Genome Plasticity in Pathogenic and Nonpathogenic Enterobacteria

Dobrindt, Ulrich; Hentschel, Ute; Kaper, James B.; Hacker, Jörg

doi:10.1007/978-3-662-09217-0_9

Cited by 17 publications

(15 citation statements)

References 87 publications

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“…The above criteria have been used to characterize GIs from several microorganisms, and the ORF composition of GI 1 is also in accordance with what has been verified in other systems, including 41 hypothetical proteins, six conserved hypothetical proteins, five phage-related factors (including a hemolysin-like enzyme), one lipid A biosynthesis enzyme, one fimbrillin, and the virulenceassociated factor VapE from Dichelobacter nodosus (Bloomfield et al 1997). These latter factors are typically present in pathogenicity islands (PAIs), a subset of GIs that transfer virulence-related genes among microorganisms and are currently viewed as key virulence determinants in many pathogenic (Bjorkholm et al 2001;Dobrindt et al 2002;Dziejman et al 2002;Tauschek et al 2002;Walker and Verma 2002). The changes associated with this region suggest that GI 1 might be partly or entirely duplicated in the citrus strains, but absent in bacteria from the other hosts (except for coffee), indicating a remarkable level of transpositional activity during the evolution of the Xf group.…”

Section: Genomic Comparison Of Xf Strainsmentioning

confidence: 53%

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Nunes¹,

Rosato²,

Muto³

et al. 2003

Genome Res.

104

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Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species

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Section: Genomic Comparison Of Xf Strainsmentioning

confidence: 53%

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Nunes¹,

Rosato²,

Muto³

et al. 2003

Genome Res.

104

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“…Although no such CTL escape mutants have yet been isolated in bacteria, several lines of evidence suggest that they can evolve. Recent studies have revealed microbial genomes to have more plasticity than previously thought (35,36). Comparative genome analysis of different Escherichia coli strains has demonstrated that DNA sequence variation exists throughout the chromosome, and that the genome contains a high number of putative open reading frames and mobile genetic elements (37).…”

Section: Discussionmentioning

confidence: 99%

Activation of Antigen-Specific CD8 T Cells Results in Minimal Killing of Bystander Bacteria

Jiang

Zenewicz

Mateo

et al. 2003

The Journal of Immunology

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Memory CD8 T cells play a critical role in protective immunity against intracellular pathogens. In addition to their ability to specifically recognize and lyse infected targets, activated CD8 T cells secrete cytokines that induce phagocytic cells to engulf and kill bacterial pathogens. In this study, we asked whether activation of Ag-specific CD8 T cells results in nonspecific killing of bystander bacteria during a mixed infection. Mice with epitope-specific memory CD8 T cells were coinfected with two isogenic strains of recombinant Listeria monocytogenes that differ in the cognate epitope. Recall responses by epitope-specific CD8 T cells rapidly inhibited the growth of epitope-bearing bacteria, impeding the course of infection within 6 h after challenge. This rapid inhibition was highly specific and did not affect the growth of coinfecting bacteria without the epitope. CTL recall did not enhance activation of innate immune cells, as evidenced by the absence of inducible NO synthase production in infectious foci. Our observations demonstrate the remarkable specificity of the bactericidal mechanisms of CTL and reveal the possibility for escape mutants to prevail in the hostile environment of a specific immune response. This implication has a bearing on subunit vaccine design strategies and understanding failure of immunization against bacterial infection.

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“…Future work will show whether this reflects general principles of adaptation or if there are other important strategies for optimizing metabolism. A full appreciation of the plasticity of genomes 32,33 and the capacity of bacteria to rapidly adapt to new environments will emerge as genome-scale technologies such as CGS are applied to study experimental evolution.…”

Section: Mutation Frequencies In Evolving Populationsmentioning

confidence: 99%

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

et al. 2006

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We applied whole-genome resequencing of Escherichia coli to monitor the acquisition and fixation of mutations that conveyed a selective growth advantage during adaptation to a glycerol-based growth medium. We identified 13 different de novo mutations in five different E. coli strains and monitored their fixation over a 44-d period of adaptation. We obtained proof that the observed spontaneous mutations were responsible for improved fitness by creating single, double and triple site-directed mutants that had growth rates matching those of the evolved strains. The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts.Comparative genomics has been almost entirely focused on genomic changes over long periods of time, on the order of millions of years. A new microarray-based method of whole-genome resequencing called comparative genome sequencing (CGS) 1 now makes it cost efficient to monitor bacterial evolution comprehensively over short time periods as well. This capability is important because many microbial phenomena, such as the emergence of new pathogens and the acquisition of antibiotic resistance factors, can occur over relatively short time scales. Experimental evolution of bacteria and viruses 2,3 is a facile approach to study these topics. It has been used to test predictions of evolutionary theory 4 and to study parallel changes in populations evolved for 20,000 generations 5 , acquisition of antibiotic resistance 1 and in vitro symbiosis 6 . Our laboratory has used experimental evolution as a tool for metabolic engineering 7 and to study the recovery of strains with gene knockouts in central metabolic genes 8 . Nevertheless, much remains unknown about genome plasticity over short evolutionary timescales.It is a common mistake to think of bacteria as static; that is, to assume that a culture grown overnight is the same as it was the day before. It has been estimated that nearly 10% of the individual bacteria in a Salmonella enterica population carry large-scale genome rearrangements 9 , and in a suboptimal environment, selection can alter a population very rapidly. The 10-20 generations that occur in the process of growing a bacterial culture are sufficient to create a heterogeneous population, depending on the magnitude of the selective advantage of adaptive mutations. This problem is avoided by using strains of bacteria that are adapted to common laboratory media, but there are interesting cases where a seemingly straightforward growth medium poses a great challenge to a bacterium.An example is E. coli K-12 grown in minimal medium supplemented with glycerol as the carbon and energy source. Despite a complete pathway for glycerol catabolism, large variations in the growth rates of various strains have been noted 10 . Growth of the sequenced strain MG1655 has been observed to differ from computational predictions based on flux balance analysis 11 . Upon extended logarithmic growth in glycerol minimal medium, the growth rate...

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Genome Plasticity in Pathogenic and Nonpathogenic Enterobacteria

Cited by 17 publications

References 87 publications

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Activation of Antigen-Specific CD8 T Cells Results in Minimal Killing of Bystander Bacteria

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

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