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Abstract
Inferring gene regulatory networks from expression data is a very challenging problem that has raised the interest of the scientific community. Different algorithms have been proposed to try to solve this issue, but it has been shown that different methods have some particular biases and strengths, and none of them is the best across all types of data and datasets. As a result, the idea of aggregating various network inferences through a consensus mechanism naturally arises. In this chapter, a common framework to standardize already proposed consensus methods is presented, and based on this framework different proposals are introduced and analyzed in two different scenarios: Homogeneous and Heterogeneous. The first scenario reflects situations where the networks to be aggregated are rather similar because they are obtained with inference algorithms working on the same data, whereas the second scenario deals with very diverse networks because various sources of data are used to generate the individual networks. A procedure for combining multiple network inference algorithms is analyzed in a systematic way. The results show that there is a very significant difference between these two scenarios, and that the best way to combine networks in the Heterogeneous scenario is not the most commonly used. We show in particular that aggregation in the Heterogeneous scenario can be very beneficial if the individual networks are combined with our new proposed method ScaleLSum.
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LaVoie SP, Summers AO. Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. BMC Genomics 2018; 19:52. [PMID: 29338696 PMCID: PMC5769350 DOI: 10.1186/s12864-017-4413-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Background The protean chemical properties of mercury have long made it attractive for diverse applications, but its toxicity requires great care in its use, disposal, and recycling. Mercury occurs in multiple chemical forms, and the molecular basis for the distinct toxicity of its various forms is only partly understood. Global transcriptomics applied over time can reveal how a cell recognizes a toxicant and what cellular subsystems it marshals to repair and recover from the damage. The longitudinal effects on the transcriptome of exponential phase E. coli were compared during sub-acute exposure to mercuric chloride (HgCl2) or to phenylmercuric acetate (PMA) using RNA-Seq. Results Differential gene expression revealed common and distinct responses to the mercurials throughout recovery. Cultures exhibited growth stasis immediately after each mercurial exposure but returned to normal growth more quickly after PMA exposure than after HgCl2 exposure. Correspondingly, PMA rapidly elicited up-regulation of a large number of genes which continued for 30 min, whereas fewer genes were up-regulated early after HgCl2 exposure only some of which overlapped with PMA up-regulated genes. By 60 min gene expression in PMA-exposed cells was almost indistinguishable from unexposed cells, but HgCl2 exposed cells still had many differentially expressed genes. Relative expression of energy production and most metabolite uptake pathways declined with both compounds, but nearly all stress response systems were up-regulated by one or the other mercurial during recovery. Conclusions Sub-acute exposure influenced expression of ~45% of all genes with many distinct responses for each compound, reflecting differential biochemical damage by each mercurial and the corresponding resources available for repair. This study is the first global, high-resolution view of the transcriptional responses to any common toxicant in a prokaryotic model system from exposure to recovery of active growth. The responses provoked by these two mercurials in this model bacterium also provide insights about how higher organisms may respond to these ubiquitous metal toxicants. Electronic supplementary material The online version of this article (10.1186/s12864-017-4413-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen P LaVoie
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Liu D, Albergante L, Newman TJ. Universal attenuators and their interactions with feedback loops in gene regulatory networks. Nucleic Acids Res 2017; 45:7078-7093. [PMID: 28575450 PMCID: PMC5499555 DOI: 10.1093/nar/gkx485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022] Open
Abstract
Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LRCs act as attenuators. This observation implies a progressively weaker functionality of LRCs as their length increases. When analyzing the preponderance of LRCs in the GRNs of Escherichia coli K12 and several other organisms, we find that very long LRCs are essentially absent. In both E. coli and M. tuberculosis we find that four-gene LRCs are intimately linked to identical feedback loops that are involved in potentially chaotic stress response, indicating that the dynamics of these potentially destabilising motifs are strongly restrained under homeostatic conditions. The same relationship is observed in a human cancer cell line (K562), and we postulate that four-gene LRCs act as ‘universal attenuators’. These findings suggest a role for long LRCs in dampening variation in gene expression, thereby protecting cell identity, and in controlling dramatic shifts in cell-wide gene expression through inhibiting chaos-generating motifs.
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Affiliation(s)
- Dianbo Liu
- School of Life sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.,The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.,Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA
| | - Luca Albergante
- School of Life sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005 Paris, France
| | - Timothy J Newman
- School of Life sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Carneiro S, Villas-Bôas S, Ferreira EC, Rocha I. A Comparative Proteome Analysis of Escherichia coli Δ relA Mutant Cells. Front Bioeng Biotechnol 2016; 4:78. [PMID: 27833909 PMCID: PMC5081369 DOI: 10.3389/fbioe.2016.00078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/26/2016] [Indexed: 11/15/2022] Open
Abstract
The bacterial RelA-dependent stringent response exerts a strong influence over various processes. In this work, the impact of the relA gene mutation in Escherichia coli cells was evaluated by a quantitative proteomics analysis, employing stable-isotope labeling and high-resolution mass spectrometry. Chemostat cultures of E. coli W3110 and ΔrelA mutant strains were performed at two dilution rates (0.1 and 0.2 h−1) to assess the influence of the relA gene mutation in steady-state protein levels. A total of 121 proteins showed significant alterations in their abundance when comparing the proteome of mutant to wild-type cells. The relA gene mutation induced changes on key cellular processes, including the amino acids and nucleotide biosynthesis, the lipid metabolism, transport activities, transcription and translation processes, and responses to stress. Furthermore, some of those changes were more pronounced under specific growth conditions, as the most significant differences in protein ratios were observed at one of the dilution rates. An effect of the relA gene mutation in the acetate overflow was also observed, which confers interesting characteristics to this mutant strain that could be useful in the production of recombinant proteins. Overall, these results provide a valuable insight into the E. coli stringent response under defined steady-state conditions, suggesting that this stress response might influence multiple metabolic processes like the acetate overflow or the catabolite repression.
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Affiliation(s)
- Sónia Carneiro
- CEB - Centre of Biological Engineering, University of Minho , Braga , Portugal
| | - Silas Villas-Bôas
- Centre for Microbial Innovation, School of Biological Sciences, The University of Auckland , Auckland , New Zealand
| | - Eugénio C Ferreira
- CEB - Centre of Biological Engineering, University of Minho , Braga , Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho , Braga , Portugal
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Kremling A, Geiselmann J, Ropers D, de Jong H. Understanding carbon catabolite repression in Escherichia coli using quantitative models. Trends Microbiol 2014; 23:99-109. [PMID: 25475882 DOI: 10.1016/j.tim.2014.11.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/26/2014] [Accepted: 11/05/2014] [Indexed: 01/14/2023]
Abstract
Carbon catabolite repression (CCR) controls the order in which different carbon sources are metabolized. Although this system is one of the paradigms of the regulation of gene expression in bacteria, the underlying mechanisms remain controversial. CCR involves the coordination of different subsystems of the cell that are responsible for the uptake of carbon sources, their breakdown for the production of energy and precursors, and the conversion of the latter to biomass. The complexity of this integrated system, with regulatory mechanisms cutting across metabolism, gene expression, and signaling, and that are subject to global physical and physiological constraints, has motivated important modeling efforts over the past four decades, especially in the enterobacterium Escherichia coli. Different hypotheses concerning the dynamic functioning of the system have been explored by a variety of modeling approaches. We review these studies and summarize their contributions to the quantitative understanding of CCR, focusing on diauxic growth in E. coli. Moreover, we propose a highly simplified representation of diauxic growth that makes it possible to bring out the salient features of the models proposed in the literature and confront and compare the explanations they provide.
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Affiliation(s)
- A Kremling
- Fachgebiet für Systembiotechnologie, Technische Universität München, Boltzmannstrasse 15, 85748 Garching, Germany.
| | - J Geiselmann
- Laboratoire Interdisciplinaire de Physique, Université Joseph Fourier, Grenoble I, CNRS UMR 5588, 140 Avenue de la Physique, BP 87, 38402 Saint Martin d'Hères, France; Institut National de Recherche en Informatique et en Automatique (INRIA), Centre de recherche Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France
| | - D Ropers
- Institut National de Recherche en Informatique et en Automatique (INRIA), Centre de recherche Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France
| | - H de Jong
- Institut National de Recherche en Informatique et en Automatique (INRIA), Centre de recherche Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot, 38334 Saint Ismier CEDEX, France.
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Zhong R, Allen JD, Xiao G, Xie Y. Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PLoS One 2014; 9:e106319. [PMID: 25390635 PMCID: PMC4229114 DOI: 10.1371/journal.pone.0106319] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 08/01/2014] [Indexed: 11/19/2022] Open
Abstract
Reverse engineering approaches to constructing gene regulatory networks (GRNs) based on genome-wide mRNA expression data have led to significant biological findings, such as the discovery of novel drug targets. However, the reliability of the reconstructed GRNs needs to be improved. Here, we propose an ensemble-based network aggregation approach to improving the accuracy of network topologies constructed from mRNA expression data. To evaluate the performances of different approaches, we created dozens of simulated networks from combinations of gene-set sizes and sample sizes and also tested our methods on three Escherichia coli datasets. We demonstrate that the ensemble-based network aggregation approach can be used to effectively integrate GRNs constructed from different studies – producing more accurate networks. We also apply this approach to building a network from epithelial mesenchymal transition (EMT) signature microarray data and identify hub genes that might be potential drug targets. The R code used to perform all of the analyses is available in an R package entitled “ENA”, accessible on CRAN (http://cran.r-project.org/web/packages/ENA/).
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Affiliation(s)
- Rui Zhong
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jeffrey D. Allen
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Mol Syst Biol 2014; 10:740. [PMID: 25028489 PMCID: PMC4299497 DOI: 10.15252/msb.20145160] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
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Affiliation(s)
- Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | - Antoine Allard
- Département de Physique, de Génie Physique et d'Optique, Université Laval, Québec, QC, Canada
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Diego M Salvanha
- Institute for Systems Biology, Seattle, WA, USA LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil
| | | | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA Lawrence Berkeley National Laboratories, Berkeley, CA, USA
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