple sites. The library design tool can be accessed via http://www.dynamcc.com/dynamcc_d/.
Graphical Abstract
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Affiliation(s)
- Gur Pines
- Department of Entomology, Institute of Plant Protection, Agricultural Research Organization, Rishon LeTsiyon, 7528809, Israel
| | | | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS6060, Oak Ridge, Tennessee, 37831, USA
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3
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Shimko TC, Fordyce PM, Orenstein Y. DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinformatics 2020; 36:3357-3364. [PMID: 32176271 DOI: 10.1093/bioinformatics/btaa162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/13/2020] [Accepted: 03/13/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High-throughput protein screening is a critical technique for dissecting and designing protein function. Libraries for these assays can be created through a number of means, including targeted or random mutagenesis of a template protein sequence or direct DNA synthesis. However, mutagenic library construction methods often yield vastly more nonfunctional than functional variants and, despite advances in large-scale DNA synthesis, individual synthesis of each desired DNA template is often prohibitively expensive. Consequently, many protein-screening libraries rely on the use of degenerate codons (DCs), mixtures of DNA bases incorporated at specific positions during DNA synthesis, to generate highly diverse protein-variant pools from only a few low-cost synthesis reactions. However, selecting DCs for sets of sequences that covary at multiple positions dramatically increases the difficulty of designing a DC library and leads to the creation of many undesired variants that can quickly outstrip screening capacity. RESULTS We introduce a novel algorithm for total DC library optimization, degenerate codon design (DeCoDe), based on integer linear programming. DeCoDe significantly outperforms state-of-the-art DC optimization algorithms and scales well to more than a hundred proteins sharing complex patterns of covariation (e.g. the lab-derived avGFP lineage). Moreover, DeCoDe is, to our knowledge, the first DC design algorithm with the capability to encode mixed-length protein libraries. We anticipate DeCoDe to be broadly useful for a variety of library generation problems, ranging from protein engineering attempts that leverage mutual information to the reconstruction of ancestral protein states. AVAILABILITY AND IMPLEMENTATION github.com/OrensteinLab/DeCoDe. CONTACT yaronore@bgu.ac.il. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Polly M Fordyce
- Department of Genetics
- Department of Bioengineering
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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4
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Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
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Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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5
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Verma D, Grigoryan G, Bailey-Kellogg C. Pareto Optimization of Combinatorial Mutagenesis Libraries. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1143-1153. [PMID: 30040654 PMCID: PMC8262366 DOI: 10.1109/tcbb.2018.2858794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In order to increase the hit rate of discovering diverse, beneficial protein variants via high-throughput screening, we have developed a computational method to optimize combinatorial mutagenesis libraries for overall enrichment in two distinct properties of interest. Given scoring functions for evaluating individual variants, POCoM (Pareto Optimal Combinatorial Mutagenesis) scores entire libraries in terms of averages over their constituent members, and designs optimal libraries as sets of mutations whose combinations make the best trade-offs between average scores. This represents the first general-purpose method to directly design combinatorial libraries for multiple objectives characterizing their constituent members. Despite being rigorous in mapping out the Pareto frontier, it is also very fast even for very large libraries (e.g., designing 30 mutation, billion-member libraries in only hours). We here instantiate POCoM with scores based on a target's protein structure and its homologs' sequences, enabling the design of libraries containing variants balancing these two important yet quite different types of information. We demonstrate POCoM's generality and power in case study applications to green fluorescent protein, cytochrome P450, and β-lactamase. Analysis of the POCoM library designs provides insights into the trade-offs between structure- and sequence-based scores, as well as the impacts of experimental constraints on library designs. POCoM libraries incorporate mutations that have previously been found favorable experimentally, while diversifying the contexts in which these mutations are situated and maintaining overall variant quality.
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6
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Abstract
Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids. Here, we provide detailed information on the Dynamic Management for Codon Compression (DYNAMCC) approaches that allow us to precisely define the desired amino acid composition to be introduced to a specific target site. DYNAMCC allows us to set usage thresholds and to eliminate undesirable stop and wild-type codons, thus allowing us to control library size and subsequently downstream screening efforts. The DYNAMCC algorithms are free of charge and are implemented in a website for easy access and usage: www.dynamcc.com .
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Affiliation(s)
- Gur Pines
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA. .,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA.,Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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7
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Verma D, Grigoryan G, Bailey-Kellogg C. Structure-based design of combinatorial mutagenesis libraries. Protein Sci 2015; 24:895-908. [PMID: 25611189 DOI: 10.1002/pro.2642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/14/2014] [Accepted: 01/11/2015] [Indexed: 01/27/2023]
Abstract
The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states.
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Affiliation(s)
- Deeptak Verma
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire
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8
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Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol 2014; 31:1581-92. [PMID: 24567513 PMCID: PMC4032126 DOI: 10.1093/molbev/msu081] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mutations are central to evolution, providing the genetic variation upon which selection acts. A mutation’s effect on the suitability of a gene to perform a particular function (gene fitness) can be positive, negative, or neutral. Knowledge of the distribution of fitness effects (DFE) of mutations is fundamental for understanding evolutionary dynamics, molecular-level genetic variation, complex genetic disease, the accumulation of deleterious mutations, and the molecular clock. We present comprehensive DFEs for point and codon mutants of the Escherichia coli TEM-1 β-lactamase gene and missense mutations in the TEM-1 protein. These DFEs provide insight into the inherent benefits of the genetic code’s architecture, support for the hypothesis that mRNA stability dictates codon usage at the beginning of genes, an extensive framework for understanding protein mutational tolerance, and evidence that mutational effects on protein thermodynamic stability shape the DFE. Contrary to prevailing expectations, we find that deleterious effects of mutation primarily arise from a decrease in specific protein activity and not cellular protein levels.
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Affiliation(s)
- Elad Firnberg
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
| | - Jason W Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University
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9
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Bordner AJ, Mittelmann HD. A new formulation of protein evolutionary models that account for structural constraints. Mol Biol Evol 2013; 31:736-49. [PMID: 24307688 DOI: 10.1093/molbev/mst240] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid sites. This is mainly due to the difficulty in formulating a computationally tractable model since rate matrices can no longer be used. Here, we introduce a general framework, based on factor graphs, for constructing probabilistic models of protein evolution with site interdependence. Conveniently, efficient approximate inference algorithms, such as Belief Propagation, can be used to calculate likelihoods for these models. We fit an amino acid substitution model of this type that accounts for both solvent accessibility and site-site correlations. Comparisons of the new model with rate matrix models and alternative structure-dependent models demonstrate that it better fits the sequence data. We also examine evolution within a family of homohexameric enzymes and find that site-site correlations between most contacting subunits contribute to a higher likelihood. In addition, we show that the new substitution model has a similar mathematical form to the one introduced in Rodrigue et al. (Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217), although with different parameter interpretations and values. We also perform a statistical analysis of the effects of amino acids at neighboring sites on substitution probabilities and find a significant perturbation of most probabilities, further supporting the significant role of site-site interactions in protein evolution and motivating the development of new evolutionary models similar to the one described here. Finally, we discuss possible extensions and applications of the new substitution model.
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10
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Kikis EA, Gidalevitz T, Morimoto RI. Protein homeostasis in models of aging and age-related conformational disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 694:138-59. [PMID: 20886762 DOI: 10.1007/978-1-4419-7002-2_11] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The stability of the proteome is crucial to the health of the cell, and contributes significantly to the lifespan of the organism. Aging and many age-related diseases have in common the expression of misfolded and damaged proteins. The chronic expression of damaged proteins during disease can have devastating consequences on protein homeostasis (proteostasis), resulting in disruption ofnumerous biological processes. This chapter discusses our current understanding of the various contributors to protein misfolding, and the mechanisms by which misfolding, and accompanied aggregation/toxicity, is accelerated by stress and aging. Invertebrate models have been instrumental in studying the processes related to aggregation and toxicity of disease-associated proteins and how dysregulation ofproteostasis leads to neurodegenerative diseases of aging.
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Affiliation(s)
- Elise A Kikis
- Department of Biochemistry, Molecular Biology and Cell Biology, Rice Institute for Biomedical Research, 2205 Tech Drive, Hogan 2-100, Northwestern University, Evanston, Illinois 60208, USA
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11
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DePristo MA, Weinreich DM, Hartl DL. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 2006; 6:678-87. [PMID: 16074985 DOI: 10.1038/nrg1672] [Citation(s) in RCA: 484] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteins are finicky molecules; they are barely stable and are prone to aggregate, but they must function in a crowded environment that is full of degradative enzymes bent on their destruction. It is no surprise that many common diseases are due to missense mutations that affect protein stability and aggregation. Here we review the literature on biophysics as it relates to molecular evolution, focusing on how protein stability and aggregation affect organismal fitness. We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution.
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Affiliation(s)
- Mark A DePristo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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12
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Clemente MT, Márquez AJ. Site-directed mutagenesis of Cys-92 from the alpha-polypeptide of Phaseolus vulgaris glutamine synthetase reveals that this highly conserved residue is not essential for enzyme activity but it is involved in thermal stability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 154:189-197. [PMID: 10729618 DOI: 10.1016/s0168-9452(00)00197-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The residue Cys-92 from the alpha-polypeptide of Phaseolus vulgaris glutamine synthetase is a highly conserved residue in prokaryotic and eukaryotic glutamine synthetase genes. This cysteine residue was previously proposed as a good candidate for being essential for enzyme activity. We have examined through heterologous expression in Escherichia coli and site-directed mutagenesis the functional importance of this residue. We have found that the thiol group of Cys-92 is not essential either for glutamine synthetase biosynthetic or transferase enzyme activities. The characteristic inhibition by p-hydroxymercuribenzoate (a specific sulphydryl reagent) was not substantially altered as a consequence of replacement of Cys-92 by Ala. Immunoreactivity of the glutamine synthetase mutant protein, examined both under native and denaturing conditions, was similar to the wild-type, indicating that no significant conformational changes were produced as a consequence of the introduced mutation. However, the mutant enzyme C92A was considerably less stable than the wild-type. These results indicate that Cys-92 is not an essential residue for enzyme activity but it is important for stability of the glutamine synthetase protein.
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Affiliation(s)
- MT Clemente
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Apartado 553, 41080-, Sevilla, Spain
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13
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Mouz N, Gordon E, Di Guilmi AM, Petit I, Pétillot Y, Dupont Y, Hakenbeck R, Vernet T, Dideberg O. Identification of a structural determinant for resistance to beta-lactam antibiotics in Gram-positive bacteria. Proc Natl Acad Sci U S A 1998; 95:13403-6. [PMID: 9811812 PMCID: PMC24831 DOI: 10.1073/pnas.95.23.13403] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is the main causal agent of pathologies that are increasingly resistant to antibiotic treatment. Clinical resistance of S. pneumoniae to beta-lactam antibiotics is linked to multiple mutations of high molecular mass penicillin-binding proteins (H-PBPs), essential enzymes involved in the final steps of bacterial cell wall synthesis. H-PBPs from resistant bacteria have a reduced affinity for beta-lactam and a decreased hydrolytic activity on substrate analogues. In S. pneumoniae, the gene coding for one of these H-PBPs, PBP2x, is located in the cell division cluster (DCW). We present here structural evidence linking multiple beta-lactam resistance to amino acid substitutions in PBP2x within a buried cavity near the catalytic site that contains a structural water molecule. Site-directed mutation of amino acids in contact with this water molecule in the "sensitive" form of PBP2x produces mutants similar, in terms of beta-lactam affinity and substrate hydrolysis, to altered PBP2x produced in resistant clinical isolates. A reverse mutation in a PBP2x variant from a clinically important resistant clone increases the acylation efficiency for beta-lactams and substrate analogues. Furthermore, amino acid residues in contact with the structural water molecule are conserved in the equivalent H-PBPs of pathogenic Gram-positive cocci. We suggest that, probably via a local structural modification, the partial or complete loss of this water molecule reduces the acylation efficiency of PBP2x substrates to a point at which cell wall synthesis still occurs, but the sensitivity to therapeutic concentrations of beta-lactam antibiotics is lost.
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Affiliation(s)
- N Mouz
- Laboratoire d'Ingénierie des Macromolécules, Institut de Biologie Structurale Jean-Pierre Ebel (Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique), 41, avenue des Martyrs, F-38027 Grenoble Cedex 1, France
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14
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Fastrez J. In vivo versus in vitro screening or selection for catalytic activity in enzymes and abzymes. Mol Biotechnol 1997; 7:37-55. [PMID: 9163721 DOI: 10.1007/bf02821543] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The recent development of catalytic antibodies and the introduction of new techniques to generate huge libraries of random mutants of existing enzymes have created the need for powerful tools for finding in large populations of cells those producing the catalytically most active proteins. Several approaches have been developed and used to reach this goal. The screening techniques aim at easily detecting the clones producing active enzymes or abzymes; the selection techniques are designed to extract these clones from mixtures. These techniques have been applied both in vivo and in vitro. This review describes the advantages and limitations of the various methods in terms of ease of use, sensitivity, and convenience for handling large libraries. Examples are analyzed and tentative rules proposed. These techniques prove to be quite powerful to study the relationship between structure and function and to alter the properties of enzymes.
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Affiliation(s)
- J Fastrez
- Laboratoire de Biochimie Physique et des Biopolymères, Louvain-la-Neuve, Belgium
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15
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Hosseini-Mazinani SM, Nakajima E, Ihara Y, Kameyama KZ, Sugimoto K. Recovery of active beta-lactamases from Proteus vulgaris and RTEM-1 hybrid by random mutagenesis by using a dnaQ strain of Escherichia coli. Antimicrob Agents Chemother 1996; 40:2152-9. [PMID: 8878598 PMCID: PMC163490 DOI: 10.1128/aac.40.9.2152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Proteus vulgaris and RTEM-1 beta-lactamases that belong to molecular class A with 37% amino acid similarity were examined to find the relationship between amino acid residues and activity of enzymes. MICs of ampicillin were > 2,000 micrograms/ml for Escherichia coli cells producing these enzymes. We have made 18 hybrid genes by substituting the coding region of the P. vulgaris beta-lactamase gene with the equivalent portions from the RTEM-1 gene. Most of these hybrids produced inactive proteins, but a few hybrid enzymes had partial or trace activity. From one of the hybrid genes (MIC of ampicillin, 100 micrograms/ml), we recovered three kinds of active mutants which provided ampicillin MICs of 1,000 micrograms/ml by the selection of spontaneous mutations in a dnaQ strain of E. coli. In these mutants, Leu-148, Met-182, and Tyr-274 were replaced with Val, Thr, and His, respectively. These amino acids have not been identified as residues with functional roles in substrate hydrolysis. Furthermore, from these hybrid mutants, we obtained a second set of mutants which conferred ampicillin MICs of 1,500 micrograms/ml. Interestingly, the second mutations were limited to these three amino acid substitutions. These amino acid residues which do not directly interact with substrates have an effect on enzyme activity. These mutant enzymes exhibited lower K(m) values for cephaloridine than both parental enzymes.
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16
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Ono A, Matsuda A, Zhao J, Santi DV. The synthesis of blocked triplet-phosphoramidites and their use in mutagenesis. Nucleic Acids Res 1995; 23:4677-82. [PMID: 8524660 PMCID: PMC307443 DOI: 10.1093/nar/23.22.4677] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 triplet-amidite blocks consisting of codon sequences requires 16 dimer blocks, just seven dimer blocks are required to synthesize all required antisense sequences. The antisense sequences are then converted to codons in template mediated replication. Using a mixture of four triplet-amidites and conventional automated solid-phase DNA synthesis, short (6mer) and medium length (30mer) oligonucleotide mixtures were synthesized and analyzed. The latter was replicated in vitro and used as a mutagenic cassette to produce four mutants of Asp 221 in the enzyme thymidylate synthase. The method establishes the direction and utility for the production and use of triplet-amidite blocks in DNA synthesis.
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Affiliation(s)
- A Ono
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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17
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Bush K, Jacoby GA, Medeiros AA. A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 1995; 39:1211-33. [PMID: 7574506 PMCID: PMC162717 DOI: 10.1128/aac.39.6.1211] [Citation(s) in RCA: 1553] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- K Bush
- American Cyanamid Company, Lederle Laboratories, Pearl River, New York 10965, USA
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18
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Barthélémy M, Péduzzi J, Rowlands D, Paul G, Moreau G, Labia R. Val-237 for Ala substitution in the TEM-2 beta-lactamase dramatically alters the catalytic efficiencies towards carbenicillin and ticarcillin. FEMS Microbiol Lett 1994; 117:333-9. [PMID: 8200509 DOI: 10.1111/j.1574-6968.1994.tb06788.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The mutant 554 of TEM-2 beta-lactamase was selected for a decrease in the resistance to carbenicillin of an Escherichia coli K12 carrier. The amino acid sequence of the mutant beta-lactamase was determined by manual Edman degradation analysis of proteolytic peptides. A single substitution Val for Ala was localized at position 237. The mutant exhibited only 2% of the catalytic efficiency of the wild-type enzyme towards carbenicillin and ticarcillin, whereas it retained 30-60% of the hydrolytic activity towards other penicillin and cephalosporin substrates. Carfecillin, the phenyl ester of the side-chain carboxyl group of carbenicillin, was hydrolysed as a good substrate. This suggests that the behaviour of the mutant enzyme towards carbenicillin may result from ionic rather than steric constraints. A molecular model of the Val-237 TEM-2 mutant suggests possible electrostatic interaction between Glu-171 and the carboxylic group of the side chain of carbenicillin.
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Affiliation(s)
- M Barthélémy
- Muséum National Histoire Naturelle, CNRS URA 401, Paris, France
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19
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Palzkill T, Botstein D. Probing beta-lactamase structure and function using random replacement mutagenesis. Proteins 1992; 14:29-44. [PMID: 1329081 DOI: 10.1002/prot.340140106] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new analytical mutagenesis technique is described that involves randomizing the DNA sequence of a short stretch of a gene (3-6 codons) and determining the percentage of all possible random sequences that produce a functional protein. A low percentage of functional random sequences in a complete library of random substitutions indicates that the region mutagenized is important for the structure and/or function of the protein. Repeating the mutagenesis over many regions throughout a protein gives a global perspective of which amino acid sequences in a protein are critical. We applied this method to 66 codons of the gene encoding TEM-1 beta-lactamase in 19 separate experiments. We found that TEM-1 beta-lactamase is extremely tolerant of amino acid substitutions: on average, 44% of all mutants with random substitutions function and 20% of the substitutions are expressed, secreted, and fold well enough to function at levels similar to those for the wild-type enzyme. We also found a few exceptional regions where only a few random sequences function. Examination of the X-ray structures of homologous beta-lactamases indicates that the regions most sensitive to substitution are in the vicinity of the active site pocket or buried in the hydrophobic core of the protein. DNA sequence analysis of functional random sequences has been used to obtain more detailed information about the amino acid sequence requirements for several regions and this information has been compared to sequence conservation among several related beta-lactamases.
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Affiliation(s)
- T Palzkill
- Department of Genetics, School of Medicine, Stanford University, California 94305
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20
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Bourguignon-Bellefroid C, Joris B, Van Beeumen J, Ghuysen JM, Frère JM. Point mutations of two arginine residues in the Streptomyces R61 DD-peptidase. Biochem J 1992; 283 ( Pt 1):123-8. [PMID: 1567359 PMCID: PMC1131003 DOI: 10.1042/bj2830123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Incubation of the exocellular DD-carboxypeptidase/transpeptidase of Streptomyces R61 with phenylglyoxal resulted in a time-dependent decrease in the enzyme activity. This inactivation was demonstrated to be due to modification of the Arg-99 side chain. In consequence, the role of that residue was investigated by site-directed mutagenesis. Mutation of Arg-99 into leucine appeared to be highly detrimental to enzyme stability, reflecting a determining structural role for this residue. The conserved Arg-103 residue was also substituted by using site-directed mutagenesis. The modification to a serine residue yielded a stable enzyme, the catalytic properties of which were similar to those of the wild-type enzyme. Thus Arg-103, although strictly conserved or replaced by a lysine residue in most of the active-site penicillin-recognizing proteins, did not appear to fulfil any essential role in either the enzyme activity or structure.
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21
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Lee S, Koh H, Yu M. Molecular properties of global suppressors of temperature-sensitive folding mutations in P22 tailspike endorhamnosidase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54482-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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22
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Bottema CD, Ketterling RP, Ii S, Yoon HS, Phillips JA, Sommer SS. Missense mutations and evolutionary conservation of amino acids: evidence that many of the amino acids in factor IX function as "spacer" elements. Am J Hum Genet 1991; 49:820-38. [PMID: 1680287 PMCID: PMC1683179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report 31 point mutations in the factor IX gene and explore the relationship between the level of evolutionary conservation of an amino acid and the probability of a mutation causing hemophilia B. From our total sample of 125 hemophiliacs and from those reported by others, we identify 95 independent missense mutations, 94 of which occur at amino acids that are evolutionarily conserved in the available mammalian factor IX sequences. The likelihood of a missense mutation causing hemophilia B depends on whether the residue is also conserved in the factor IX-related proteases: factor VII, factor X, and protein C. Most of the possible missense mutations in generically conserved residues (i.e., those conserved in factor IX and in all the related proteases) should cause disease. In contrast, missense mutations in factor IX-specific residues (i.e., those conserved in human, cow, dog, and mouse factor IX but not in the related proteases) are sixfold less likely to cause disease. Missense mutations at nonconserved residues are 33-fold less likely to cause disease. At least three models are compatible with these observations. A comparison of sequence alignments from four and nine species of factor IX and an examination of the missense mutations occurring at CpG residues suggest a model in which most residues fall on opposite ends of a spectrum. In about 40% of residues, virtually any missense mutation in a minority of the residues will cause disease, while virtually no missense mutations will cause disease in most of the remaining residues. Thus, many of the residues in factor IX are spacers; that is, the main chains are presumably necessary to keep other amino acid interactions in register, but the nature of the side chain is unimportant.
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Affiliation(s)
- C D Bottema
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN 55905
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23
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Lim HM, Iyer RK, Pène JJ. Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 beta-lactamase II. Biochem J 1991; 276 ( Pt 2):401-4. [PMID: 1904717 PMCID: PMC1151105 DOI: 10.1042/bj2760401] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of beta-lactam antibiotics by the zinc-containing Bacillus cereus beta-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 beta-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution of asparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for beta-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glu90 lead to the synthesis of inactive enzyme, suggesting that the spatial position of the beta-carboxy group of Asp90 is critical for enzyme function.
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Affiliation(s)
- H M Lim
- School of Life and Health Sciences, University of Delaware, Newark 19716
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24
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Sowek JA, Singer SB, Ohringer S, Malley MF, Dougherty TJ, Gougoutas JZ, Bush K. Substitution of lysine at position 104 or 240 of TEM-1pTZ18R beta-lactamase enhances the effect of serine-164 substitution on hydrolysis or affinity for cephalosporins and the monobactam aztreonam. Biochemistry 1991; 30:3179-88. [PMID: 1901218 DOI: 10.1021/bi00227a004] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
By site-directed mutagenesis, TEM-1 beta-lactamase was altered to contain single amino acid changes of E104K, R164S, and E240K, in addition to double changes of E104K/R164S or R164S/E240K and the triple change of E104K/R164S/E240K. Hydrolysis rates for cephaloridine and benzylpenicillin were lowered at least 1 order of magnitude for all enzymes containing R164S substitutions. All mutant enzymes exhibited increased kcat values for beta-lactam antibiotics containing an aminothiazole oxime side chain. Hydrolysis of ceftazidime was most affected, with kcat values increased 3-4 orders of magnitude in all enzymes with the substituted R164S moiety. Km values decreased for all substrates except ceftazidime in the enzymes with multiple mutations. Aztreonam was most affected, with Km values lowered 23-56-fold in the enzymes bearing multiple mutations. When the crystal structures of aztreonam and related monobactams were studied and projected into an active-site model of the PC1 beta-lactamase, it became apparent that the two lysine residues might serve equivalent roles by interacting with the carboxylate of the aminothiazole oxime side chain. Hydrogen-bonding interactions involving the oxime and N7 of the lysine, particularly Lys-104, may also be important in some antibiotics. Ser-164 apparently serves an indirect role, since it is somewhat distant from the active-site cleft.
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Affiliation(s)
- J A Sowek
- Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492
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25
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Chang TK, Iverson SA, Rodrigues CG, Kiser CN, Lew AY, Germanas JP, Richards JH. Gene synthesis, expression, and mutagenesis of the blue copper proteins azurin and plastocyanin. Proc Natl Acad Sci U S A 1991; 88:1325-9. [PMID: 1899926 PMCID: PMC51010 DOI: 10.1073/pnas.88.4.1325] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Genes for the blue copper proteins Populus nigra var. italica plastocyanin and Pseudomonas aeruginosa azurin have been constructed by a stepwise procedure. The leader sequence for azurin has been placed before the genes directing plastocyanin and azurin transport to the periplasmic space when the genes are expressed in Escherichia coli. Site-saturation mutagenesis has been used to alter two copper-binding residues of azurin (Met-121 and His-46) and Met-92 of plastocyanin. While the plastocyanin mutants do not appear to bind copper, the azurin variants all bind copper and show characteristic type I blue copper centers. In particular, the electronic spectra reflect the dominance of the charge transfer interaction between copper and the thiolate of Cys-112, being relatively insensitive to changes in Met-121 or His-46. In contrast, removal of Met-121 appreciably alters the EPR spectra of the mutants, although, to a first order, the spectra of all mutants are themselves similar, suggesting a more distorted geometry around copper in the mutants than in the wild type.
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Affiliation(s)
- T K Chang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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26
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Adachi H, Ohta T, Matsuzawa H. Site-directed mutants, at position 166, of RTEM-1 beta-lactamase that form a stable acyl-enzyme intermediate with penicillin. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)49972-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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27
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Pastor N, Piñero D, Valdés AM, Soberón X. Molecular evolution of class A beta-lactamases: phylogeny and patterns of sequence conservation. Mol Microbiol 1990; 4:1957-65. [PMID: 2082152 DOI: 10.1111/j.1365-2958.1990.tb02045.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present a multiple alignment of the amino acid sequences of eight class A beta-lactamases and utilized it to propose a phylogeny, based on the nucleotide sequences of their corresponding genes. We have also used the alignment, together with the alpha-carbon co-ordinates of the Staphylococcus aureus protein, to search systematically for neighbouring residues that share the same pattern of conservation among the different members of the protein family. The distribution of invariant residues and of groups of residues with co-ordinate changes map, predominantly, at the region of the active site and at interfaces between structural elements, respectively. We have also contrasted the distribution of conserved residues with the positions which are known to differ in mutants and variants of class A beta-lactamases.
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Affiliation(s)
- N Pastor
- Centro de Investigacíon sobre Ingeniería Genética y Biotecnología, Universidad Nacional Autónoma de México
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28
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Climie S, Ruiz-Perez L, Gonzalez-Pacanowska D, Prapunwattana P, Cho S, Stroud R, Santi D. Saturation site-directed mutagenesis of thymidylate synthase. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)30579-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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Jacob F, Joris B, Lepage S, Dusart J, Frère JM. Role of the conserved amino acids of the 'SDN' loop (Ser130, Asp131 and Asn132) in a class A beta-lactamase studied by site-directed mutagenesis. Biochem J 1990; 271:399-406. [PMID: 2173561 PMCID: PMC1149568 DOI: 10.1042/bj2710399] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ser130, Asp131 and Asn132 ('SDN') are highly conserved residues in class A beta-lactamases forming one wall of the active-site cavity. All three residues of the SDN loop in Streptomyces albus G beta-lactamase were modified by site-directed mutagenesis. The mutant proteins were expressed in Streptomyces lividans, purified from culture supernatants and their kinetic parameters were determined for several substrates. Ser130 was substituted by Asn, Ala and Gly. The first modification yielded an almost totally inactive protein, whereas the smaller-side-chain mutants (A and G) retained some activity, but were less stable than the wild-type enzyme. Ser130 might thus be involved in maintaining the structure of the active-site cavity. Mutations of Asp131 into Glu and Gly proved to be highly detrimental to enzyme stability, reflecting significant structural perturbations. Mutation of Asn132 into Ala resulted in a dramatically decreased enzymic activity (more than 100-fold) especially toward cephalosporin substrates, kcat. being the most affected parameter, which would indicate a role of Asn132 in transition-state stabilization rather than in ground-state binding. Comparison of the N132A and the previously described N132S mutant enzymes underline the importance of an H-bond-forming residue at position 132 for the catalytic process.
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Affiliation(s)
- F Jacob
- Laboratoire d'Enzymologie, Université de Liège, Belgium
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30
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Tsukamoto K, Ohno R, Sawai T. Extension of the substrate spectrum by an amino acid substitution at residue 219 in the Citrobacter freundii cephalosporinase. J Bacteriol 1990; 172:4348-51. [PMID: 2115867 PMCID: PMC213260 DOI: 10.1128/jb.172.8.4348-4351.1990] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cephalosporinase of Citrobacter freundii GN346 is a class C beta-lactamase, consisting of 361 amino acids and exhibiting the substrate profile of a typical cephalosporinase. On the conversion of a conserved glutamic acid at residue 219 to lysine, the substrate spectrum of the cephalosporinase was extended to oxyimino cephalosporins, aztreonam and carbenicillin, which are essentially undesirable substrates for the enzyme. Escherichia coli cells carrying the mutant gene showed higher resistance levels to cefuroxime, aztreonam, and carbenicillin, but a lower resistance level to cefoxitin, than cells carrying the wild gene. The kcat values of the purified mutant enzyme for ceftazidime, cefuroxime, and cefmenoxime were 77,100, and 300 times those of the wild enzyme, respectively. The relative Vmax values of the mutant enzyme for aztreonam and carbenicillin were determined to be 11 and 23 times those of the wild enzyme, respectively, but the value of the mutant enzyme for cefoxitin was only one-third that of the wild enzyme.
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Affiliation(s)
- K Tsukamoto
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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31
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Kojima S, Obata S, Kumagai I, Miura K. Alteration of the Specificity of the Streptomyces Subtilisin Inhibitor by Gene Engineering. Nat Biotechnol 1990; 8:449-52. [PMID: 1366538 DOI: 10.1038/nbt0590-449] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have altered the amino acid at the center of the reactive site (methionine 73) of Streptomyces subtilisin inhibitor (SSI) by site-directed and cassette mutagenesis. Replacement by lysine or arginine resulted in trypsin inhibitory activity, replacement only by lysine gave inhibition of lysyl endopeptidase, and replacement by tyrosine or tryptophan resulted in inhibition of alpha-chymotrypsin. The four mutant SSIs retained their native activity against subtilisin BPN'. Thus by altering only one amino acid residue at the reactive site of SSI to the substrate specificity of the respective protease we could successfully change its inhibitory profile.
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Affiliation(s)
- S Kojima
- Department of Industrial Chemistry, Faculty of Engineering, University of Tokyo, Japan
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32
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Chang YH, Labgold MR, Richards JH. Altering enzymatic activity: recruitment of carboxypeptidase activity into an RTEM beta-lactamase/penicillin-binding protein 5 chimera. Proc Natl Acad Sci U S A 1990; 87:2823-7. [PMID: 2181451 PMCID: PMC53783 DOI: 10.1073/pnas.87.7.2823] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The D-Ala-D-Ala carboxypeptidases/transpeptidases (penicillin-binding proteins, PBPs) share considerable structural homology with class A beta-lactamases (EC 3.5.2.6), although these beta-lactamases have no observable D-Ala-D-Ala carboxypeptidase activity. With the objective of recruiting such activity into a beta-lactamase background, we have prepared a chimeric protein by inserting a 28-amino acid segment of PBP-5 of Escherichia coli in place of the corresponding region of the RTEM-1 beta-lactamase. The segment thus inserted encompasses two residues conserved in both families: Ser-70, which forms the acyl-enzyme intermediate during beta-lactam hydrolysis, and Lys-73, whose presence has been shown to be necessary for catalysis. This chimera involves changes of 18 residues and gives a protein that differs at 7% of the residues from the parent. Whereas RTEM beta-lactamase has no D-Ala-D-Ala carboxypeptidase activity, that of the chimera is significant and is, in fact, about 1% the activity of PBP-5 on diacetyl-L-Lys-D-Ala-D-Ala; in terms of free energy of activation, the chimera stabilizes the transition state for the reaction to within about 2.7 kcal/mol of the stabilization achieved by PBP-5. Furthermore, the chimera catalyzes hydrolysis exclusively at the carboxyl-terminal amide bond which is the site of cleavage by D-Ala-D-Ala carboxypeptidase. Though containing all those residues that are conserved throughout class A beta-lactamases and are thought to be essential for beta-lactamase activity, the chimera has considerably reduced activity (approximately 10(-5) on penams such as penicillins and ampicillins as substrates. As a catalyst, the chimera shows an induction period of approximately 30 min, reflecting a slow conformational rearrangement from an inactive precursor to the active enzyme.
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Affiliation(s)
- Y H Chang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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33
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Christensen H, Martin MT, Waley SG. Beta-lactamases as fully efficient enzymes. Determination of all the rate constants in the acyl-enzyme mechanism. Biochem J 1990; 266:853-61. [PMID: 2158301 PMCID: PMC1131217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
The rate constants for both acylation and deacylation of beta-lactamase PC1 from Staphylococcus aureus and the RTEM beta-lactamase from Escherichia coli were determined by the acid-quench method [Martin & Waley (1988) Biochem. J. 254, 923-925] with several good substrates, and, for a wider range of substrates, of beta-lactamase I from Bacillus cereus. The values of the acylation and deacylation rate constants for benzylpenicillin were approximately the same (i.e. differing by no more than 2-fold) for each enzyme. The variation of kcat./Km for benzylpenicillin with the viscosity of the medium was used to obtain values for all four rate constants in the acyl-enzyme mechanism for all three enzymes. The reaction is partly diffusion-controlled, and the rate constant for the dissociation of the enzyme-substrate complex has approximately the same value as the rate constants for acylation and deacylation. Thus all three first-order rate constants have comparable values. Here there is no single rate-determining step for beta-lactamase action. This is taken to be a sign of a fully efficient enzyme.
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Affiliation(s)
- H Christensen
- Sir William Dunn School of Pathology, University of Oxford, U.K
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34
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Tsukamoto K, Tachibana K, Yamazaki N, Ishii Y, Ujiie K, Nishida N, Sawai T. Role of lysine-67 in the active site of class C beta-lactamase from Citrobacter freundii GN346. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:15-22. [PMID: 1969344 DOI: 10.1111/j.1432-1033.1990.tb15365.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Citrobacter freundii GN346 produces a class C beta-lactamase exhibiting the substrate profile of a typical cephalosporinase. The structural and promoter regions of the cephalosporinase gene, comprising 1408 nucleotides, were completely sequenced. The amino acid sequence of the mature enzyme, comprising 361 amino acids, and its molecular mass, 39,878 Da, were determined. The active site was confirmed to be Ser-64. The amino acid sequence of the enzyme differs from that of the cephalosporinase of C. freundii OS60 by nine residues. The nucleotide sequence of the promoter region suggests a possible attenuator structure. Lys-67, one of the most conserved residues found in class A and C beta-lactamases and penicillin-binding proteins, was converted into arginine, threonine or glutamic acid through site-directed mutagenesis. The Glu-67 enzyme had lost the catalytic activity and the Thr-67 enzyme only showed a trace of activity. The Arg-67 enzyme, which retained a significant amount of the activity, was purified. The Km values of the Arg-67 enzyme for cephalothin, cephaloridine and benzylpenicillin are 13-19 times those of the wild-type enzyme; the kcat values for the three substrates are 37%, 3%, and 36% those of the wild-type enzyme, respectively.
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Affiliation(s)
- K Tsukamoto
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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35
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Boissinot M, Levesque RC. Nucleotide sequence of the PSE-4 carbenicillinase gene and correlations with the Staphylococcus aureus PC1 beta-lactamase crystal structure. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40181-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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36
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Moews PC, Knox JR, Dideberg O, Charlier P, Frère JM. Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution. Proteins 1990; 7:156-71. [PMID: 2326252 DOI: 10.1002/prot.340070205] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two crystal forms (A and B) of the 29,500 Da Class A beta-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 A resolution, the starting model for which was a 3.5 A structure obtained from A-form crystals. The beta-lactamase has an alpha + beta structure with 11 helices and 5 beta-strands seen also in a penicillin target DD-peptidase of Streptomyces R61. Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 A resolution. The R factor is 0.208 for the 27,330 data greater than 3 sigma (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conserved Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of beta-lactam substrates is facilitated by interactions with Lys-234, Thr-235, and Ala-237 in a conserved beta-strand peptide, which is antiparallel to the beta-lactam's acylamido linkage; an exposed cavity near Asn-170 exists for acylamido substituents. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth beta-strand. A very similar binding site architecture is seen in the DD-peptidase.
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Affiliation(s)
- P C Moews
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269
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37
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Matagne A, Misselyn-Bauduin AM, Joris B, Erpicum T, Granier B, Frère JM. The diversity of the catalytic properties of class A beta-lactamases. Biochem J 1990; 265:131-46. [PMID: 2302162 PMCID: PMC1136623 DOI: 10.1042/bj2650131] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The catalytic properties of four class A beta-lactamases were studied with 24 different substrates. They exhibit a wide range of variation. Similarly, the amino acid sequences are also quite different. However, no relationships were found between the sequence similarities and the substrate profiles. Lags and bursts were observed with various compounds containing a large sterically hindered side chain. As a group, the enzymes could be distinguished from the class C beta-lactamases on the basis of the kappa cat. values for several substrates, particularly oxacillin, cloxacillin and carbenicillin. Surprisingly, that distinction was impossible with the kappa cat./Km values, which represent the rates of acylation of the active-site serine residue by the beta-lactam. For several cephalosporin substrates (e.g. cefuroxime and cefotaxime) class A enzymes consistently exhibited higher kappa cat. values than class C enzymes, thus belying the usual distinction between 'penicillinases' and 'cephalosporinases'. The problem of the repartition of class A beta-lactamases into sub-classes is discussed.
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Affiliation(s)
- A Matagne
- Université de Liège, Institute de Chimie, Belgium
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38
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Lim HM, Pène JJ. Mutations affecting the catalytic activity of Bacillus cereus 5/B/6 β-lactamase II. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)80118-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Ner SS, Atkinson TC, Smith M. A method for introducing random single point deletions in specific DNA target sequences using oligonucleotides. Nucleic Acids Res 1989; 17:4015-23. [PMID: 2662137 PMCID: PMC317915 DOI: 10.1093/nar/17.11.4015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We describe a method for the generation of random point deletions in any target DNA sequence using synthetic mixed oligonucleotides. A mixed pool of oligonucleotides, which contain single nucleotide deletions randomly distributed throughout the full length, was generated by a modification of the synthesis cycle of an automated DNA synthesiser that allowed the inefficient incorporation of nucleotide monomers during each cycle of synthesis. A family of oligonucleotides was used to prime in vitro synthesis of the complementary strand of a cloned DNA fragment in an M13 vector which had previously been passaged through a dut-, ung- Escherichia coli host. Strong selection for progeny from the newly synthesised strand is provided by transforming the heteroduplex into a dut+, ung+ host. This procedure introduced point deletions at 10-25% efficiency. It has been used to introduce point deletions into operator sequences which bind the yeast regulatory proteins encoded by MATa1 and MAT alpha 2.
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Affiliation(s)
- S S Ner
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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40
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Needels MC, Fried SR, Love R, Rosenberg JM, Boyer HW, Greene PJ. Determinants of EcoRI endonuclease sequence discrimination. Proc Natl Acad Sci U S A 1989; 86:3579-83. [PMID: 2657723 PMCID: PMC287181 DOI: 10.1073/pnas.86.10.3579] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The arginine at position 200 of EcoRI endonuclease is thought to make two hydrogen bonds to the guanine of the sequence GAATTC and thus be an important determinant of sequence discrimination. Arg-200 was replaced by each of the other 19 naturally occurring amino acids, and the mutant endonucleases were assessed for activities in vivo and in vitro. The mutant endonuclease with lysine at position 200 exhibits the most in vivo activity of all the position 200 mutants, although the in vitro activity is less than 1/100th of wild-type activity. Five other mutants show more drastically reduced levels of in vivo activity (Cys, Pro, Val, Ser, and Trp). The Cys, Val, and Ser mutant enzymes appear to have in vivo activity which is specific for the wild-type canonical site despite the loss of hydrogen bonding potential at position 200. The Pro and Trp mutants retain in vivo activity which is independent of the presence of the EcoRI methylase. In crude cell lysates, only the Cys mutant shows a very low level of in vitro activity. None of the mutant enzymes show a preference for alternative sites in assays in vitro. The implications of these results are discussed.
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Affiliation(s)
- M C Needels
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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41
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Affiliation(s)
- K Bush
- Squibb Institute for Medical Research, Princeton, New Jersey 08540
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42
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Tripathi G. Biocatalysis made to order. Appl Biochem Biotechnol 1988; 19:33-59. [PMID: 3060014 DOI: 10.1007/bf02921464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recombinant DNA technology is now being explored to engineer enzyme molecules. It has many far-reaching applications in biocatalytic processes of enzyme engineering. The facts have pursued certain important industrial, biomedical, and environmental problems. These current excitements are mainly focused on the basis of gene cloning and in vitro mutagenesis for overproduction and redesigning of enzymes, as well as their probable implications in industry, antibiotic research, and waste degradation.
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Affiliation(s)
- G Tripathi
- Department of Zoology, Banaras Hindu University, Varanasi, India
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Mutagenesis of the alpha subunit of the F1Fo-ATPase from Escherichia coli. Mutations at Glu-196, Pro-190, and Ser-199. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68683-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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44
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Joris B, Ghuysen JM, Dive G, Renard A, Dideberg O, Charlier P, Frère JM, Kelly JA, Boyington JC, Moews PC. The active-site-serine penicillin-recognizing enzymes as members of the Streptomyces R61 DD-peptidase family. Biochem J 1988; 250:313-24. [PMID: 3128280 PMCID: PMC1148858 DOI: 10.1042/bj2500313] [Citation(s) in RCA: 307] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Homology searches and amino acid alignments, using the Streptomyces R61 DD-peptidase/penicillin-binding protein as reference, have been applied to the beta-lactamases of classes A and C, the Oxa-2 beta-lactamase (considered as the first known member of an additional class D), the low-Mr DD-peptidases/penicillin-binding proteins (protein no. 5 of Escherichia coli and Bacillus subtilis) and penicillin-binding domains of the high-Mr penicillin-binding proteins (PBP1A, PBP1B, PBP2 and PBP3 of E. coli). Though the evolutionary distance may vary considerably, all these penicillin-interactive proteins and domains appear to be members of a single superfamily of active-site-serine enzymes distinct from the classical trypsin or subtilisin families. The amino acid alignments reveal several conserved boxes that consist of strict identities or homologous amino acids. The significance of these boxes is highlighted by the known results of X-ray crystallography, chemical derivatization and site-directed-mutagenesis experiments.
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Affiliation(s)
- B Joris
- Service de Microbiologie, Université de Liège, Belgium
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45
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Ner SS, Goodin DB, Smith M. A simple and efficient procedure for generating random point mutations and for codon replacements using mixed oligodeoxynucleotides. DNA (MARY ANN LIEBERT, INC.) 1988; 7:127-34. [PMID: 3282853 DOI: 10.1089/dna.1988.7.127] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A very simple and highly efficient procedure for the generation of single and multiple substitutions in segments of DNA is described which has no requirements for conveniently placed restriction sites, and allows all DNA sequences to be equally accessible. A mixed pool of oligodeoxynucleotides is synthesized by contaminating the monomeric nucleotides with low levels of the other three nucleotides such that the full-length oligonucleotide contains on the average one to two changes per molecule. This pool is used in priming in vitro synthesis of the complementary strand of cloned DNA fragments in M13 or pEMBL vectors which have previously been passed through a dut-, ung- Escherichia coli host. Strong selection for the newly synthesized strand is provided by transforming the heteroduplex into a dut+, ung+ host. Single and multiple substitutions in the carboxy-terminal coding region of the MATa1 gene of Saccharomyces cerevisiae are introduced at high efficiency (25-55%) and the changes are identified by direct sequencing alone. The same principle can be used to generate multiple sets of changes at any specified codon.
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Affiliation(s)
- S S Ner
- Department of Biochemistry, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Profy AT, Schimmel P. Complementary use of chemical modification and site-directed mutagenesis to probe structure-activity relationships in enzymes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1988; 35:1-26. [PMID: 3065821 DOI: 10.1016/s0079-6603(08)60608-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Goff SA, Short-Russell SR, Dice JF. Efficient saturation mutagenesis of a pentapeptide coding sequence using mixed oligonucleotides. DNA (MARY ANN LIEBERT, INC.) 1987; 6:381-8. [PMID: 3652908 DOI: 10.1089/dna.1987.6.381] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Site-directed mutagenesis using oligonucleotides that are degenerate at a specific codon was employed to construct a set of mutations in a pentapeptide sequence targeting cytosolic proteins to lysosomes during serum withdrawal. Low-temperature annealing of the mixed oligonucleotides to single-stranded phage DNA and a genetic selection for the DNA strand carrying the mutations were utilized. The use of mixed oligonucleotides by this technique provides an economical means of generating a large set of substitution mutations. A single codon can be changed to codons for most other amino acids in one step. This approach eliminates the need for restriction enzyme cleavage sites flanking the target for mutagenesis and, therefore, is useful for targeting mutations to any DNA fragment cloned into an appropriate single-stranded bacteriophage.
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Affiliation(s)
- S A Goff
- Department of Physiology, Tufts University School of Medicine, Boston, MA 02111
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48
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Schultz SC, Dalbadie-McFarland G, Neitzel JJ, Richards JH. Stability of wild-type and mutant RTEM-1 beta-lactamases: effect of the disulfide bond. Proteins 1987; 2:290-7. [PMID: 3502362 DOI: 10.1002/prot.340020405] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Uniquely among class A beta-lactamases, the RTEM-1 and RTEM-2 enzymes contain a single disulfide bond between Cys 77 and Cys 123. To study the possible role of this naturally occurring disulfide in stabilizing RTEM-1 beta-lactamase and its mutants at residue 71, this bond was removed by introducing a Cys 77----Ser mutation. Both the wild-type enzyme and the single mutant Cys 77----Ser confer the same high levels of resistance to ampicillin in vivo to Escherichia coli; at 30 degrees C the specific activity of purified Cys 77----Ser mutant is also the same as that of the wild-type enzyme. Also, neither wild-type enzyme nor the Cys 77----Ser mutant is inactivated by brief exposure to p-hydroxymercuribenzoate. However, above 40 degrees C the mutant enzyme is less stable than wild-type enzyme. After introduction of the Cys 77----Ser mutation, none of the double mutants (containing the second mutations at residue 71) confer resistance to ampicillin in vivo at 37 degrees C; proteins with Ala, Val, Leu, Ile, Met, Pro, His, Cys, and Ser at residue 71 confer low levels of resistance to ampicillin in vivo at 30 degrees C. The use of electrophoretic blots stained with antibodies against beta-lactamase to analyze the relative quantities of mutant proteins in whole-cell extracts of E. coli suggests that all 19 of the doubly mutant enzymes are proteolyzed much more readily than their singly mutant analogues (at Thr 71) that contain a disulfide bond.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S C Schultz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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Bryan PN, Rollence ML, Pantoliano MW, Wood J, Finzel BC, Gilliland GL, Howard AJ, Poulos TL. Proteases of enhanced stability: characterization of a thermostable variant of subtilisin. Proteins 1986; 1:326-34. [PMID: 3329733 DOI: 10.1002/prot.340010406] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A procedure has been developed for the isolation and identification of mutants in the bacterial serine protease subtilisin that exhibit enhanced thermal stability. The cloned subtilisin BPN' gene from Bacillus amyloliquefaciens was treated with bisulfite, a chemical mutagen that deaminates cytosine to uracil in single-stranded DNA. Strains containing the cloned, mutagenized subtilisin gene which produced subtilisin with enhanced thermal stability were selected by a simple plate assay procedure which screens for esterase activity on nitrocellulose filters after preincubation at elevated temperatures. One thermostable subtilisin variant, designated 7150, has been fully characterized and found to differ from wild-type subtilisin by a single substitution of Ser for Asn at position 218. The 7150 enzyme was found to undergo thermal inactivation at one-fourth the rate of the wild-type enzyme when incubated at elevated temperatures. Moreover, the mid-point in the thermally induced transition from the folded to unfolded state was found to be 2.4-3.9 degrees C higher for 7150 as determined by differential scanning calorimetry under a variety of conditions. The refined, 1.8-A crystal structures of the wild-type and 7150 subtilisin have been compared in detail, leading to the conclusion that slight improvements in hydrogen bond parameters in the vicinity of position 218 result in the enhanced thermal stability of 7150.
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Affiliation(s)
- P N Bryan
- Genex Corporation, Gaithersburg, Maryland 20877
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