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Environmental versatility promotes modularity in genome-scale metabolic networks
[article]
2011
arXiv
pre-print
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We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. ...
An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. ...
support through Swiss National Science Foundation grants 315200-116814, 315200-119697, and 315230-129708, as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in ...
arXiv:1108.4951v1
fatcat:qcn74cgfv5emlcr6xywpaqykly
Environmental versatility promotes modularity in genome-scale metabolic networks
2011
BMC Systems Biology
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We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. ...
An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. ...
support through Swiss National Science Foundation grants 315200-116814, 315200-119697, and 315230-129708, as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in ...
doi:10.1186/1752-0509-5-135
pmid:21864340
pmcid:PMC3184077
fatcat:vi76aluf5rhpfej5wkbryq6lji
The evolution of modularity in bacterial metabolic networks
2008
Proceedings of the National Academy of Sciences of the United States of America
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Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. ...
Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species ...
, supporting the hypothesis that environmental variability promotes modularity. ...
doi:10.1073/pnas.0712149105
pmid:18460604
pmcid:PMC2383979
fatcat:awkppmfdyfb2jk2ubsj24gnkq4
Network-based approaches for linking metabolism with environment
2008
Genome Biology
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e en nv vi ir ro on nm me en nt t A Ab bs st tr ra ac ct t Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking ...
Genome B Bi io ol lo og gy y 2008, 9 9: :239 Minireview N Ne et tw wo or rk k--b ba as se ed d a ap pp pr ro oa ac ch he es s f fo or r l li in nk ki in ng g m me et ta ab bo ol li is sm m w wi it th h ...
[13] that variability in the natural habitat of an organism promotes modularity in its metabolic network. Kreimer et al. ...
doi:10.1186/gb-2008-9-11-239
pmid:19040774
pmcid:PMC2614483
fatcat:owyq662qcvhybn6seuzo56ijhq
Human disease classification in the postgenomic era: A complex systems approach to human pathobiology
2007
Molecular Systems Biology
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modification in protein networks (Qian et al, 2001; Bhan et al, 2002; Pastor-Satorras et al, 2003; Vazquez et al, 2003) , as well as the variable chemical versatility of the metabolic intermediates in ...
In this construct, disease can be considered the result of a modular collection of genomic, proteomic, metabolomic, and environmental networks that interact to yield the pathophenotype. ...
doi:10.1038/msb4100163
pmid:17625512
pmcid:PMC1948102
fatcat:f3acqm2rejcuzgmv5shnqvnup4
Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks
2011
BMC Evolutionary Biology
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Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. ...
Results: A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. ...
Acknowledgements Foremost, we are grateful to Tony Pawson for his advice and support, and to Tim Nott for his assistance in protein structure modeling. ...
doi:10.1186/1471-2148-11-242
pmid:21849086
pmcid:PMC3167776
fatcat:7hx4omb6ynbrpaneedrihmxk6i
Harnessing nature's toolbox: regulatory elements for synthetic biology
2009
Journal of the Royal Society Interface
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Achieving higher complexity in engineered biological organisms will require manipulating numerous systems of biological regulation: transcription; RNA interactions; protein signalling; and metabolic fluxes ...
Exploiting the natural modularity at each level of biological regulation will promote the development of standardized tools for designing biological systems. concentration or rate of those enzymes. ...
There is evidence that higher order modularity exists in metabolic networks. Metabolic networks appear to be both scale free and hierarchical (Ravasz et al. 2002) . ...
doi:10.1098/rsif.2008.0521.focus
pmid:19324675
pmcid:PMC2843961
fatcat:nhxrpowjqrh4hcjixne6dlcypq
Phenotypic constraints promote latent versatility and carbon efficiency in metabolic networks
2015
Physical Review E
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Here we study the effect of direct selective pressure for growth or viability in particular environments on two properties of metabolic networks: latent versatility to function in additional environments ...
We find that the latent versatility of sampled metabolic networks increases with the number of directly constrained environments and with the size of the networks. ...
Matias Rodrigues for sharing their database of reactions used in this study. ...
doi:10.1103/physreve.92.012809
pmid:26274227
fatcat:sdzs4uu7bbb4dcdbm2w2mgtzoi
CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks
2006
BMC Genomics
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These large-scale reconstructions can be converted into in silico models of bacterial cells that allow a systematic analysis of network behavior in response to changing environmental conditions. ...
The application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. ...
Consequently, CoryneRegNet is a versatile systems biology tool to support the large-scale analysis of transcriptional regulation of gene expression in microorganisms. ...
doi:10.1186/1471-2164-7-24
pmid:16478536
pmcid:PMC1382212
fatcat:ke6glarww5ddznroohdymih2cq
SYSTEMS BIOLOGY: Life's Complexity Pyramid
2002
Science
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Indeed, scale-free connectivity with embedded hierarchical modularity has been documented for a wide range of nonbiological networks. ...
Finally, the scale-free nature (7) of the network's large-scale organization is known to characterize all intracellular relationships documented in metabolic, protein interaction, genetic, and protein ...
doi:10.1126/science.1078563
pmid:12399572
fatcat:4wae5sqwbvbrxntlyst6sm2gam
Evolutionary design principles in metabolism
2019
Proceedings of the Royal Society of London. Biological Sciences
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In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. ...
Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. ...
The metabolic networks that are more versatile, i.e. that can grow in many different environments, have been shown to be highly modular [62] . ...
doi:10.1098/rspb.2019.0098
pmid:30836874
pmcid:PMC6458322
fatcat:uytbj6de4zavvmsdw5zpafjkyu
Plant Biosystems Design Research Roadmap 1.0
2020
BioDesign Research
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Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. ...
both quantity and quality, resulting from the rapid increase in world population and expected standards of living. ...
(b) A plant genemetabolite network; adapted from Gonçalves et al.
Figure 3 : 3 Mechanistic modeling for plant biosystem design. (a) General steps in reconstructing a genome-scale metabolic network. ...
doi:10.34133/2020/8051764
fatcat:sfdo7mm76rfrnbyvlgtirqmizi
Data-driven integration of genome-scale regulatory and metabolic network models
2015
Frontiers in Microbiology
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Citation: Imam S, Schäuble S, Brooks AN, Baliga NS and Price ND (2015) Data-driven integration of genome-scale regulatory and metabolic network models. Front. Microbiol. 6:409. ...
networks in a data-driven fashion. ...
Acknowledgments This work was funded in part by DOE-ABY (DEEE0006315) (NSB, NDP), DOE ARPA-E program (DE-AR0000426) (NDP), ...
doi:10.3389/fmicb.2015.00409
pmid:25999934
pmcid:PMC4419725
fatcat:vp3skde33rgs3asbda7vhgrqly
Synthetic biology: applications come of age
2010
Nature reviews genetics
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Meanwhile, breakthroughs in genomic research and genetic engineering (for example, recombinant DNA technology) were supplying the inventory and methods necessary to physically construct and assemble biomolecular ...
Synthetic biology, equipped with the engineering-driven approaches of modularization, rationalization and modelling, has progressed rapidly and generated an ever-increasing suite of genetic devices and ...
Furthermore, the design is transcriptionally modular in that different sets of environment-responsive promoters can be interfaced to the AND gate. ...
doi:10.1038/nrg2775
pmid:20395970
pmcid:PMC2896386
fatcat:eihjga2srrabxkzihpyvazjiba
The role of predictive modelling in rationally re-engineering biological systems
2009
Nature Reviews Microbiology
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Technologies to synthesize and transplant a complete genome into a cell have opened limitless potential to redesign organisms for complex, specialized tasks. ...
Multidisciplinary approaches in science have always resulted in new ideas, broader and deeper levels of understanding, and of course, controversies. ...
; ESI, electrospray ionization; FDA, Food and Drug Administration; GFP, green fluorescent protein; GRN, gene regulatory network; GMO, genetically modified organism; GSMR, genome-scale metabolic reconstruction ...
doi:10.1038/nrmicro2107
pmid:19252506
pmcid:PMC2734281
fatcat:bqo77xkgujhcdk4msqnubsvcie
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