4451
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Industrial Biotechnology: A Unique Potential for Pollution Prevention. Ind Biotechnol (New Rochelle N Y) 2017. [DOI: 10.1089/ind.2017.29088.bio] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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4452
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Lopes H, Rocha I. Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Res 2017; 17:3950252. [PMID: 28899034 PMCID: PMC5812505 DOI: 10.1093/femsyr/fox050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/21/2023] Open
Abstract
Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed.
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Affiliation(s)
- Helder Lopes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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4453
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Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. Cell Syst 2017; 5:95-104. [PMID: 28755958 DOI: 10.1016/j.cels.2017.06.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 11/22/2022]
Abstract
Bacteria and other cells show a puzzling behavior. At high growth rates, E. coli switch from respiration (which is ATP-efficient) to using fermentation for additional ATP (which is inefficient). This overflow metabolism results in a several-fold decrease in ATP produced per glucose molecule provided as food. By integrating diverse types of experimental data into a simple biophysical model, we give evidence that this onset is the result of the membrane real estate hypothesis: Fast growth drives cells to be bigger, reducing their surface-to-volume ratios. This decreases the membrane area available for respiratory proteins despite growing demand, causing increased crowding. Only when respiratory proteins reach their crowding limit does the cell activate fermentation, since fermentation allows faster ATP production per unit membrane area. Surface limitation thus creates a Pareto trade-off between membrane efficiency and ATP yield that links metabolic choice to the size and shape of a bacterial cell. By exploring the predictions that emerge from this trade-off, we show how consideration of molecular structures, energetics, rates, and equilibria can provide important insight into cellular behavior.
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4454
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Bothfeld W, Kapov G, Tyo KEJ. A Glucose-Sensing Toggle Switch for Autonomous, High Productivity Genetic Control. ACS Synth Biol 2017; 6:1296-1304. [PMID: 28274123 DOI: 10.1021/acssynbio.6b00257] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Many biosynthetic strategies are coupled to growth, which is inherently limiting, as (1) excess feedstock (e.g., sugar) may be converted to biomass, instead of product, (2) essential genes must be maintained, and (3) growth toxicity must be managed. A decoupled growth and production phase strategy could avoid these issues. We have developed a toggle switch that uses glucose sensing to enable this two-phase strategy. Temporary glucose starvation precisely and autonomously activates product pathway expression in rich or minimal media, obviating the requirement for expensive inducers. The switch remains stably in the new state even after reintroduction of glucose. In the context of polyhydroxybutyrate (PHB) biosynthesis, our system enables shorter growth phases and comparable titers to a constitutively expressing PHB strain. This two-phase production strategy, and specifically the glucose toggle switch, should be broadly useful to initiate many types of genetic program for metabolic engineering applications.
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Affiliation(s)
- William Bothfeld
- Department of Chemical
and
Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Grace Kapov
- Department of Chemical
and
Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Keith E. J. Tyo
- Department of Chemical
and
Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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4455
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Abstract
Increasing demand for plant oil for food, feed, and fuel production has led to food-fuel competition, higher plant lipid cost, and more need for agricultural land. On the other hand, the growing global production of biodiesel has increased the production of glycerol as a by-product. Efficient utilization of this by-product can reduce biodiesel production costs. We engineered Yarrowia lipolytica (Y. lipolytica) at various metabolic levels of lipid biosynthesis, degradation, and regulation for enhanced lipid and citric acid production. We used a one-step double gene knock-in and site-specific gene knock-out strategy. The resulting final strain combines the overexpression of homologous DGA1 and DGA2 in a POX-deleted background, and deletion of the SNF1 lipid regulator. This increased lipid and citric acid production in the strain under nitrogen-limiting conditions (C/N molar ratio of 60). The engineered strain constitutively accumulated lipid at a titer of more than 4.8 g/L with a lipid content of 53% of dry cell weight (DCW). The secreted citric acid reached a yield of 0.75 g/g (up to ~45 g/L) from pure glycerol in 3 days of batch fermentation using a 1-L bioreactor. This yeast cell factory was capable of simultaneous lipid accumulation and citric acid secretion. It can be used in fed-batch or continuous bioprocessing for citric acid recovery from the supernatant, along with lipid extraction from the harvested biomass.
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4456
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van der Ark KCH, van Heck RGA, Martins Dos Santos VAP, Belzer C, de Vos WM. More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes. MICROBIOME 2017; 5:78. [PMID: 28705224 PMCID: PMC5512848 DOI: 10.1186/s40168-017-0299-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 07/05/2017] [Indexed: 05/14/2023]
Abstract
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions. We provide showcase examples for the application of GEMs for gut microbes and focus on (i) the prediction of minimal, synthetic, or defined media; (ii) the prediction of possible functions and phenotypes; and (iii) the prediction of interspecies interactions. All three applications are key in understanding the role of individual species in the gut ecosystem as well as the role of the microbiota as a whole. Using GEMs in the described fashions has led to designs of minimal growth media, an increased understanding of microbial phenotypes and their influence on the host immune system, and dietary interventions to improve human health. Ultimately, an increased understanding of the gut ecosystem will enable targeted interventions in gut microbial composition to restore homeostasis and appropriate host-microbe crosstalk.
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Affiliation(s)
- Kees C H van der Ark
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruben G A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Haartmanikatu 4, 002940, Helsinki, Finland.
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4457
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4458
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Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun 2017; 8:16022. [PMID: 28699633 PMCID: PMC5510182 DOI: 10.1038/ncomms16022] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
The decreasing cost of genomic technologies has enabled the molecular characterization of large-scale clinical disease samples and of molecular changes upon drug treatment in various disease models. Exploring methods to relate diseases to potentially efficacious drugs through various molecular features is critically important in the discovery of new therapeutics. Here we show that the potency of a drug to reverse cancer-associated gene expression changes positively correlates with that drug's efficacy in preclinical models of breast, liver and colon cancers. Using a systems-based approach, we predict four compounds showing high potency to reverse gene expression in liver cancer and validate that all four compounds are effective in five liver cancer cell lines. The in vivo efficacy of pyrvinium pamoate is further confirmed in a subcutaneous xenograft model. In conclusion, this systems-based approach may be complementary to the traditional target-based approach in connecting diseases to potentially efficacious drugs.
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Affiliation(s)
- Bin Chen
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
| | - Li Ma
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Hyojung Paik
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA.,Biomedical HPC Technology Research Center, Korea Institute of Science and Technology Information, 245, Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Marina Sirota
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
| | - Wei Wei
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Mei-Sze Chua
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Samuel So
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Atul J Butte
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
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4459
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Moses T, Mehrshahi P, Smith AG, Goossens A. Synthetic biology approaches for the production of plant metabolites in unicellular organisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4057-4074. [PMID: 28449101 DOI: 10.1093/jxb/erx119] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synthetic biology is the repurposing of biological systems for novel objectives and applications. Through the co-ordinated and balanced expression of genes, both native and those introduced from other organisms, resources within an industrial chassis can be siphoned for the commercial production of high-value commodities. This developing interdisciplinary field has the potential to revolutionize natural product discovery from higher plants, by providing a diverse array of tools, technologies, and strategies for exploring the large chemically complex space of plant natural products using unicellular organisms. In this review, we emphasize the key features that influence the generation of biorefineries and highlight technologies and strategic solutions that can be used to overcome engineering pitfalls with rational design. Also presented is a succinct guide to assist the selection of unicellular chassis most suited for the engineering and subsequent production of the desired natural product, in order to meet the global demand for plant natural products in a safe and sustainable manner.
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Affiliation(s)
- Tessa Moses
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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4460
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Powers BL, Hall MC. Re-examining the role of Cdc14 phosphatase in reversal of Cdk phosphorylation during mitotic exit. J Cell Sci 2017; 130:2673-2681. [PMID: 28663385 DOI: 10.1242/jcs.201012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/26/2017] [Indexed: 01/12/2023] Open
Abstract
Inactivation of cyclin-dependent kinase (Cdk) and reversal of Cdk phosphorylation are universally required for mitotic exit. In budding yeast (Saccharomyces cerevisiae), Cdc14 is essential for both and thought to be the major Cdk-counteracting phosphatase. However, Cdc14 is not required for mitotic exit in many eukaryotes, despite highly conserved biochemical properties. The question of how similar enzymes could have such disparate influences on mitotic exit prompted us to re-examine the contribution of budding yeast Cdc14. By using an auxin-inducible degron, we show that severe Cdc14 depletion has no effect on the kinetics of mitotic exit and bulk Cdk substrate dephosphorylation, but causes a cell separation defect and is ultimately lethal. Phosphoproteomic analysis revealed that Cdc14 is highly selective for distinct Cdk sites in vivo and does not catalyze widespread Cdk substrate dephosphorylation. We conclude that additional phosphatases likely contribute substantially to Cdk substrate dephosphorylation and coordination of mitotic exit in budding yeast, similar to in other eukaryotes, and the critical mitotic exit functions of Cdc14 require trace amounts of enzyme. We propose that Cdc14 plays very specific, and often different, roles in counteracting Cdk phosphorylation in all species.
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Affiliation(s)
- Brendan L Powers
- Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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4461
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Lopes-Bastos B, Jin L, Ruge F, Owen S, Sanders A, Cogle C, Chester J, Jiang WG, Cai J. Association of breast carcinoma growth with a non-canonical axis of IFNγ/IDO1/TSP1. Oncotarget 2017; 8:85024-85039. [PMID: 29156701 PMCID: PMC5689591 DOI: 10.18632/oncotarget.18781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/29/2017] [Indexed: 01/21/2023] Open
Abstract
Reciprocal interactions between cancers and the surrounding microenvironment have an important role in tumour evolution. In this study, our data suggested that through thrombospondin 1 (TSP1), tumour-associated microvessel provides a dormant niche to sustain inactive status of breast invasive ductal carcinoma (IDC) cells. TSP1 levels in the tumour stroma were negatively correlated with vascular indoleamine 2,3-dioxygenase 1 (IDO1) in IDC tissues. IDO1 is an intracellular enzyme initiating the first and rate-limited step of tryptophan breakdown. Lower stromal TSP1 levels and positive tumour vascular IDO1 staining seems to associate with poor survive of patients with IDC. IDC cells induced a significantly increase in IDO1 expression in endothelial cells (ECs). IFNγ exerts a similar effect on ECs. We hypothesized a tryptophan starvation theory that since tryptophan is essential for the synthesis of TSP1, IDO1 induce a decrease in tryptophan availability and a reduction in TSP1 synthesis in ECs, leading to overcoming the dormancy state of IDC cells and exacerbating conditions such as tumour invasion and metastasis. These findings identify a non-canonical role of IFNγ/IDO1/TSP1 axis in microvascular niche-dominated dormancy of breast invasive ductal carcinoma with a solid foundation for further investigation of therapeutic and prognostic relevance.
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Affiliation(s)
- Bruno Lopes-Bastos
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Liang Jin
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Fiona Ruge
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Sioned Owen
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Andrew Sanders
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Christopher Cogle
- School of Medicine, University of Florida, Gainesville, Florida 32610-0278, USA
| | - John Chester
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Jun Cai
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
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4462
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Abstract
What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.
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4463
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Abstract
The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y. lipolytica and identified how two opposite regulatory states both result in lipid accumulation. This study involved comparison of a strain overexpressing diacylglycerol acyltransferase (DGA1) with a control strain grown under either nitrogen or carbon limitation conditions. A strong correlation was observed between the responses on the transcript and protein levels. Combination of DGA1 overexpression with nitrogen limitation resulted in a high level of lipid accumulation accompanied by downregulation of several amino acid biosynthetic pathways, including that of leucine in particular, and these changes were further correlated with a decrease in metabolic fluxes. This downregulation was supported by the measured decrease in the level of 2-isopropylmalate, an intermediate of leucine biosynthesis. Combining the multi-omics data with putative transcription factor binding motifs uncovered a contradictory role for TORC1 in controlling lipid accumulation, likely mediated through 2-isopropylmalate and a Leu3-like transcription factor.IMPORTANCE The ubiquitous metabolism of lipids involves refined regulation, and an enriched understanding of this regulation would have wide implications. Various factors can influence lipid metabolism, including the environment and genetics. We demonstrated, using a multi-omics and multifactorial experimental setup, that multiple factors affect lipid accumulation in the yeast Yarrowia lipolytica Using integrative analysis, we identified novel interactions between nutrient restriction and genetic factors involving regulators that are highly conserved among eukaryotes. Given that lipid metabolism is involved in many diseases but is also vital to the development of microbial cell factories that can provide us with sustainable fuels and oleochemicals, we envision that our report introduces foundational work to further unravel the regulation of lipid accumulation in eukaryal cells.
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4464
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Jolly MK, Tripathi SC, Somarelli JA, Hanash SM, Levine H. Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? Mol Oncol 2017; 11:739-754. [PMID: 28548388 PMCID: PMC5496493 DOI: 10.1002/1878-0261.12084] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 05/18/2017] [Indexed: 12/17/2022] Open
Abstract
Phenotypic plasticity, the ability of cells to reversibly alter their phenotypes in response to signals, presents a significant clinical challenge to treating solid tumors. Tumor cells utilize phenotypic plasticity to evade therapies, metastasize, and colonize distant organs. As a result, phenotypic plasticity can accelerate tumor progression. A well‐studied example of phenotypic plasticity is the bidirectional conversions among epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M) phenotype(s). These conversions can alter a repertoire of cellular traits associated with multiple hallmarks of cancer, such as metabolism, immune evasion, invasion, and metastasis. To tackle the complexity and heterogeneity of these transitions, mathematical models have been developed that seek to capture the experimentally verified molecular mechanisms and act as ‘hypothesis‐generating machines’. Here, we discuss how these quantitative mathematical models have helped us explain existing experimental data, guided further experiments, and provided an improved conceptual framework for understanding how multiple intracellular and extracellular signals can drive E/M plasticity at both the single‐cell and population levels. We also discuss the implications of this plasticity in driving multiple aggressive facets of tumor progression.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
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4465
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Liang Y, Kelemen A. Computational dynamic approaches for temporal omics data with applications to systems medicine. BioData Min 2017. [PMID: 28638442 PMCID: PMC5473988 DOI: 10.1186/s13040-017-0140-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era. In this paper, we present various recently developed dynamic trajectory and causal network approaches for temporal omics data, which are extremely useful for those researchers who want to start working in this challenging research area. Moreover, applications to various biological systems, health conditions and disease status, and examples that summarize the state-of-the art performances depending on different specific mining tasks are presented. We critically discuss the merits, drawbacks and limitations of the approaches, and the associated main challenges for the years ahead. The most recent computing tools and software to analyze specific problem type, associated platform resources, and other potentials for the dynamic trajectory and interaction methods are also presented and discussed in detail.
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Affiliation(s)
- Yulan Liang
- Department of Family and Community Health, University of Maryland, Baltimore, MD 21201 USA
| | - Arpad Kelemen
- Department of Organizational Systems and Adult Health, University of Maryland, Baltimore, MD 21201 USA
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4466
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Selekman JA, Qiu J, Tran K, Stevens J, Rosso V, Simmons E, Xiao Y, Janey J. High-Throughput Automation in Chemical Process Development. Annu Rev Chem Biomol Eng 2017; 8:525-547. [DOI: 10.1146/annurev-chembioeng-060816-101411] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua A. Selekman
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jun Qiu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Kristy Tran
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jason Stevens
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Victor Rosso
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Eric Simmons
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Yi Xiao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
| | - Jacob Janey
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903;, , , , , , ,
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4467
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Gov E, Kori M, Arga KY. RNA-based ovarian cancer research from 'a gene to systems biomedicine' perspective. Syst Biol Reprod Med 2017; 63:219-238. [PMID: 28574782 DOI: 10.1080/19396368.2017.1330368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery. Whole RNA sequencing and coding and non-coding RNA expression array datasets have shed light on the mechanisms underlying disease progression and have identified mRNAs, miRNAs, and lncRNAs involved in ovarian cancer progression. In addition, the results from these analyses indicate that various signalling pathways and biological processes are associated with ovarian cancer. Here, we present a comprehensive literature review on RNA-based ovarian cancer research and highlight the benefits of integrative approaches within the systems biomedicine concept for future ovarian cancer research. We invite the ovarian cancer and systems biomedicine research fields to join forces to achieve the interdisciplinary caliber and rigor required to find real-life solutions to common, devastating, and complex diseases such as ovarian cancer. ABBREVIATIONS CAF: cancer-associated fibroblasts; COG: Cluster of Orthologous Groups; DEA: disease enrichment analysis; EOC: epithelial ovarian carcinoma; ESCC: oesophageal squamous cell carcinoma; GSI: gamma secretase inhibitor; GO: Gene Ontology; GSEA: gene set enrichment analyzes; HAS: Hungarian Academy of Sciences; lncRNAs: long non-coding RNAs; MAPK/ERK: mitogen-activated protein kinase/extracellular signal-regulated kinases; NGS: next-generation sequencing; ncRNAs: non-coding RNAs; OvC: ovarian cancer; PI3K/Akt/mTOR: phosphatidylinositol-3-kinase/protein kinase B/mammalian target of rapamycin; RT-PCR: real-time polymerase chain reaction; SNP: single nucleotide polymorphism; TF: transcription factor; TGF-β: transforming growth factor-β.
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Affiliation(s)
- Esra Gov
- a Department of Bioengineering , Marmara University , Istanbul , Turkey.,b Department of Bioengineering , Adana Science and Technology University , Adana , Turkey
| | - Medi Kori
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
| | - Kazim Yalcin Arga
- a Department of Bioengineering , Marmara University , Istanbul , Turkey
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4468
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Gibbs DL, Shmulevich I. Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PLoS Comput Biol 2017; 13:e1005591. [PMID: 28628618 PMCID: PMC5495484 DOI: 10.1371/journal.pcbi.1005591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 07/03/2017] [Accepted: 05/24/2017] [Indexed: 02/07/2023] Open
Abstract
The Influence Maximization Problem (IMP) aims to discover the set of nodes with the greatest influence on network dynamics. The problem has previously been applied in epidemiology and social network analysis. Here, we demonstrate the application to cell cycle regulatory network analysis for Saccharomyces cerevisiae. Fundamentally, gene regulation is linked to the flow of information. Therefore, our implementation of the IMP was framed as an information theoretic problem using network diffusion. Utilizing more than 26,000 regulatory edges from YeastMine, gene expression dynamics were encoded as edge weights using time lagged transfer entropy, a method for quantifying information transfer between variables. By picking a set of source nodes, a diffusion process covers a portion of the network. The size of the network cover relates to the influence of the source nodes. The set of nodes that maximizes influence is the solution to the IMP. By solving the IMP over different numbers of source nodes, an influence ranking on genes was produced. The influence ranking was compared to other metrics of network centrality. Although the top genes from each centrality ranking contained well-known cell cycle regulators, there was little agreement and no clear winner. However, it was found that influential genes tend to directly regulate or sit upstream of genes ranked by other centrality measures. The influential nodes act as critical sources of information flow, potentially having a large impact on the state of the network. Biological events that affect influential nodes and thereby affect information flow could have a strong effect on network dynamics, potentially leading to disease. Code and data can be found at: https://github.com/gibbsdavidl/miergolf.
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Affiliation(s)
- David L. Gibbs
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
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4469
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Sánchez-Pascuala A, de Lorenzo V, Nikel PI. Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol 2017; 6:793-805. [PMID: 28121421 PMCID: PMC5440799 DOI: 10.1021/acssynbio.6b00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
Embden–Meyerhof–Parnas (EMP) pathway is generally
considered to be the biochemical standard for glucose catabolism.
Alas, its native genomic organization and the control of gene expression
in Escherichia coli are both very intricate, which
limits the portability of the EMP pathway to other biotechnologically
important bacterial hosts that lack the route. In this work, the genes
encoding all the enzymes of the linear EMP route have been individually
recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals,
and synthesized de novo following a standard (GlucoBrick)
that enables their grouping in the form of functional modules at the
user’s will. After verifying their activity in several glycolytic
mutants of E. coli, the versatility of these
GlucoBricks was demonstrated in quantitative physiology tests and
biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous
hosts. Specific configurations of GlucoBricks were also adopted to
streamline the downward circulation of carbon from hexoses to pyruvate
in E. coli recombinants, thereby resulting in
a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose.
Refactoring whole metabolic blocks in the fashion described in this
work thus eases the engineering of biochemical processes where the
optimization of carbon traffic is facilitated by the operation of
the EMP pathway—which yields more ATP than other glycolytic
routes such as the Entner–Doudoroff pathway.
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Affiliation(s)
- Alberto Sánchez-Pascuala
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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4470
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Shah S, Lubeck E, Zhou W, Cai L. seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus. Neuron 2017; 94:752-758.e1. [DOI: 10.1016/j.neuron.2017.05.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/20/2017] [Accepted: 05/02/2017] [Indexed: 11/29/2022]
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4471
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Taherian Fard A, Ragan MA. Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach. Front Genet 2017; 8:48. [PMID: 28458684 PMCID: PMC5394169 DOI: 10.3389/fgene.2017.00048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/31/2017] [Indexed: 12/25/2022] Open
Abstract
Genome-wide regulatory networks enable cells to function, develop, and survive. Perturbation of these networks can lead to appearance of a disease phenotype. Inspired by Conrad Waddington's epigenetic landscape of cell development, we use a Hopfield network formalism to construct an attractor landscape model of disease progression based on protein- or gene-correlation networks of Parkinson's disease, glioma, and colorectal cancer. Attractors in this landscape correspond to normal and disease states of the cell. We introduce approaches to estimate the size and robustness of these attractors, and take a network-based approach to study their biological features such as the key genes and their functions associated with the attractors. Our results show that the attractor of cancer cells is wider than the attractor of normal cells, suggesting a heterogeneous nature of cancer. Perturbation analysis shows that robustness depends on characteristics of the input data (number of samples per time-point, and the fraction which converge to an attractor). We identify unique gene interactions at each stage, which reflect the temporal rewiring of the gene regulatory network (GRN) with disease progression. Our model of the attractor landscape, constructed from large-scale gene expression profiles of individual patients, captures snapshots of disease progression and identifies gene interactions specific to different stages, opening the way for development of stage-specific therapeutic strategies.
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Affiliation(s)
- Atefeh Taherian Fard
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
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4472
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Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin AP, Keasling JD, Martín HG. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinformatics 2017; 18:205. [PMID: 28381205 PMCID: PMC5382524 DOI: 10.1186/s12859-017-1615-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/25/2017] [Indexed: 01/25/2023] Open
Abstract
Background Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell. In addition to flux analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed. Results The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes and leveraging other -omics data for the scientific study of cellular metabolism and bioengineering purposes. Firstly, it presents a complete toolbox for simultaneously performing two different types of flux analysis that are typically disjoint: Flux Balance Analysis and 13C Metabolic Flux Analysis. Moreover, it introduces the capability to use 13C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13C Metabolic Flux Analysis (2S-13C MFA). In addition, the library includes a demonstration of a method that uses proteomics data to produce actionable insights to increase biofuel production. Finally, the use of the jQMM library is illustrated through the addition of several Jupyter notebook demonstration files that enhance reproducibility and provide the capability to be adapted to the user’s specific needs. Conclusions jQMM will facilitate the design and metabolic engineering of organisms for biofuels and other chemicals, as well as investigations of cellular metabolism and leveraging -omics data. As an open source software project, we hope it will attract additions from the community and grow with the rapidly changing field of metabolic engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1615-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Garrett W Birkel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA
| | - Amit Ghosh
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA.,School of Energy Science and Engineering, Indian Institute of Technology (IIT), Kharagpur, India
| | - Vinay S Kumar
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA
| | - Daniel Weaver
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA
| | - David Ando
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA
| | - Tyler W H Backman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA
| | - Adam P Arkin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Bioengineering, University of California, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Joint BioEnergy Institute, Emeryville, CA, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.,Department of Bioengineering, University of California, Berkeley, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, DK2970, Denmark
| | - Héctor García Martín
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Joint BioEnergy Institute, Emeryville, CA, USA. .,DOE Agile BioFoundry, Emeryville, CA, USA. .,BCAM, Basque Center for Applied Mathematics, Bilbao, Spain.
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4473
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Biomedical applications of cell- and tissue-specific metabolic network models. J Biomed Inform 2017; 68:35-49. [DOI: 10.1016/j.jbi.2017.02.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/17/2022]
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4474
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Butzin NC, Hochendoner P, Ogle CT, Mather WH. Entrainment of a Bacterial Synthetic Gene Oscillator through Proteolytic Queueing. ACS Synth Biol 2017; 6:455-462. [PMID: 27935286 DOI: 10.1021/acssynbio.6b00157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Internal chemical oscillators (chemical clocks) direct the behavior of numerous biological systems, and maintenance of a given period and phase among many such oscillators may be important for their proper function. However, both environmental variability and fundamental molecular noise can cause biochemical oscillators to lose coherence. One solution to maintaining coherence is entrainment, where an external signal provides a cue that resets the phase of the oscillators. In this work, we study the entrainment of gene networks by a queueing interaction established by competition between proteins for a common proteolytic pathway. Principles of queueing entrainment are investigated for an established synthetic oscillator in Escherichia coli. We first explore this theoretically using a standard chemical reaction network model and a map-based model, both of which suggest that queueing entrainment can be achieved through pulsatile production of an additional protein competing for a common degradation pathway with the oscillator proteins. We then use a combination of microfluidics and fluorescence microscopy to verify that pulse trains modulating the production rate of a fluorescent protein targeted to the same protease (ClpXP) as the synthetic oscillator can entrain the oscillator.
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Affiliation(s)
- Nicholas C. Butzin
- Department
of Physics, Virginia Tech, 850 West Campus Drive, Blacksburg, Virginia 24061-0435, United States
| | - Philip Hochendoner
- Department
of Physics, Virginia Tech, 850 West Campus Drive, Blacksburg, Virginia 24061-0435, United States
| | - Curtis T. Ogle
- Department
of Physics, Virginia Tech, 850 West Campus Drive, Blacksburg, Virginia 24061-0435, United States
| | - William H. Mather
- Department
of Physics, Virginia Tech, 850 West Campus Drive, Blacksburg, Virginia 24061-0435, United States
- Department
of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, Virginia 24061-0406, United States
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4475
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Yamaguchi S, Yoshino J. Adipose tissue NAD + biology in obesity and insulin resistance: From mechanism to therapy. Bioessays 2017; 39. [PMID: 28295415 DOI: 10.1002/bies.201600227] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD+ ) biosynthetic pathway, mediated by nicotinamide phosphoribosyltransferase (NAMPT), a key NAD+ biosynthetic enzyme, plays a pivotal role in controlling many biological processes, such as metabolism, circadian rhythm, inflammation, and aging. Over the past decade, NAMPT-mediated NAD+ biosynthesis, together with its key downstream mediator, namely the NAD+ -dependent protein deacetylase SIRT1, has been demonstrated to regulate glucose and lipid metabolism in a tissue-dependent manner. These discoveries have provided novel mechanistic and therapeutic insights into obesity and its metabolic complications, such as insulin resistance, an important risk factor for developing type 2 diabetes and cardiovascular disease. This review will focus on the importance of adipose tissue NAMPT-mediated NAD+ biosynthesis and SIRT1 in the pathophysiology of obesity and insulin resistance. We will also critically explore translational and clinical aspects of adipose tissue NAD+ biology.
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Affiliation(s)
- Shintaro Yamaguchi
- Center for Human Nutrition, Division of Geriatrics and Nutritional Science, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jun Yoshino
- Center for Human Nutrition, Division of Geriatrics and Nutritional Science, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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4476
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Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife 2017; 6:20487. [PMID: 28296635 PMCID: PMC5352225 DOI: 10.7554/elife.20487] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 02/06/2023] Open
Abstract
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development. DOI:http://dx.doi.org/10.7554/eLife.20487.001
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Affiliation(s)
- Sumin Jang
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Sandeep Choubey
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Leon Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Biophysics Program, Harvard University, Cambridge, United States
| | - Ling-Nan Zou
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
| | - Adele Doyle
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
| | - Ethan B Loew
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | | | - Linda Madisen
- Allen Institute for Brain Science, Seattle, United States
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Allen Institute for Brain Science, Seattle, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States
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4477
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Immethun CM, DeLorenzo DM, Focht CM, Gupta D, Johnson CB, Moon TS. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803. Biotechnol Bioeng 2017; 114:1561-1569. [PMID: 28244586 DOI: 10.1002/bit.26275] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/19/2017] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheryl M Immethun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Drew M DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Caroline M Focht
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Dinesh Gupta
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Charles B Johnson
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
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4478
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Martin AJ, Contreras-Riquelme S, Dominguez C, Perez-Acle T. LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks. PeerJ 2017; 5:e3052. [PMID: 28265516 PMCID: PMC5333545 DOI: 10.7717/peerj.3052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/31/2017] [Indexed: 11/24/2022] Open
Abstract
One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.
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Affiliation(s)
- Alberto J Martin
- Computational Biology Laboratory (DLab), Fundacion Ciencia y Vida, Santiago, Chile; Centro Interdisciplinario de Neurociencia de Valparaíso, Valparaiso, Chile
| | - Sebastián Contreras-Riquelme
- Computational Biology Laboratory (DLab), Fundacion Ciencia y Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Calixto Dominguez
- Computational Biology Laboratory (DLab), Fundacion Ciencia y Vida , Santiago , Chile
| | - Tomas Perez-Acle
- Computational Biology Laboratory (DLab), Fundacion Ciencia y Vida, Santiago, Chile; Centro Interdisciplinario de Neurociencia de Valparaíso, Valparaiso, Chile
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4479
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Seviour EG, Sehgal V, Mishra D, Rupaimoole R, Rodriguez-Aguayo C, Lopez-Berestein G, Lee JS, Sood AK, Kim MP, Mills GB, Ram PT. Targeting KRas-dependent tumour growth, circulating tumour cells and metastasis in vivo by clinically significant miR-193a-3p. Oncogene 2017; 36:1339-1350. [PMID: 27669434 PMCID: PMC5344721 DOI: 10.1038/onc.2016.308] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/16/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
KRas is mutated in a significant number of human cancers and so there is an urgent therapeutic need to target KRas signalling. To target KRas in lung cancers we used a systems approach of integrating a genome-wide miRNA screen with patient-derived phospho-proteomic signatures of the KRas downstream pathway, and identified miR-193a-3p, which directly targets KRas. Unique aspects of miR-193a-3p biology include two functionally independent target sites in the KRas 3'UTR and clinically significant correlation between miR-193a-3p and KRas expression in patients. Rescue experiments with mutated KRas 3'UTR showed very significantly that the anti-tumour effect of miR-193a-3p is via specific direct targeting of KRas and not due to other targets. Ex vivo and in vivo studies utilizing nanoliposome packaged miR-193a-3p demonstrated significant inhibition of tumour growth, circulating tumour cell viability and decreased metastasis. These studies show the broader applicability of using miR-193a-3p as a therapeutic agent to target KRas-mutant cancer.
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Affiliation(s)
- Elena G. Seviour
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX
| | - Vasudha Sehgal
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, UTMDACC, Houston, TX
- Center for RNA Interference and Non-Coding RNA, UTMDACC
| | - Ju-Seog Lee
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX
- Center for RNA Interference and Non-Coding RNA, UTMDACC
| | - Anil K. Sood
- Department of Gynecologic Oncology, UTMDACC
- Center for RNA Interference and Non-Coding RNA, UTMDACC
| | - Min P. Kim
- Methodist Hospital Research Institute, Houston, TX
| | - Gordon B. Mills
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX
| | - Prahlad T. Ram
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX
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4480
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Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V. Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. Cancer Res 2017; 77:1063-1074. [PMID: 27932399 PMCID: PMC5532541 DOI: 10.1158/0008-5472.can-16-1467] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/07/2016] [Accepted: 11/07/2016] [Indexed: 11/16/2022]
Abstract
Small cell lung cancer (SCLC) is a devastating disease due to its propensity for early invasion and refractory relapse after initial treatment response. Although these aggressive traits have been associated with phenotypic heterogeneity, our understanding of this association remains incomplete. To fill this knowledge gap, we inferred a set of 33 transcription factors (TF) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes. The topology of this SCLC TF network was derived from prior knowledge and was simulated using Boolean modeling. These simulations predicted that the network settles into attractors, or TF expression patterns, that correlate with NE or ML phenotypes, suggesting that TF network dynamics underlie the emergence of heterogeneous SCLC phenotypes. However, several cell lines and patient tumor specimens failed to correlate with either the NE or ML attractors. By flow cytometry, single cells within these cell lines simultaneously expressed surface markers of both NE and ML differentiation, confirming the existence of a "hybrid" phenotype. Upon exposure to standard-of-care cytotoxic drugs or epigenetic modifiers, NE and ML cell populations converged toward the hybrid state, suggesting possible escape from treatment. Our findings indicate that SCLC phenotypic heterogeneity can be specified dynamically by attractor states of a master regulatory TF network. Thus, SCLC heterogeneity may be best understood as states within an epigenetic landscape. Understanding phenotypic transitions within this landscape may provide insights to clinical applications. Cancer Res; 77(5); 1063-74. ©2016 AACR.
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Affiliation(s)
| | - David J Wooten
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Megan Hoeksema
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Mukesh Bansal
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrea Califano
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Lourdes Estrada
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | - Vito Quaranta
- Vanderbilt University School of Medicine, Nashville, Tennessee.
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4481
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Oguz C, Watson LT, Baumann WT, Tyson JJ. Predicting network modules of cell cycle regulators using relative protein abundance statistics. BMC SYSTEMS BIOLOGY 2017; 11:30. [PMID: 28241833 PMCID: PMC5329933 DOI: 10.1186/s12918-017-0409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/17/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studies have shown that one usually finds a set of "feasible" parameter vectors that fit the available experimental data equally well, and that these alternative vectors can make different predictions under novel experimental conditions. In this study, we characterize the feasible region of a complex model of the budding yeast cell cycle under a large set of discrete experimental constraints in order to test whether the statistical features of relative protein abundance predictions are influenced by the topology of the cell cycle regulatory network. RESULTS Using differential evolution, we generate an ensemble of feasible parameter vectors that reproduce the phenotypes (viable or inviable) of wild-type yeast cells and 110 mutant strains. We use this ensemble to predict the phenotypes of 129 mutant strains for which experimental data is not available. We identify 86 novel mutants that are predicted to be viable and then rank the cell cycle proteins in terms of their contributions to cumulative variability of relative protein abundance predictions. Proteins involved in "regulation of cell size" and "regulation of G1/S transition" contribute most to predictive variability, whereas proteins involved in "positive regulation of transcription involved in exit from mitosis," "mitotic spindle assembly checkpoint" and "negative regulation of cyclin-dependent protein kinase by cyclin degradation" contribute the least. These results suggest that the statistics of these predictions may be generating patterns specific to individual network modules (START, S/G2/M, and EXIT). To test this hypothesis, we develop random forest models for predicting the network modules of cell cycle regulators using relative abundance statistics as model inputs. Predictive performance is assessed by the areas under receiver operating characteristics curves (AUC). Our models generate an AUC range of 0.83-0.87 as opposed to randomized models with AUC values around 0.50. CONCLUSIONS By using differential evolution and random forest modeling, we show that the model prediction statistics generate distinct network module-specific patterns within the cell cycle network.
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Affiliation(s)
- Cihan Oguz
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA.
| | - Layne T Watson
- Department of Computer Science, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Mathematics, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Aerospace and Ocean Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - William T Baumann
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA
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4482
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Völler JS, Budisa N. Coupling genetic code expansion and metabolic engineering for synthetic cells. Curr Opin Biotechnol 2017; 48:1-7. [PMID: 28237511 DOI: 10.1016/j.copbio.2017.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/16/2022]
Abstract
Orthogonal protein translation with noncanonical amino acids (ncAAs) has become a standard method in biosciences. Whereas much effort is made to broaden the chemical space of ncAAs, only few attempts on their systematic low-cost in situ production are reported until now. The main aim is to engineer cells with newly designed biosynthetic pathways coupled with orthogonal aminoacyl-tRNA synthetase/tRNA pairs (o-pairs). These should provide cost-effective solutions to industrially relevant bio-production problems, such as peptide/protein production beyond the canonical set of natural molecules and to expand the arsenal of chemistries available for living cells. Therefore, coupling genetic code expansion (GCE) with metabolic engineering is the basic prerequisite to transform orthogonal translation from a standard technique in academic research to industrial biotechnology.
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Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
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4483
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Korla K, Chandra N. A Systems Perspective of Signalling Networks in Host–Pathogen Interactions. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4484
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Méndez-López LF, Davila-Velderrain J, Domínguez-Hüttinger E, Enríquez-Olguín C, Martínez-García JC, Alvarez-Buylla ER. Gene regulatory network underlying the immortalization of epithelial cells. BMC SYSTEMS BIOLOGY 2017; 11:24. [PMID: 28209158 PMCID: PMC5314717 DOI: 10.1186/s12918-017-0393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/11/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin. To this end, we first integrate published functional and well-curated molecular data of the components and interactions that have been found to be involved in such cell states and transitions into a network of 41 molecular components. We then reduce this initial network by removing simple mediators (i.e., linear pathways), and formalize the resulting regulatory core into logical rules that govern the dynamics of each of the network components as a function of the states of its regulators. RESULTS Computational dynamic analysis shows that our proposed Gene Regulatory Network model recovers exactly three attractors, each of them defined by a specific gene expression profile that corresponds to the epithelial, senescent, and mesenchymal stem-like cellular phenotypes, respectively. We show that although a mesenchymal stem-like state can be attained even under unperturbed physiological conditions, the likelihood of converging to this state is increased when pro-inflammatory conditions are simulated, providing a systems-level mechanistic explanation for the carcinogenic role of chronic inflammatory conditions observed in the clinic. We also found that the regulatory core yields an epigenetic landscape that restricts temporal patterns of progression between the steady states, such that recovered patterns resemble the time-ordered transitions observed during the spontaneous immortalization of epithelial cells, both in vivo and in vitro. CONCLUSION Our study strongly suggests that the in vitro tumorigenic transformation of epithelial cells, which strongly correlates with the patterns observed during the pathological progression of epithelial carcinogenesis in vivo, emerges from underlying regulatory networks involved in epithelial trans-differentiation during development.
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Affiliation(s)
- Luis Fernando Méndez-López
- Centro de Investigación y Desarrollo en Ciencias de la Salud (CIDICS), Universidad Autonoma de Nuevo Leon, A. P. 14-740, México, 07300 D.F México
| | | | - Elisa Domínguez-Hüttinger
- Instituto de Ecología, UNAM, Cd. Universitaria, México, 04510 D.F México
- Centro de Ciencias de la Complejidad, UNAM, Cd. Universitaria, México, 04510 D.F México
| | | | | | - Elena R. Alvarez-Buylla
- Instituto de Ecología, UNAM, Cd. Universitaria, México, 04510 D.F México
- Centro de Ciencias de la Complejidad, UNAM, Cd. Universitaria, México, 04510 D.F México
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4485
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Noronha A, Daníelsdóttir AD, Gawron P, Jóhannsson F, Jónsdóttir S, Jarlsson S, Gunnarsson JP, Brynjólfsson S, Schneider R, Thiele I, Fleming RMT. ReconMap: an interactive visualization of human metabolism. Bioinformatics 2017; 33:605-607. [PMID: 27993782 PMCID: PMC5408809 DOI: 10.1093/bioinformatics/btw667] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/22/2016] [Accepted: 10/26/2016] [Indexed: 12/22/2022] Open
Abstract
Motivation A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualize its content integrated with omics data and simulation results. Results We manually drew a comprehensive map, ReconMap 2.0, that is consistent with the content of Recon 2. We present it within a web interface that allows content query, visualization of custom datasets and submission of feedback to manual curators. Availability and Implementation ReconMap can be accessed via http://vmh.uni.lu , with network export in a Systems Biology Graphical Notation compliant format released under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. A Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension to interact with ReconMap is available via https://github.com/opencobra/cobratoolbox . Contact ronan.mt.fleming@gmail.com.
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Affiliation(s)
- Alberto Noronha
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | | | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Freyr Jóhannsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Soffía Jónsdóttir
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Sindri Jarlsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | | | | | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Ronan M T Fleming
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
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4486
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Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica. mSphere 2017; 2:mSphere00038-17. [PMID: 28217743 PMCID: PMC5311114 DOI: 10.1128/msphere.00038-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 01/31/2017] [Indexed: 11/30/2022] Open
Abstract
Nitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeast Y. lipolytica to determine how the nitrogen source regulates lipid metabolism. We show that disruption of both activators and repressors of nitrogen catabolite repression leads to increased lipid accumulation via activation of carbon catabolite repression through an as yet uncharacterized method. Fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeast Yarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism in Y. lipolytica. Deletion of the GATA transcription factor genes gzf3 and gzf2 resulted in nitrogen source-specific growth defects and greater accumulation of lipids when the cells were growing on a simple nitrogen source. Deletion of gzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion of gzf3 results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, while gzf2 is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressor mig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism. IMPORTANCE Nitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeast Y. lipolytica to determine how the nitrogen source regulates lipid metabolism. We show that disruption of both activators and repressors of nitrogen catabolite repression leads to increased lipid accumulation via activation of carbon catabolite repression through an as yet uncharacterized method.
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4487
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Mustafin ZS, Lashin SA, Matushkin YG, Gunbin KV, Afonnikov DA. Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. BMC Bioinformatics 2017; 18:1427. [PMID: 28466792 PMCID: PMC5333177 DOI: 10.1186/s12859-016-1427-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape (http://cytoscape.org/) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged ‘network evolution’ found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Results Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Conclusion Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1427-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sergey Alexandrovich Lashin
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.
| | | | | | - Dmitry Arkadievich Afonnikov
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia
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4488
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Abstract
PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users. We present an example where we used PathLinker to compute and analyze the network of interactions connecting proteins that are perturbed by the drug lovastatin.
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Affiliation(s)
- Daniel P Gil
- Department of Computer Science, Virginia Tech, Blacksburg, USA
| | - Jeffrey N Law
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, USA
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, USA.,ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, USA
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4489
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HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research. NPJ Syst Biol Appl 2017. [PMID: 28649429 PMCID: PMC5445586 DOI: 10.1038/s41540-016-0001-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The HD Physiology Project is a Japanese research consortium that aimed to develop methods and a computational platform in which physiological and pathological information can be described in high-level definitions across multiple scales of time and size. During the 5 years of this project, an appropriate software platform for multilevel functional simulation was developed and a whole-heart model including pharmacokinetics for the assessment of the proarrhythmic risk of drugs was developed. In this article, we outline the description and scientific strategy of this project and present the achievements and influence on multilevel integrative systems biology and physiome research.
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4490
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Tsigkinopoulou A, Baker SM, Breitling R. Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology. Trends Biotechnol 2017; 35:518-529. [PMID: 28094080 DOI: 10.1016/j.tibtech.2016.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/05/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
Although there is still some skepticism in the biological community regarding the value and significance of quantitative computational modeling, important steps are continually being taken to enhance its accessibility and predictive power. We view these developments as essential components of an emerging 'respectful modeling' framework which has two key aims: (i) respecting the models themselves and facilitating the reproduction and update of modeling results by other scientists, and (ii) respecting the predictions of the models and rigorously quantifying the confidence associated with the modeling results. This respectful attitude will guide the design of higher-quality models and facilitate the use of models in modern applications such as engineering and manipulating microbial metabolism by synthetic biology.
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Affiliation(s)
- Areti Tsigkinopoulou
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Syed Murtuza Baker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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4491
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Simmons A, Burrage PM, Nicolau DV, Lakhani SR, Burrage K. Environmental factors in breast cancer invasion: a mathematical modelling review. Pathology 2017; 49:172-180. [PMID: 28081961 DOI: 10.1016/j.pathol.2016.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/07/2016] [Accepted: 11/13/2016] [Indexed: 12/17/2022]
Abstract
This review presents a brief overview of breast cancer, focussing on its heterogeneity and the role of mathematical modelling and simulation in teasing apart the underlying biophysical processes. Following a brief overview of the main known pathophysiological features of ductal carcinoma, attention is paid to differential equation-based models (both deterministic and stochastic), agent-based modelling, multi-scale modelling, lattice-based models and image-driven modelling. A number of vignettes are presented where these modelling approaches have elucidated novel aspects of breast cancer dynamics, and we conclude by offering some perspectives on the role mathematical modelling can play in understanding breast cancer development, invasion and treatment therapies.
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Affiliation(s)
- Alex Simmons
- School of Mathematical Sciences, and ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Gardens Point, Brisbane, Qld, Australia
| | - Pamela M Burrage
- School of Mathematical Sciences, and ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Gardens Point, Brisbane, Qld, Australia
| | - Dan V Nicolau
- School of Mathematical Sciences, and ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Gardens Point, Brisbane, Qld, Australia; Mathematical Institute, University of Oxford, Oxford, United Kingdom; Molecular Sense Ltd, Oxford, United Kingdom
| | - Sunil R Lakhani
- The University of Queensland, Centre for Clinical Research and School of Medicine and Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Kevin Burrage
- School of Mathematical Sciences, and ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Gardens Point, Brisbane, Qld, Australia; Department of Computer Science, University of Oxford, United Kingdom.
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4492
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Clomburg JM, Crumbley AM, Gonzalez R. Industrial biomanufacturing: The future of chemical production. Science 2017; 355:355/6320/aag0804. [DOI: 10.1126/science.aag0804] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/21/2016] [Indexed: 12/18/2022]
Abstract
The current model for industrial chemical manufacturing employs large-scale megafacilities that benefit from economies of unit scale. However, this strategy faces environmental, geographical, political, and economic challenges associated with energy and manufacturing demands. We review how exploiting biological processes for manufacturing (i.e., industrial biomanufacturing) addresses these concerns while also supporting and benefiting from economies of unit number. Key to this approach is the inherent small scale and capital efficiency of bioprocesses and the ability of engineered biocatalysts to produce designer products at high carbon and energy efficiency with adjustable output, at high selectivity, and under mild process conditions. The biological conversion of single-carbon compounds represents a test bed to establish this paradigm, enabling rapid, mobile, and widespread deployment, access to remote and distributed resources, and adaptation to new and changing markets.
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4493
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Engineering glucose metabolism of Escherichia coli under nitrogen starvation. NPJ Syst Biol Appl 2017; 3:16035. [PMID: 28725483 PMCID: PMC5516864 DOI: 10.1038/npjsba.2016.35] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/07/2016] [Accepted: 10/05/2016] [Indexed: 12/02/2022] Open
Abstract
A major aspect of microbial metabolic engineering is the development of chassis hosts that have favorable global metabolic phenotypes, and can be further engineered to produce a variety of compounds. In this work, we focus on the problem of decoupling growth and production in the model bacterium Escherichia coli, and in particular on the maintenance of active metabolism during nitrogen-limited stationary phase. We find that by overexpressing the enzyme PtsI, a component of the glucose uptake system that is inhibited by α-ketoglutarate during nitrogen limitation, we are able to achieve a fourfold increase in metabolic rates. Alternative systems were also tested: chimeric PtsI proteins hypothesized to be insensitive to α-ketoglutarate did not improve metabolic rates under the conditions tested, whereas systems based on the galactose permease GalP suffered from energy stress and extreme sensitivity to expression level. Overexpression of PtsI is likely to be a useful arrow in the metabolic engineer’s quiver as productivity of engineered pathways becomes limited by central metabolic rates during stationary phase production processes.
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4494
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Vasdekis AE, Silverman AM, Stephanopoulos G. Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica. PLoS One 2017; 12:e0168889. [PMID: 28052085 PMCID: PMC5215641 DOI: 10.1371/journal.pone.0168889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/07/2016] [Indexed: 01/14/2023] Open
Abstract
Despite substantial achievements in elucidating the metabolic pathways of lipogenesis, a mechanistic representation of lipid accumulation and degradation has not been fully attained to-date. Recent evidence suggests that lipid accumulation can occur through increases of either the cytosolic copy-number of lipid droplets (LDs), or the LDs size. However, the prevailing phenotype, or how such mechanisms pertain to lipid degradation remain poorly understood. To address this shortcoming, we employed the-recently discovered-innate bioprocessing fluctuations in Yarrowia lipolytica, and performed single-cell fluctuation analysis using optical microscopy and microfluidics that generate a quasi-time invariant microenvironment. We report that lipid accumulation at early stationary phase in rich medium is substantially more likely to occur through variations in the LDs copy-number, rather than the LDs size. Critically, these mechanistics are also preserved during lipid degradation, as well as upon exposure to a protein translation inhibitor. The latter condition additionally induced a lipid accumulation phase, accompanied by the downregulation of lipid catabolism. Our results enable an in-depth mechanistic understanding of lipid biogenesis, and expand longitudinal single-cell fluctuation analyses from gene regulation to metabolism.
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Affiliation(s)
- Andreas E. Vasdekis
- Department of Physics, University of Idaho, Moscow, ID, United States of America
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
- * E-mail: (AEV); (GS)
| | - Andrew M. Silverman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail: (AEV); (GS)
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4495
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Zhao C, Isenberg JS, Popel AS. Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model. PLoS Comput Biol 2017; 13:e1005272. [PMID: 28045898 PMCID: PMC5207393 DOI: 10.1371/journal.pcbi.1005272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 01/09/2023] Open
Abstract
Hypoxia is an important physiological stress signal that drives angiogenesis, the formation of new blood vessels. Besides an increase in the production of pro-angiogenic signals such as vascular endothelial growth factor (VEGF), hypoxia also stimulates the production of anti-angiogenic signals. Thrombospondin-1 (TSP-1) is one of the anti-angiogenic factors whose synthesis is driven by hypoxia. Cellular synthesis of TSP-1 is tightly regulated by different intermediate biomolecules including proteins that interact with hypoxia-inducible factors (HIFs), transcription factors that are activated by receptor and intracellular signaling, and microRNAs which are small non-coding RNA molecules that function in post-transcriptional modification of gene expression. Here we present a computational model that describes the mechanistic interactions between intracellular biomolecules and cooperation between signaling pathways that together make up the complex network of TSP-1 regulation both at the transcriptional and post-transcriptional level. Assisted by the model, we conduct in silico experiments to compare the efficacy of different therapeutic strategies designed to modulate TSP-1 synthesis in conditions that simulate tumor and peripheral arterial disease microenvironment. We conclude that TSP-1 production in endothelial cells depends on not only the availability of certain growth factors but also the fine-tuned signaling cascades that are initiated by hypoxia.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| | - Jeffrey S. Isenberg
- Vascular Medicine Institute, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aleksander S. Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
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4496
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Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE. A molecular genetic toolbox for Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:2. [PMID: 28066508 PMCID: PMC5210315 DOI: 10.1186/s13068-016-0687-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. RESULTS We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. CONCLUSIONS These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.
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Affiliation(s)
- Erin L. Bredeweg
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Kyle R. Pomraning
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Ziyu Dai
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
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4497
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Taguchi YH. Identification of Candidate Drugs for Heart Failure Using Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Integrated Analysis of Gene Expression Between Heart Failure and DrugMatrix Datasets. INTELLIGENT COMPUTING THEORIES AND APPLICATION 2017. [DOI: 10.1007/978-3-319-63312-1_45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4498
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Rahman J, Noronha A, Thiele I, Rahman S. Leigh map: A novel computational diagnostic resource for mitochondrial disease. Ann Neurol 2017; 81:9-16. [PMID: 27977873 PMCID: PMC5347854 DOI: 10.1002/ana.24835] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Joyeeta Rahman
- Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alberto Noronha
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Shamima Rahman
- Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health and Metabolic Department, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
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4499
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Nishimura Y. [Drug discovery using transcriptome data]. Nihon Yakurigaku Zasshi 2017; 149:138. [PMID: 28260744 DOI: 10.1254/fpj.149.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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4500
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Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW. Xylose induces cellulase production in Thermoascus aurantiacus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:271. [PMID: 29167701 PMCID: PMC5688616 DOI: 10.1186/s13068-017-0965-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an important resource for renewable production of biofuels and bioproducts. Enzymes that deconstruct this biomass are critical for the viability of biomass-based biofuel production processes. Current commercial enzyme mixtures have limited thermotolerance. Thermophilic fungi may provide enzyme mixtures with greater thermal stability leading to more robust processes. Understanding the induction of biomass-deconstructing enzymes in thermophilic fungi will provide the foundation for strategies to construct hyper-production strains. RESULTS Induction of cellulases using xylan was demonstrated during cultivation of the thermophilic fungus Thermoascus aurantiacus. Simulated fed-batch conditions with xylose induced comparable levels of cellulases. These fed-batch conditions were adapted to produce enzymes in 2 and 19 L bioreactors using xylose and xylose-rich hydrolysate from dilute acid pretreatment of corn stover. Enzymes from T. aurantiacus that were produced in the xylose-fed bioreactor demonstrated comparable performance in the saccharification of deacetylated, dilute acid-pretreated corn stover when compared to a commercial enzyme mixture at 50 °C. The T. aurantiacus enzymes retained this activity at of 60 °C while the commercial enzyme mixture was largely inactivated. CONCLUSIONS Xylose induces both cellulase and xylanase production in T. aurantiacus and was used to produce enzymes at up to the 19 L bioreactor scale. The demonstration of induction by xylose-rich hydrolysate and saccharification of deacetylated, dilute acid-pretreated corn stover suggests a scenario to couple biomass pretreatment with onsite enzyme production in a biorefinery. This work further demonstrates the potential for T. aurantiacus as a thermophilic platform for cellulase development.
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Affiliation(s)
- Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Chyi-Shin Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Matthew Miller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Fabrice Masson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Qian He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Sarah Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Mona Mirshiaghi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ling Liang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Lauren M. Tom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Todd R. Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
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