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Environmental versatility promotes modularity in genome-scale metabolic networks [article]

Areejit Samal, Andreas Wagner, Olivier C. Martin
2011 arXiv   pre-print
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

Areejit Samal, Andreas Wagner, Olivier C Martin
2011 BMC Systems Biology  
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

A. Kreimer, E. Borenstein, U. Gophna, E. Ruppin
2008 Proceedings of the National Academy of Sciences of the United States of America  
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

Sarath Janga, M Madan Babu
2008 Genome Biology  
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

Joseph Loscalzo, Isaac Kohane, Albert-Laszlo Barabasi
2007 Molecular Systems Biology  
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

Xueying Xie, Jing Jin, Yongyi Mao
2011 BMC Evolutionary Biology  
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

P. M. Boyle, P. A. Silver
2009 Journal of the Royal Society Interface  
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

Marco Bardoscia, Matteo Marsili, Areejit Samal
2015 Physical Review E  
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

Jan Baumbach, Karina Brinkrolf, Lisa F Czaja, Sven Rahmann, Andreas Tauch
2006 BMC Genomics  
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

Z. N. Oltvai
2002 Science  
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

Gayathri Sambamoorthy, Himanshu Sinha, Karthik Raman
2019 Proceedings of the Royal Society of London. Biological Sciences  
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

Xiaohan Yang, June I. Medford, Kasey Markel, Patrick M. Shih, Henrique C. De Paoli, Cong T. Trinh, Alistair J. McCormick, Raphael Ployet, Steven G. Hussey, Alexander A. Myburg, Poul Erik Jensen, Md Mahmudul Hassan (+24 others)
2020 BioDesign Research  
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

Saheed Imam, Sascha Schäuble, Aaron N. Brooks, Nitin S. Baliga, Nathan D. Price
2015 Frontiers in Microbiology  
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

Ahmad S. Khalil, James J. Collins
2010 Nature reviews genetics  
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

Tie Koide, Wyming Lee Pang, Nitin S. Baliga
2009 Nature Reviews Microbiology  
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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