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Barry G Hall

Publications and source records attributed to Barry G Hall.

At least 19 recordsLinked to original sources
PubMed2006

Simple and accurate estimation of ancestral protein sequences.

There are a variety of reasons to reconstruct the sequences of ancient proteins, but whatever the reason, the value of the reconstructed protein depends on the accuracy with which the ancient sequence is inferred. This study uses sequences simulated by a sequence-evolution simulation program that compares parsimony, maximum likelihood, and the Bayesian methods of inferring ancestral sequences and concludes that the Bayesian method, as implemented by MRBAYES 3.11, is preferred. Estimated ancestral sequences are of necessity the same length as the alignment on which the underlying phylogeny is based. A highly accurate method for correcting the estimated sequences is introduced, and it is shown that the correction permits inferring the sequences of ancient protein sequences with a very high degree of accuracy.

Base Sequence↗
PubMed2005

Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases.

Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates.

Base Sequence↗
PubMed2005

Structure-based phylogeny of the metallo-beta-lactamases.

The metallo-beta-lactamases fall into two groups: Ambler class B subgroups B1 and B2 and Ambler class B subgroup B3. The two groups are so distantly related that there is no detectable sequence homology between members of the two different groups, but homology is clearly detectable at the protein structure level. The multiple structure alignment program MAPS has been used to align the structures of eight metallo-beta-lactamases and five structurally homologous proteins from the metallo-beta-lactamase superfamily, and that alignment has been used to construct a phylogenetic tree of the metallo-beta-lactamases. The presence of genes from Eubacteria, Archaebacteria, and Eukaryota on that tree is consistent with a very ancient origin of the metallo-beta-lactamase family.

Amino Acid Sequence↗
PubMed2004

Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.

A biologically realistic method was used to simulate evolutionary trees. The method uses a real DNA coding sequence as the starting point, simulates mutation according to the mutational spectrum of Escherichia coli-including base substitutions, insertions, and deletions-and separates the processes of mutation and selection. Trees of 8, 16, 32, and 64 taxa were simulated with average branch lengths of 50, 100, 150, 200, and 250 changes per branch. The resulting sequences were aligned with ClustalX, and trees were estimated by Neighbor Joining, Parsimony, Maximum Likelihood, and Bayesian methods from both DNA sequences and the corresponding protein sequences. The estimated trees were compared with the true trees, and both topological and branch length accuracies were scored. Over the variety of conditions tested, Bayesian trees estimated from DNA sequences that had been aligned according to the alignment of the corresponding protein sequences were the most accurate, followed by Maximum Likelihood trees estimated from DNA sequences and Parsimony trees estimated from protein sequences.

Amino Acid Sequence↗
PubMed2004

Independent origins of subgroup Bl + B2 and subgroup B3 metallo-beta-lactamases.

The metallo-beta-lactamases constitute Class B in the Ambler classification of beta-lactamases and are divided into three subclasses: Bl, B2, and B3. Bayesian phylogenies of the Subclass B1 + B2 and Subclass B3 metallo-beta-lactamases and their homologs show that the beta-lactam-hydrolyzing function evolved independently within each group. In Subclass B1+B2 that function evolved about 1 billion years ago, and in Subclass B3 it evolved before the divergence of the Gram-positive and Gram-negative eubacteria, about 2 billion years ago. These results lend additional support to the proposal that the metallo-beta-lactamases should be divided into two distinct classes.

Archaea↗
PubMed2004

Evolution of the serine beta-lactamases: past, present and future.

We present a protein structure-based phylogeny of Classes A, C and D of the serine beta-lactamases, and a new, detailed, sequence-based phylogeny of the Class A beta-lactamases. In addition, we discuss the historical evolution of Classes C and D. The evolutionary histories of all three classes indicate that the serine beta-lactamases are ancient enzymes, originating over two billion years ago, and that some have been on plasmids for millions of years. We also discuss the recent, antibiotic-era, evolution of the serine beta-lactamases in response to the clinical use of beta-lactam antibiotics. We also discuss a method that is being used to predict the future evolution of beta-lactamases in response to selection with new drugs.

Anti-Bacterial Agents↗
PubMed2004

In vitro evolution predicts that the IMP-1 metallo-beta-lactamase does not have the potential to evolve increased activity against imipenem.

In vitro evolution was used to predict whether the IMP-1 metallo-beta-lactamase has the potential to evolve an increased ability to confer resistance to imipenem. Screening of eight libraries containing 9.8 x 10(6) +/- 1.4 x 10(6) (mean +/- standard error) variants per library, with an average of 1.2 mutations per variant, detected no increased resistance to imipenem. The results predict, with >99.9% confidence, that even under intense selection the IMP-1 beta-lactamase will not evolve to confer increased resistance to imipenem.

Biological Evolution↗
PubMed2003

Determining the limits of the evolutionary potential of an antibiotic resistance gene.

The AAC(6') enzymes inactivate aminoglycoside antibiotics by acetylating their substrates at the 6' position. Based on functional similarity and size similarity, the AAC(6') enzymes have been considered to be members of a single family. Our phylogenetic analysis shows that the AAC(6') enzymes instead belong to three unrelated families that we now designate as [A], [B], and [C] and that aminoglycoside acetylation at the 6' position has evolved independently at least three times. AAC(6')-Iaa is a typical member of the [A] family in that it acetylates tobramycin, kanamycin, and amikacin effectively but acetylates gentamicin ineffectively. The potential of the aac(6')-Iaa gene to increase resistance to tobramycin, kanamycin, or amikacin or to acquire resistance to gentamicin was assessed by in vitro evolution. Libraries of PCR mutagenized alleles were screened for increased resistance to tobramycin, kanamycin, and amikacin, but no isolates that conferred more resistance than the wild-type gene were recovered. The library sizes were sufficient to conclude with 99.9% confidence that no single amino acid substitution or combination of two amino acid substitutions in aac(6')-Iaa is capable of increasing resistance to the antibiotics used. It is therefore very unlikely that aac(6')-Iaa of S. typhimurium LT2 has the potential to evolve increased aminoglycoside resistance in nature. The practical implications of being able to determine the evolutionary limits for other antibiotic resistance genes are discussed.

Acetyltransferases↗
PubMed2003

The metallo-beta-lactamases fall into two distinct phylogenetic groups.

The Ambler Class B metallo-beta-lactamases fall into two distinct phylogenetic groups based on the observation that there is no significant sequence homology between the sequences of members of different groups. Structural alignments confirm that those groups are no more closely related to each other than are the three classes of serine beta-lactamases, Classes A, C, and D. We present phylogenies of these two groups and suggest a new classification scheme for the beta-lactamases.

Bacteria↗
PubMed2003

Structure-based phylogenies of the serine beta-lactamases.

The serine beta-lactamases present a special problem for phylogenetics because they have diverged so much that they fall into three classes that share no detectable sequence homology among themselves. Here we offer a solution to the problem in the form of two phylogenies that are based on a protein structure alignment. In the first, structural alignments were used as a guide for aligning amino acid sequences and in the second, the average root mean square distances between the alpha carbons of the proteins were used to create a pairwise distance matrix from which a neighbor-joining phylogeny was created. From those phylogenies, we show that the Class A and Class D beta-lactamases are sister taxa and that the divergence of the Class C beta-lactamases pre-dated the divergence of the Class A and Class D beta-lactamases.

Bacteria↗
PubMed2003

Experimental prediction of the natural evolution of antibiotic resistance.

The TEM family of beta-lactamases has evolved to confer resistance to most of the beta-lactam antibiotics, but not to cefepime. To determine whether the TEM beta-lactamases have the potential to evolve cefepime resistance, we evolved the ancestral TEM allele, TEM-1, in vitro and selected for cefepime resistance. After four rounds of mutagenesis and selection for increased cefepime resistance each of eight independent populations reached a level equivalent to clinical resistance. All eight evolved alleles increased the level of cefepime resistance by a factor of at least 32, and the best allele improved by a factor of 512. Sequencing showed that alleles contained from two to six amino acid substitutions, many of which were shared among alleles, and that the best allele contained only three substitutions.

Biological Evolution↗
PubMed2003

Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase.

Understanding of the evolutionary histories of many genes has not yet allowed us to predict the evolutionary potential of those genes. Intuition suggests that current biochemical activity of gene products should be a good predictor of the potential to evolve related activities; however, we have little evidence to support that intuition. Here we use our in vitro evolution method to evaluate biochemical activity as a predictor of future evolutionary potential. Neither the class C Citrobacter freundii CMY-2 AmpC beta-lactamase nor the class A TEM-1 beta-lactamase confer resistance to the beta-lactam antibiotic cefepime, nor do any of the naturally occurring alleles descended from them. However, the CMY-2 AmpC enzyme and some alleles descended from TEM-1 confer high-level resistance to the structurally similar ceftazidime. On the basis of the comparison of TEM-1 and CMY-2, we asked whether biochemical activity is a good predictor of the evolutionary potential of an enzyme. If it is, then CMY-2 should be more able than the TEMs to evolve the ability to confer higher levels of cefepime resistance. Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles.

Bacterial Proteins↗
PubMed2003

GeneHunter, a transposon tool for identification and isolation of cryptic antibiotic resistance genes.

GeneHunter is a transposon tool designed for the experimental activation and identification of silent antibiotic resistance genes. The method permits the identification of novel resistance genes that lack previously identified homologues. Using Salmonella enterica serovar Typhimurium strain LT2 as a test organism for the in vivo version of the GeneHunter method, we were able to activate, clone, and identify two cryptic antibiotic resistance genes, the aminoglycoside acetyltransferase aac(6')-Iaa and the probable Mar-A regulon activator rma. Because the method requires being able to electroporate the host with an efficiency of at least 10(10) transformants per microgram, the in vivo method is not applicable to most microorganisms. We therefore developed an in vitro transposition method, showed that it can also recover the cryptic rma gene from S. enterica serovar Typhimurium strain LT2, and showed that it is generally applicable to a variety of microorganisms by using it to recover a cryptic metallo-beta-lactamase gene from the gram-positive organism Bacillus cereus. It is anticipated that the GeneHunter method will be used to identify potential resistance genes during the development and testing of novel antibiotics, new variants of existing antibiotics, and drug inhibitor combinations.

Acetyltransferases↗
PubMed2003

The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose.

The EBG system of E. coli has served as a model for the evolution of novel functions. This paper reviews the experimental evolution of the catabolism of beta-galactoside sugars in strains of E. coli that carry deletions of the classical lacZ beta-galactosidase gene. Evolution of the ebgA encoded Ebg beta-galactosidase for an expanded substrate range, evolution of the ebgR encoded Ebg repressor for sensitivity to an expanded range of inducers, the amino acid replacements responsible for those changes, and the evolutionary potential of the system are discussed. The EBG system has also served as a model for studying the detailed catalytic consequences of experimental evolution at the physical-chemical level. The analysis of free-energy profiles for the wildtype and all of the various evolved Ebg enzymes has permitted rejection of the Albery-Knowles hypothesis that relates likely changes in free-energy profiles to evolutionary change.

Crosses, Genetic↗
PubMed2002

Phylogenetic analysis shows that the OXA beta-lactamase genes have been on plasmids for millions of years.

The OXA genes encode a class of beta-lactamases that confer resistance to a wide range of beta-lactam antibiotics. To determine whether the diversity of the OXA beta-lactamases is the result of recent or ancient events, and to determine whether mobilization of the OXA genes from chromosomes to plasmids occurred recently or long ago, we have constructed a Bayesian phylogeny of the OXA beta-lactamase genes. Analysis of that phylogeny shows that much of the diversity is the result of ancient events and that the OXA genes were mobilized from chromosomes to plasmids on at least two independent occasions that occurred millions of years ago. That observation contradicts the commonly held impression that mobilization of antibiotic resistance genes is strictly the result of modern use of antibiotics.

Bayes Theorem↗
PubMed2002

Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase.

To evaluate the validity of our in vitro evolution method as a model for natural evolutionary processes, the TEM-1 beta-lactamase gene was evolved in vitro and was selected for increased resistance to cefotaxime, cefuroxime, ceftazadime, and aztreonam, i.e., the "extended-spectrum" phenotype. The amino acid substitutions recovered in 10 independent in vitro evolvants were compared with the amino acid substitutions in the naturally occurring extended-spectrum TEM alleles. Of the nine substitutions that have arisen multiple times in naturally occurring extended-spectrum TEM alleles, seven were recovered multiple times in vitro. We take this result as evidence that our in vitro evolution technique accurately mimics natural evolution and can therefore be used to predict the results of natural evolutionary processes. Additionally, our results predict that a phenotype not yet observed among TEM beta-lactamases in nature-resistance to cefepime-is likely to arise in nature.

Anti-Bacterial Agents↗