Biomedical subjects

Dominique Schneider

Publications and source records attributed to Dominique Schneider.

15 recordsLinked to original sources

PubMed2006

Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli.

BACKGROUND: Genome-wide profiling has allowed the regulatory interaction networks of many organisms to be visualised and the pattern of connections between genes to be studied. These networks are non-random, following a power-law distribution with a small number of well-connected 'hubs' and many genes with only one or a few connections. Theoretical work predicts that power-law networks display several unique properties. One of the most biologically interesting of these is an intrinsic robustness to disturbance such that removal of a random gene will have little effect on network function. Conversely, targeted removal of a hub gene is expected to have a large effect. RESULTS: We compared the response of Escherichia coli to environmental and mutational stress following disruption of random or hub genes. We found that disruption of random genes had less effect on robustness to environmental stress than did the targeted disruption of hub genes. In contrast, random disruption strains were slightly less robust to the effect of mutational stress than were hub disruption strains. When we compared the effect of each disruption on environmental and mutational stress, we found a negative relationship, such that strains that were more environmentally robust tended to be less robust to mutational stress. CONCLUSION: Our results demonstrate that mutant strains of E. coli respond differently to stress, depending on whether random or hub genes are disrupted. This difference indicates that the power-law distribution of regulatory interactions has biological significance, making random disruptions less deleterious to organisms facing environmental stress. That E. coli can reduce the effect of environmental stress without reducing the phenotypic effect of additional mutations, indicates that robustness and evolvability need not be antagonistic.

Anti-Bacterial Agents↗

PubMed2006

Tests of parallel molecular evolution in a long-term experiment with Escherichia coli.

The repeatability of evolutionary change is difficult to quantify because only a single outcome can usually be observed for any precise set of circumstances. In this study, however, we have quantified the frequency of parallel and divergent genetic changes in 12 initially identical populations of Escherichia coli that evolved in identical environments for 20,000 cell generations. Unlike previous analyses in which candidate genes were identified based on parallel phenotypic changes, here we sequenced four loci (pykF, nadR, pbpA-rodA, and hokB/sokB) in which mutations of unknown effect had been discovered in one population, and then we compared the substitution pattern in these "blind" candidate genes with the pattern found in 36 randomly chosen genes. Two candidate genes, pykF and nadR, had substitutions in all 11 other populations, and the other 2 in several populations. There were very few cases, however, in which the exact same mutations were substituted, in contrast to the findings from conceptually related work performed with evolving virus populations. No random genes had any substitutions except in four populations that evolved defects in DNA repair. Tests of four different statistical aspects of the pattern of molecular evolution all indicate that adaptation by natural selection drove the parallel changes in these candidate genes.

Animals↗

PubMed2006

Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli.

Twelve populations of Escherichia coli evolved in and adapted to a glucose-limited environment from a common ancestor. We used two-dimensional protein electrophoresis to compare two evolved clones, isolated from independently derived populations after 20,000 generations. Exceptional parallelism was detected. We compared the observed changes in protein expression profiles with previously characterized global transcription profiles of the same clones; this is the first time such a comparison has been made in an evolutionary context where these changes are often quite subtle. The two methodologies exhibited some remarkable similarities that highlighted two different levels of parallel regulatory changes that were beneficial during the evolution experiment. First, at the higher level, both methods revealed extensive parallel changes in the same global regulatory network, reflecting the involvement of beneficial mutations in genes that control the ppGpp regulon. Second, both methods detected expression changes of identical gene sets that reflected parallel changes at a lower level of gene regulation. The protein profiles led to the discovery of beneficial mutations affecting the malT gene, with strong genetic parallelism across independently evolved populations. Functional and evolutionary analyses of these mutations revealed parallel phenotypic decreases in the maltose regulon expression and a high level of polymorphism at this locus in the evolved populations.

Adaptation, Physiological↗

PubMed2006

Growth-phase-dependent mobility of the lvh-encoding region in Legionella pneumophila strain Paris.

The lvh region of the Legionella pneumophila genome, which encodes a type IV secretion system, is located on a plasmid-like element in strains Paris (pP36) and Philadelphia (pLP45). The pP36 element has been described either integrated in the chromosome or excised as a multi-copy plasmid, in a similar manner to pLP45. In this paper, the chromosomal integration of pP36 in the Paris strain genome was described, occurring through site-specific recombination at the 3' end of a transfer-messenger RNA gene by recombination between attachment sites, in a similar manner to pathogenicity islands. This integration was growth-phase dependent, occurring during the exponential phase. Several pP36-borne genes were expressed during the lag phase of bacterial growth, coinciding with the peak amount of the episomal form of pP36. Expression of the same genes decreased during the exponential and stationary phases, owing to the integration phenomenon and a loss of episomal copies of pP36. A similar plasmid-like element was described in the Lens strain genome, suggesting that the mobility of the lvh region is a phenomenon widespread among Legionella sp.

Attachment Sites, Microbiological↗

PubMed2006

Are maternal re-infections with Trypanosoma cruzi associated with higher morbidity and mortality of congenital Chagas disease?

BACKGROUND: Comparing two surveys performed in Bolivia in 1992-1994 and 1999-2001, we reported a significant decrease in the proportions of severe and mortal forms of congenital Chagas disease. This might be due to a reduction of vectorial density (VD) in maternal residence area, raising the question of a possible causal relationship between such VD, maternal parasitaemia and prognosis of congenital infection with Trypanosoma cruzi. METHOD: Comparisons of haematological and parasitological data obtained from Bolivian mothers infected with T. cruzi, and of clinical and biological data obtained from their infected and uninfected newborns, stratified according to VD in the area of maternal residence. RESULTS: i) Blood hematocrit rates or hemoglobin amounts were within the normal ranges and similar in all the maternal groups, whatever the VD in their areas of residence; ii) mothers living in high VD areas displayed a higher frequency of hemocultures positive for T. cruzi; iii) newborns congenitally infected with T. cruzi, but not uninfected babies born from infected mothers, displayed higher frequencies of very low Apgar scores, low birth weights, prematurity, respiratory distress syndrome or anasarca, as well as higher mortality rates when their mothers lived in areas of high VD. CONCLUSION: Frequent bites of blood sucking Reduvidae during pregnancy do not induce maternal anaemia, but, likely through multiple maternal re-infections with T. cruzi, increase maternal parasitemia and worsen congenital Chagas disease. Maternal dwelling in areas of high VD is associated with a serious increased risk of severe and mortal congenital Chagas disease.

Animals↗

PubMed2006

Congenital Chagas disease in Bolivia is not associated with DNA polymorphism of Trypanosoma cruzi.

This study aims to typify the Trypanosoma cruzi (sub)lineage(s) in umbilical cord blood of congenitally infected Bolivian newborns, using PCR amplifications of "Region Markers", mini-exon or kDNA fragments followed by hybridization or sequencing. New probes were also designed to distinguish three variants within the TcIId sublineage. The IIb, IId, or IIe T. cruzi sublineages, as well as different variants of the IId sublineage, were detected in infected neonates, whereas mixed infections were not found. The frequencies of the IId sublineage were similar in neonates (95.1%) and adults of the same area (94.1%). The IId-infected newborns displayed either asymptomatic, or severe and fatal clinical forms of congenital Chagas disease, as well as low or high parasitemia. Altogether these data show that T. cruzi DNA polymorphism, based on the presently available markers, is not associated with the occurrence of congenital infection or the development of severe clinical forms of congenital Chagas disease.

Animals↗

PubMed2005

Qualitative simulation of the carbon starvation response in Escherichia coli.

In case of nutritional stress, like carbon starvation, Escherichia coli cells abandon their exponential-growth state to enter a more resistant, non-growth state called stationary phase. This growth-phase transition is controlled by a genetic regulatory network integrating various environmental signals. Although E. coli is a paradigm of the bacterial world, it is little understood how its response to carbon starvation conditions emerges from the interactions between the different components of the regulatory network. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift.

Carbon↗

PubMed2005

Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism.

We investigated the phylogenetic history of a balanced polymorphism that evolved in an experimental population of Escherichia coli. Previous work showed that two ecologically and morphologically distinct types, designated L (large) and S (small), arose by generation 6000 and coexisted for more than 12,000 generations thereafter. Here, we performed RFLP analyses using Insertion Sequence elements to resolve the phylogenetic history of L and S. Specifically, we sought to determine whether the derived S morph was monophyletic, indicating a long history of coexistence with L or, alternatively, S was repeatedly regenerated from L, indicating a series of periods with only transiently stable coexistence. Phylogenetic analysis of some 200 clones collected throughout the history of this population demonstrates that S is monophyletic. We then performed competition assays using clones of both morphs from different generations to determine whether either or both lineages continued to undergo genetic adaptation. Indeed, both lineages continued to adapt, and their continued evolution contributed to fluctuations in their relative abundance over evolutionary time. Based on their phylogenetic history and independent evolutionary trajectories, S and L fulfill Cohan's criteria for being different asexual species.

Adaptation, Physiological↗

PubMed2005

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

MOTIVATION: The modeling and simulation of genetic regulatory networks have created the need for tools for model validation. The main challenges of model validation are the achievement of a match between the precision of model predictions and experimental data, as well as the efficient and reliable comparison of the predictions and observations. RESULTS: We present an approach towards the validation of models of genetic regulatory networks addressing the above challenges. It combines a method for qualitative modeling and simulation with techniques for model checking, and is supported by a new version of the computer tool Genetic Network Analyzer (GNA). The model-validation approach has been applied to the analysis of the network controlling the nutritional stress response in Escherichia coli. AVAILABILITY: GNA and the model of the stress response network are available at http://www-helix.inrialpes.fr/gna.

Bacterial Physiological Phenomena↗

PubMed2004

Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection.

The genetic bases of adaptation are being investigated in 12 populations of Escherichia coli, founded from a common ancestor and serially propagated for 20,000 generations, during which time they achieved substantial fitness gains. Each day, populations alternated between active growth and nutrient exhaustion. DNA supercoiling in bacteria is influenced by nutritional state, and DNA topology helps coordinate the overall pattern of gene expression in response to environmental changes. We therefore examined whether the genetic controls over supercoiling might have changed during the evolution experiment. Parallel changes in topology occurred in most populations, with the level of DNA supercoiling increasing, usually in the first 2000 generations. Two mutations in the topA and fis genes that control supercoiling were discovered in a population that served as the focus for further investigation. Moving the mutations, alone and in combination, into the ancestral background had an additive effect on supercoiling, and together they reproduced the net change in DNA topology observed in this population. Moreover, both mutations were beneficial in competition experiments. Clonal interference involving other beneficial DNA topology mutations was also detected. These findings define a new class of fitness-enhancing mutations and indicate that the control of DNA supercoiling can be a key target of selection in evolving bacterial populations.

Adaptation, Physiological↗

PubMed2004

Improvement of pCVD442, a suicide plasmid for gene allele exchange in bacteria.

Allelic exchange experiments allow investigation of the functions of many unknown genes identified during the sequencing of entire genomes. Isogenic strains differing by only specific mutations can be constructed. Among other tools, suicide plasmids are widely used for this task. They present many advantages because they leave no scars on the chromosome, and therefore allow combining several mutations in the same genetic background. While using the previously described pCVD442 suicide plasmid [Infect. Immun. 59 (1991) 4310], we found untargeted recombination events due to the presence of an IS1 element on this plasmid. The plasmid was therefore improved by removal of the IS1 element. We also replaced the bla gene of pCVD442, conferring ampicillin resistance, by the cat gene conferring chloramphenicol resistance, leading to the new suicide plasmid pDS132. The plasmid was entirely sequenced. We demonstrate that this new vector can be easily used to introduce various types of mutations into different genetics backgrounds: removal of IS elements, introduction of point mutations or deletions. It can be introduced into bacterial strains by either transformation or conjugation.

Alleles↗

PubMed2004

Dynamics of insertion sequence elements during experimental evolution of bacteria.

We review the intersection between two areas of microbial evolution that were research foci of Michel Blot. One focus is the behavior of insertion sequence (IS) elements, including their role in promoting the evolutionary adaptation of their hosts. The other focus is experimental evolution, an approach that allows the dynamics of genomic and phenotypic change to be observed in the laboratory. This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness.

DNA Transposable Elements↗

PubMed2003

Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX.

sigma(S) (RpoS), the master regulator of the general stress response in Escherichia coli, is a model system for regulated proteolysis in bacteria. sigma(S) turnover requires ClpXP and the response regulator RssB, whose phosphorylated form exhibits high affinity for sigma(S). Here, we demonstrate that recognition by the RssB/ClpXP system involves two distinct regions in sigma(S). Region 2.5 of sigma(S) (a long alpha-helix) is sufficient for binding of phosphorylated RssB. However, this interaction alone is not sufficient to trigger proteolysis. A second region located in the N-terminal part of sigma(S), which is exposed only upon RssB-sigma(S) interaction, serves as a binding site for the ClpX chaperone. Binding of the ClpX hexameric ring to sigma(S)-derived reporter proteins carrying the ClpX-binding site (but not the RssB-binding site) is also not sufficient to commit the protein to degradation. Our data indicate that RssB plays a second role in the initiation of sigma(S) proteolysis that goes beyond targeting of sigma(S) to ClpX, and suggest a model for the sequence of events in the initiation of sigma(S) proteolysis.

Adenosine Triphosphatases↗

PubMed2003

Bacterial evolution through the selective loss of beneficial Genes. Trade-offs in expression involving two loci.

The loss of preexisting genes or gene activities during evolution is a major mechanism of ecological specialization. Evolutionary processes that can account for gene loss or inactivation have so far been restricted to one of two mechanisms: direct selection for the loss of gene activities that are disadvantageous under the conditions of selection (i.e., antagonistic pleiotropy) and selection-independent genetic drift of neutral (or nearly neutral) mutations (i.e., mutation accumulation). In this study we demonstrate with an evolved strain of Escherichia coli that a third, distinct mechanism exists by which gene activities can be lost. This selection-dependent mechanism involves the expropriation of one gene's upstream regulatory element by a second gene via a homologous recombination event. Resulting from this genetic exchange is the activation of the second gene and a concomitant inactivation of the first gene. This gene-for-gene expression tradeoff provides a net fitness gain, even if the forfeited activity of the first gene can play a positive role in fitness under the conditions of selection.

Adaptation, Physiological↗

PubMed2002

Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers.

BACKGROUND: Insertion Sequence (IS) elements are mobile genetic elements widely distributed among bacteria. Their activities cause mutations, promoting genetic diversity and sometimes adaptation. Previous studies have examined their copy number and distribution in Escherichia coli K-12 and natural isolates. Here, we map most of the IS elements in E. coli B and compare their locations with the published genomes of K-12 and O157:H7. RESULTS: The genomic locations of IS elements reveal numerous differences between B, K-12, and O157:H7. IS elements occur in hok-sok loci (homologous to plasmid stabilization systems) in both B and K-12, whereas these same loci lack IS elements in O157:H7. IS elements in B and K-12 are often found in locations corresponding to O157:H7-specific sequences, which suggests IS involvement in chromosomal rearrangements including the incorporation of foreign DNA. Some sequences specific to B are identified, as reported previously for O157:H7. The extent of nucleotide sequence divergence between B and K-12 is < 2% for most sequences adjacent to IS elements. By contrast, B and K-12 share only a few IS locations besides those in hok-sok loci. Several phenotypic features of B are explained by IS elements, including differential porin expression from K-12. CONCLUSIONS: These data reveal a high level of IS activity since E. coli B, K-12, and O157:H7 diverged from a common ancestor, including IS association with deletions and incorporation of horizontally acquired genes as well as transpositions. These findings indicate the important role of IS elements in genome plasticity and divergence.

Chromosome Mapping↗