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1.
PLoS Genet ; 9(7): e1003617, 2013.
Article in English | MEDLINE | ID: mdl-23874220

ABSTRACT

The metabolic capabilities and regulatory networks of bacteria have been optimized by evolution in response to selective pressures present in each species' native ecological niche. In a new environment, however, the same bacteria may grow poorly due to regulatory constraints or biochemical deficiencies. Adaptation to such conditions can proceed through the acquisition of new cellular functionality due to gain of function mutations or via modulation of cellular networks. Using selection experiments on transposon-mutagenized libraries of bacteria, we illustrate that even under conditions of extreme nutrient limitation, substantial adaptation can be achieved solely through loss of function mutations, which rewire the metabolism of the cell without gain of enzymatic or sensory function. A systematic analysis of similar experiments under more than 100 conditions reveals that adaptive loss of function mutations exist for many environmental challenges. Drawing on a wealth of examples from published articles, we detail the range of mechanisms through which loss-of-function mutations can generate such beneficial regulatory changes, without the need for rare, specific mutations to fine-tune enzymatic activities or network connections. The high rate at which loss-of-function mutations occur suggests that null mutations play an underappreciated role in the early stages of adaption of bacterial populations to new environments.


Subject(s)
Adaptation, Physiological/genetics , Bacteria/genetics , Directed Molecular Evolution , Selection, Genetic , DNA Transposable Elements/genetics , Environment , Food , Mutation
2.
PLoS Pathog ; 7(10): e1002298, 2011 Oct.
Article in English | MEDLINE | ID: mdl-22028649

ABSTRACT

Bacteria in biofilms have higher antibiotic tolerance than their planktonic counterparts. A major outstanding question is the degree to which the biofilm-specific cellular state and its constituent genetic determinants contribute to this hyper-tolerant phenotype. Here, we used genome-wide functional profiling of a complex, heterogeneous mutant population of Pseudomonas aeruginosa MPAO1 in biofilm and planktonic growth conditions with and without tobramycin to systematically quantify the contribution of each locus to antibiotic tolerance under these two states. We identified large sets of mutations that contribute to antibiotic tolerance predominantly in the biofilm or planktonic setting only, offering global insights into the differences and similarities between biofilm and planktonic antibiotic tolerance. Our mixed population-based experimental design recapitulated the complexity of natural biofilms and, unlike previous studies, revealed clinically observed behaviors including the emergence of quorum sensing-deficient mutants. Our study revealed a substantial contribution of the cellular state to the antibiotic tolerance of biofilms, providing a rational foundation for the development of novel therapeutics against P. aeruginosa biofilm-associated infections.


Subject(s)
Anti-Bacterial Agents/pharmacology , Biofilms/drug effects , Drug Tolerance/genetics , Genetic Fitness/drug effects , Pseudomonas aeruginosa/drug effects , Tobramycin/pharmacology , Amino Acid Sequence , Base Sequence , Biofilms/growth & development , Gene Expression Regulation, Bacterial , Genes, Bacterial/genetics , Genetic Fitness/genetics , Genome-Wide Association Study , Genomics , Meta-Analysis as Topic , Molecular Sequence Data , Mutation , Oligonucleotide Array Sequence Analysis , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/growth & development
3.
Methods Mol Biol ; 765: 83-97, 2011.
Article in English | MEDLINE | ID: mdl-21815088

ABSTRACT

Successful strain engineering involves perturbing key nodes within the cellular network. How the -network's connectivity affects the phenotype of interest and the ideal nodes to modulate, however, are frequently not readily apparent. To guide the generation of a list of candidate nodes for detailed investigation, designers often examine the behavior of a representative set of strains, such as a library of transposon insertion mutants, in the environment of interest. Here, we first present design principles for creating a maximally informative competitive selection. Then, we describe how to globally quantify the change in distribution of strains within a transposon library in response to a competitive selection by amplifying the DNA adjacent to the transposons and hybridizing it to a microarray. Finally, we detail strategies for analyzing the resulting hybridization data to identify genes and pathways that contribute both negatively and positively to fitness in the desired environment.


Subject(s)
DNA Footprinting , DNA Transposable Elements/genetics , Gene Library , Mutagenesis, Insertional/genetics , Oligonucleotide Array Sequence Analysis , Selection, Genetic
4.
Mol Syst Biol ; 6: 378, 2010 Jun 08.
Article in English | MEDLINE | ID: mdl-20531407

ABSTRACT

Understanding the genetic basis of adaptation is a central problem in biology. However, revealing the underlying molecular mechanisms has been challenging as changes in fitness may result from perturbations to many pathways, any of which may contribute relatively little. We have developed a combined experimental/computational framework to address this problem and used it to understand the genetic basis of ethanol tolerance in Escherichia coli. We used fitness profiling to measure the consequences of single-locus perturbations in the context of ethanol exposure. A module-level computational analysis was then used to reveal the organization of the contributing loci into cellular processes and regulatory pathways (e.g. osmoregulation and cell-wall biogenesis) whose modifications significantly affect ethanol tolerance. Strikingly, we discovered that a dominant component of adaptation involves metabolic rewiring that boosts intracellular ethanol degradation and assimilation. Through phenotypic and metabolomic analysis of laboratory-evolved ethanol-tolerant strains, we investigated naturally accessible pathways of ethanol tolerance. Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape.


Subject(s)
Adaptation, Physiological/drug effects , Directed Molecular Evolution , Escherichia coli/drug effects , Escherichia coli/physiology , Ethanol/pharmacology , Laboratories , Metabolic Networks and Pathways/drug effects , Acids , Cell Wall/drug effects , Cell Wall/metabolism , Escherichia coli/genetics , Ethanol/metabolism , Stress, Physiological/drug effects
5.
Mol Cell ; 35(2): 247-53, 2009 Jul 31.
Article in English | MEDLINE | ID: mdl-19647521

ABSTRACT

Protein-DNA interactions are fundamental to core biological processes, including transcription, DNA replication, and chromosomal organization. We have developed in vivo protein occupancy display (IPOD), a technology that reveals protein occupancy across an entire bacterial chromosome at the resolution of individual binding sites. Application to Escherichia coli reveals thousands of protein occupancy peaks, highly enriched within and in close proximity to noncoding regulatory regions. In addition, we discovered extensive (>1 kilobase) protein occupancy domains (EPODs), some of which are localized to highly expressed genes, enriched in RNA-polymerase occupancy. However, the majority are localized to transcriptionally silent loci dominated by conserved hypothetical ORFs. These regions are highly enriched in both predicted and experimentally determined binding sites of nucleoid proteins and exhibit extreme biophysical characteristics such as high intrinsic curvature. Our observations implicate these transcriptionally silent EPODs as the elusive organizing centers, long proposed to topologically isolate chromosomal domains.


Subject(s)
Chromosomes, Bacterial/metabolism , DNA-Binding Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/genetics , Genome, Bacterial , Binding Sites , Chromosomes, Bacterial/chemistry , DNA Footprinting , DNA-Binding Proteins/genetics , DNA-Directed RNA Polymerases/metabolism , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Gene Expression Profiling , Hybridization, Genetic , RNA, Messenger/metabolism
6.
Nat Methods ; 6(8): 581-3, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19597501

ABSTRACT

Although modern DNA sequencing enables rapid identification of genetic variation, characterizing the phenotypic consequences of individual mutations remains a labor-intensive task. Here we describe array-based discovery of adaptive mutations (ADAM), a technology that searches an entire bacterial genome for mutations that contribute to selectable phenotypic variation between an evolved strain and its parent. We found that ADAM identified adaptive mutations in laboratory-evolved Escherichia coli strains with high sensitivity and specificity.


Subject(s)
DNA Mutational Analysis/methods , Escherichia coli/genetics , Mutation , Adaptation, Biological , DNA Transposable Elements , Drug Resistance, Bacterial/genetics , Escherichia coli Proteins/genetics , Sensitivity and Specificity
7.
PLoS One ; 4(5): e5629, 2009 May 20.
Article in English | MEDLINE | ID: mdl-19462005

ABSTRACT

BACKGROUND: Antibiotic exposure rapidly selects for more resistant bacterial strains, and both a drug's chemical structure and a bacterium's cellular network affect the types of mutations acquired. METHODOLOGY/PRINCIPAL FINDINGS: To better characterize the genetic determinants of antibiotic susceptibility, we exposed a transposon-mutagenized library of Escherichia coli to each of 17 antibiotics that encompass a wide range of drug classes and mechanisms of action. Propagating the library for multiple generations with drug concentrations that moderately inhibited the growth of the isogenic parental strain caused the abundance of strains with even minor fitness advantages or disadvantages to change measurably and reproducibly. Using a microarray-based genetic footprinting strategy, we then determined the quantitative contribution of each gene to E. coli's intrinsic antibiotic susceptibility. We found both loci whose removal increased general antibiotic tolerance as well as pathways whose down-regulation increased tolerance to specific drugs and drug classes. The beneficial mutations identified span multiple pathways, and we identified pairs of mutations that individually provide only minor decreases in antibiotic susceptibility but that combine to provide higher tolerance. CONCLUSIONS/SIGNIFICANCE: Our results illustrate that a wide-range of mutations can modulate the activity of many cellular resistance processes and demonstrate that E. coli has a large mutational target size for increasing antibiotic tolerance. Furthermore, the work suggests that clinical levels of antibiotic resistance might develop through the sequential accumulation of chromosomal mutations of small individual effect.


Subject(s)
Drug Resistance, Microbial/genetics , Aerobiosis/drug effects , Aminoglycosides/pharmacology , Anti-Bacterial Agents/classification , Anti-Bacterial Agents/pharmacology , DNA Transposable Elements/genetics , Electron Transport/drug effects , Escherichia coli/drug effects , Escherichia coli/enzymology , Escherichia coli/genetics , Escherichia coli Proteins/metabolism , Flagella/drug effects , Flagella/metabolism , Folic Acid/biosynthesis , Genes, Bacterial , Microbial Sensitivity Tests , Mutagenesis, Insertional/drug effects , Mutation/genetics , Racemases and Epimerases/metabolism , Reproducibility of Results , Selection, Genetic , Tetrahydrofolate Dehydrogenase/metabolism , beta-Lactams/pharmacology
8.
Nat Biotechnol ; 25(5): 584-92, 2007 May.
Article in English | MEDLINE | ID: mdl-17401361

ABSTRACT

Using 62 probe-level datasets obtained with a custom-designed Caulobacter crescentus microarray chip, we identify transcriptional start sites of 769 genes, 53 of which are transcribed from multiple start sites. Transcriptional start sites are identified by analyzing probe signal cross-correlation matrices created from probe pairs tiled every 5 bp upstream of the genes. Signals from probes binding the same message are correlated. The contribution of each promoter for genes transcribed from multiple promoters is identified. Knowing the transcription start site enables targeted searching for regulatory-protein binding motifs in the promoter regions of genes with similar expression patterns. We identified 27 motifs, 17 of which share no similarity to the characterized motifs of other C. crescentus transcriptional regulators. Using these motifs, we predict coregulated genes. We verified novel promoter motifs that regulate stress-response genes, including those responding to uranium challenge, a stress-response sigma factor and a stress-response noncoding RNA.


Subject(s)
Caulobacter crescentus/genetics , Conserved Sequence/genetics , DNA, Bacterial/genetics , Models, Genetic , Oligonucleotide Array Sequence Analysis/methods , Regulon/genetics , Transcription, Genetic/genetics , Base Sequence , Computer Simulation , Molecular Sequence Data , Promoter Regions, Genetic/genetics , Sequence Analysis, DNA/methods
9.
EMBO J ; 25(2): 377-86, 2006 Jan 25.
Article in English | MEDLINE | ID: mdl-16395329

ABSTRACT

We demonstrate that successive cleavage events involving regulated intramembrane proteolysis (Rip) occur as a function of time during the Caulobacter cell cycle. The proteolytic substrate PodJ(L) is a polar factor that recruits proteins required for polar organelle biogenesis to the correct cell pole at a defined time in the cell cycle. We have identified a periplasmic protease (PerP) that initiates the proteolytic sequence by truncating PodJ(L) to a form with altered activity (PodJ(S)). Expression of perP is regulated by a signal transduction system that activates cell type-specific transcription programs and conversion of PodJ(L) to PodJ(S) in response to the completion of cytokinesis. PodJ(S), sequestered to the progeny swarmer cell, is subsequently released from the polar membrane by the membrane metalloprotease MmpA for degradation during the swarmer-to-stalked cell transition. This sequence of proteolytic events contributes to the asymmetric localization of PodJ isoforms to the appropriate cell pole. Thus, temporal activation of the PerP protease and spatial restriction of the polar PodJ(L) substrate cooperatively control the cell cycle-dependent onset of Rip.


Subject(s)
Bacterial Proteins/metabolism , Caulobacter crescentus/physiology , Cell Polarity/physiology , Cytokinesis/physiology , Membrane Proteins/metabolism , Peptide Hydrolases/metabolism , Periplasmic Proteins/metabolism , Gene Expression Regulation, Bacterial/physiology , Immunoblotting , Microarray Analysis , Microscopy, Fluorescence , Signal Transduction/physiology , beta-Galactosidase
10.
Mol Microbiol ; 58(5): 1340-53, 2005 Dec.
Article in English | MEDLINE | ID: mdl-16313620

ABSTRACT

The level of DnaA, a key bacterial DNA replication initiation factor, increases during the Caulobacter swarmer-to-stalked transition just before the G1/S transition. We show that DnaA coordinates DNA replication initiation with cell cycle progression by acting as a global transcription factor. Using DnaA depletion and induction in synchronized cell populations, we have analysed global transcription patterns to identify the differential regulation of normally co-expressed genes. The DnaA regulon includes genes encoding several replisome components, the GcrA global cell cycle regulator, the PodJ polar localization protein, the FtsZ cell division protein, and nucleotide biosynthesis enzymes. In cells depleted of DnaA, the G1/S transition is temporally separated from the swarmer-to-stalked cell differentiation, which is normally coincident. In the absence of DnaA, the CtrA master regulator is cleared by proteolysis during the swarmer-to-stalked cell transition as usual, but DNA replication initiation is blocked. In this case, expression of gcrA, which is directly repressed by CtrA, does not increase in conjunction with the disappearance of CtrA until DnaA is subsequently induced, showing that gcrA expression requires DnaA. DnaA boxes are present upstream of many genes whose expression requires DnaA, and His6-DnaA binds to the promoters of gcrA, ftsZ and podJ in vitro. This redundant control of gcrA transcription by DnaA (activation) and CtrA (repression) forms a robust switch controlling the decision to proceed through the cell cycle or to remain in the G1 stage.


Subject(s)
Bacterial Proteins/metabolism , Caulobacter crescentus/metabolism , Cell Cycle/physiology , DNA Replication , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Bacterial , Transcription Factors/metabolism , Bacterial Proteins/genetics , Caulobacter crescentus/genetics , Caulobacter crescentus/growth & development , DNA-Binding Proteins/genetics , Oligonucleotide Array Sequence Analysis , Replication Origin , Transcription Factors/genetics , Transcription, Genetic
11.
Proc Natl Acad Sci U S A ; 101(10): 3480-5, 2004 Mar 09.
Article in English | MEDLINE | ID: mdl-14990797

ABSTRACT

Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.


Subject(s)
Codon/genetics , Genome , Mutation , Animals , Archaea/genetics , Bacteria/genetics , Base Composition , DNA, Intergenic , Genome, Archaeal , Genome, Bacterial , Genomics/statistics & numerical data , Mammals , Protein Biosynthesis , RNA, Archaeal/genetics , RNA, Bacterial/genetics
12.
J Bacteriol ; 186(5): 1448-61, 2004 Mar.
Article in English | MEDLINE | ID: mdl-14973021

ABSTRACT

Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation.


Subject(s)
Bacterial Proteins/metabolism , Caulobacter crescentus/growth & development , Gene Expression Profiling , Gene Expression Regulation, Bacterial , Transcription, Genetic , Amino Acid Motifs , Bacterial Proteins/genetics , Base Sequence , Caulobacter crescentus/genetics , Caulobacter crescentus/metabolism , Culture Media , Glucose/metabolism , Molecular Sequence Data , Oligonucleotide Array Sequence Analysis , Xylose/metabolism
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