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Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli
Tim F Cooper, Andrew P Morby, Annabel Gunn, Dominique Schneider
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-237
Abstract: 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.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.Genome-wide profiling has enabled researchers to organize the regulatory interactions of many organisms into global networks detailing connections between genes. To date most research has focused on describing the overall pattern formed by these connections, typically finding them to follow a power-law distribution comprising a small number of well-connected 'hub' genes and many genes with one or a few connections [reviewed in 1]. Now, as an increasing number of these networks have been described, the implications of their organization is being considered. For example, does network topology place evolutionary constraints on component nodes [2-4] and what general biological consequences emerge from power-law regulatory distributions [4-8]?Theoretical work predicts that power-law networks possess an intrinsic robustness to perturb
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network  [cached]
Dobrin Radu,Beg Qasim,Barabási Albert-László,Oltvai Zoltán
BMC Bioinformatics , 2004,
Abstract: Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs). However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs) do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
Radu Dobrin, Qasim Beg, Albert-László Barabási, Zoltán Oltvai
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-10
Abstract: By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs) do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect.Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.Many biological functions are carried out by the integrated activity of highly interacting cellular components, referred to as functional modules [1,2]. Motifs, considered as overrepresented topological interaction patterns within complex networks, may represent the simplest building blocks of such modules [3,4]. Owing to their small size, motifs can be explicitly identified and enumerated in various cellular networks, each network being characterized by its own set of distinct motifs [3-5]. For example, triangle motifs, referred to as feed-forward loops in directed networks, emerge in both transcriptional regulatory and neural networks, while four node feedback loops represent characteristic motifs in electric circuits, but not in biological systems [4]. The high degree of evolutionary conservation of the motif constituents within the yeast protein interaction network [6], and the convergent evolution observed in the transcriptional regulatory network of diverse species towards the same motif types [7,8] suggest that motifs are indeed of direct biological relevance.As
Structural and Mutational Analysis of Escherichia coli AlkB Provides Insight into Substrate Specificity and DNA Damage Searching  [PDF]
Paul J. Holland,Thomas Hollis
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008680
Abstract: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG) iron(II) dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions, but it also repairs 1-methylguanine (1-meG) and 3-methylthymine (3-meT) at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question.
Species-Specificity of the BamA Component of the Bacterial Outer Membrane Protein-Assembly Machinery  [PDF]
Elena B. Volokhina, Jan Grijpstra, Frank Beckers, Erika Lindh, Viviane Robert, Jan Tommassen, Martine P. Bos
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0085799
Abstract: The BamA protein is the key component of the Bam complex, the assembly machinery for outer membrane proteins (OMP) in gram-negative bacteria. We previously demonstrated that BamA recognizes its OMP substrates in a species-specific manner in vitro. In this work, we further studied species specificity in vivo by testing the functioning of BamA homologs of the proteobacteria Neisseria meningitidis, Neisseria gonorrhoeae, Bordetella pertussis, Burkholderia mallei, and Escherichia coli in E. coli and in N. meningitidis. We found that no BamA functioned in another species than the authentic one, except for N. gonorrhoeae BamA, which fully complemented a N. meningitidis bamA mutant. E. coli BamA was not assembled into the N. meningitidis outer membrane. In contrast, the N. meningitidis BamA protein was assembled into the outer membrane of E. coli to a significant extent and also associated with BamD, an essential accessory lipoprotein of the Bam complex.Various chimeras comprising swapped N-terminal periplasmic and C-terminal membrane-embedded domains of N. meningitidis and E. coli BamA proteins were also not functional in either host, although some of them were inserted in the OM suggesting that the two domains of BamA need to be compatible in order to function. Furthermore, conformational analysis of chimeric proteins provided evidence for a 16-stranded β-barrel conformation of the membrane-embedded domain of BamA.
Information content based model for the topological properties of the gene regulatory network of Escherichia coli  [PDF]
Berkin Malkoc,Duygu Balcan,Ayse Erzan
Quantitative Biology , 2009, DOI: 10.1016/j.jtbi.2009.11.017
Abstract: Gene regulatory networks (GRN) are being studied with increasingly precise quantitative tools and can provide a testing ground for ideas regarding the emergence and evolution of complex biological networks. We analyze the global statistical properties of the transcriptional regulatory network of the prokaryote Escherichia coli, identifying each operon with a node of the network. We propose a null model for this network using the content-based approach applied earlier to the eukaryote Saccharomyces cerevisiae. (Balcan et al., 2007) Random sequences that represent promoter regions and binding sequences are associated with the nodes. The length distributions of these sequences are extracted from the relevant databases. The network is constructed by testing for the occurrence of binding sequences within the promoter regions. The ensemble of emergent networks yields an exponentially decaying in-degree distribution and a putative power law dependence for the out-degree distribution with a flat tail, in agreement with the data. The clustering coefficient, degree-degree correlation, rich club coefficient and k-core visualization all agree qualitatively with the empirical network to an extent not yet achieved by any other computational model, to our knowledge. The significant statistical differences can point the way to further research into non-adaptive and adaptive processes in the evolution of the E. coli GRN.
Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli
Carlos Vázquez, Julio A Freyre-González, Guillermo Gosset, José Loza, Rosa Gutiérrez-Ríos
BMC Microbiology , 2009, DOI: 10.1186/1471-2180-9-176
Abstract: Transcriptome data from strains grown in Luria-Bertani medium (LB) or LB+glucose (LB+G) were analyzed, in order to identify differentially transcribed genes in B. subtilis. We detected 503 genes in B. subtilis that change their relative transcript levels in the presence of glucose. A similar previous study identified 380 genes in E. coli, which respond to glucose. Catabolic repression was detected in the case of transport and metabolic interconversion activities for both bacteria in LB+G. We detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. A comparison between orthologous genes revealed that global regulatory functions such as transcription, translation, replication and genes relating to the central carbon metabolism, presented similar changes in their levels of expression. An analysis of the regulatory network of a subset of genes in both organisms revealed that the set of regulatory proteins responsible for similar physiological responses observed in the transcriptome analysis are not orthologous. An example of this observation is that of transcription factors mediating catabolic repression for most of the genes that displayed reduced transcript levels in the case of both organisms. In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism. Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.During the last decades, an increase in the quantity of available data referring
Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli
Rosa Gutierrez-Ríos, Julio A Freyre-Gonzalez, Osbaldo Resendis, Julio Collado-Vides, Milton Saier, Guillermo Gosset
BMC Microbiology , 2007, DOI: 10.1186/1471-2180-7-53
Abstract: Transcriptome data from isogenic wild type and crp- strains grown in Luria-Bertani medium (LB) or LB + 4 g/L glucose (LB+G) were analyzed to identify differentially transcribed genes. We detected 180 and 200 genes displaying increased and reduced relative transcript levels in the presence of glucose, respectively. The observed expression pattern in LB was consistent with a gluconeogenic metabolic state including active transport and interconversion of small molecules and macromolecules, induction of protease-encoding genes and a partial heat shock response. In LB+G, catabolic repression was detected for transport and metabolic interconversion activities. We also detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. Cluster analysis of a subset of genes revealed that CRP mediates catabolite repression for most of the genes displaying reduced transcript levels in LB+G, whereas Fis participates in the upregulation of genes under this condition. An analysis of the regulatory network, in terms of topological functional units, revealed 8 interconnected modules which again exposed the importance of Fis and CRP as directly responsible for the coordinated response of the cell. This effect was also seen with other not extensively connected transcription factors such as FruR and PdhR, which showed a consistent response considering media composition.This work allowed the identification of eight interconnected regulatory network modules that includes CRP, Fis and other transcriptional factors that respond directly or indirectly to the presence of glucose. In most cases, each of these modules includes genes encoding physiologically related functions, thus indicating a connection between regulatory network topology and related cellular functions involved in nutrient sensing and metabolism.In their natural environments, bacteria must adapt to changing physicochemical conditions. Adaptation responses are controlled by a complex network of sen
Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils  [PDF]
Abasiofiok M. Ibekwe,Jincai Ma,David E. Crowley,Ching-Hong Yang,Pek Y. Lum
Frontiers in Cellular and Infection Microbiology , 2014, DOI: 10.3389/fcimb.2014.00122
Abstract: Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.
Escherichia coli enterohemorrágica
Margall,Núria; Domínguez,àngela; Prats,Guillem; Salleras,Lluís;
Revista Espa?ola de Salud Pública , 1997, DOI: 10.1590/S1135-57271997000500002
Abstract: groups of escherichia coli enteropathogen are described, with special attention to escherichia coli enterohaemorragic. some serotypes of escherichia coli vero citotoxin-producing are able to produce hemorrhagic enteritis, which can develop a complication with hemolityc uraemic syndrome. this complication is most frequent in children and has a high mortality rate. the transmission takes place via food and its capacity to cause epidemic outbreaks together with the seriousness of the complications caused by enteritys make this microorganism of great importance to public health. the epidemiology of this microorganism in spain is reviewed.
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