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Principles of Systems Biology, No. 8
Cell Systems
Cell Systems Call Principles of Systems Biology, No. 8 Advances in biological engineering headline this month’s Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. Synthetic Bacterial Lysis for Cancer Therapy
Batteries Not Included
Omar Din and Jeff Hasty Hasty, University of California, San Diego; Tal Danino, Massachusetts Institute of Technology
Giovanni Salvatore, Swiss Federal Institute of Technology; Ungyu Paik, Hanyang University; John Rogers, University of Illinois at Urbana-Champaign
Principles
Principles
Given the landscape of interactions between microbes and the human body, the use of engineered bacteria as possible therapies to address certain diseases is an emerging prospect. Here, we develop a genetic circuit to control the population dynamics of bacteria via lysis. The circuit causes bacteria to collectively lyse at a threshold density using quorum sensing machinery, allowing them to limit growth while releasing therapeutic proteins. A small group of bacteria survive and re-populate the colony to repeat the process, leading to oscillatory population dynamics where lysis events are punctuated in time. We apply this as an in vivo delivery approach on cancer, using bacteria to produce therapeutic proteins inside tumors, and then release them upon synchronized lysis. We successfully demonstrate reduced growth of grafted tumors in mice before moving to a mouse model of liver metastases. We find a survival benefit when the engineered bacteria are delivered in combination with standard chemotherapy over either therapy alone (Din et al., Nature 536, 81–85).
‘‘Electronic skin,’’ or ‘‘epidermal electronics,’’ represents an emerging class of technology with thin, soft characteristics that enable direct lamination onto the surface of the skin as a measurement interface for its rich variety of bio-signals in an accurate and unobtrusive manner. Most existing embodiments, however, require wires for power and communication with the external world. In many cases, batteries do not offer an acceptable option due to difficulties in rendering them in thin, ‘‘epidermal’’ formats. In recent work (Kim et al., Sci. Adv. 2, e1600418) we demonstrated ultra-thin, stretchable optoelectronic circuits that adhere onto the skin like a temporary tattoo and are entirely battery-free and wireless in their operation. Power and data transfer exploit resonant inductive coupling and near field communication schemes, similar to those used for wireless payments (such as Apple and Android Pay), making the devices compatible with smartphones and tablets. We demonstrated integration of multicolor and miniaturized LEDs and photodetectors that enable the monitoring of heart rate, tissue oxygenation for peripheral vascular disease assess, UV dosimetry, and four-color spectroscopic evaluation of the skin.
‘‘.bacteria. produce therapeutic proteins inside tumors, and then release them upon synchronized lysis.’’ What’s Next? We hope this approach highlights the usefulness of synthetic biology tools in the context of the microbiota and cancer immunotherapy. We plan to investigate new strategies to prolong the therapeutic lifetime of the bacteria as well as novel combinations of strains and therapeutics.
‘‘.we demonstrated ultrathin, stretchable optoelectronic circuits that adhere onto the skin like a temporary tattoo and are entirely battery-free and wireless in their operation.’’ What’s Next? Next steps consist of broadening the array of sensors based on this platform and testing the devices on hospital patients.
110 Cell Systems 3, August 24, 2016 ª 2016 Published by Elsevier Inc.
Microfluidic Stepping Stone to Therapeutics for Neuromuscular Pathologies Sebastien Uzel, Harvard University; Roger Kamm, Massachusetts Institute of Technology
Principles Engineering in vitro neuromuscular tissues is crucial to expand our understanding of the formation and function of neuromuscular junctions and to identify the mechanisms responsible for disorders such as amyotrophic lateral sclerosis (ALS) or spinal muscular atrophy (SMA). In our recent paper, we present a microfluidic device recapitulating aspects of the motor units as they are found in vivo. Specifically, our device allows for the three-dimensional and physically separated culture of motor neurons and muscle fibers (Uzel et al., Sci. Adv. published online August 3, 2016. http://dx.doi. org/10.1126/sciadv.1501429). The presence of force sensors within the culture chamber allows for quantitative measurement of the muscle contraction. In addition, optogenetic modification of the stem cells from which the motor neurons are derived provides a wellcontrolled and non-invasive way of stimulating the tissue.
‘‘.our device allows for the three-dimensional and physically separated culture of motor neurons and muscle fibers.’’ What’s Next? The immediate next step will be to demonstrate the ability for the platform to reproduce phenotypic differences between healthy and patient-derived neuromuscular tissue, the overarching goal being to use a high-throughput version of this device to identify therapeutics capable of rescuing neuromuscular junction pathologies.
Cell Systems
Cell Systems Call Inferring the Microbial Building Blocks of the Lichen Symbiosis
A Molecular Measurement Atlas for the Human Proteome
Toby Spribille, Institute of Plant Sciences, University of Graz; and John P. McCutcheon, Division of Biological Sciences, University of Montana
Ulrike Kusebauch and Robert L. Moritz, Institute for Systems Biology; Ruedi Aebersold, Institute of Molecular Systems Biology, ETH Zurich, and University of Zurich
Principles
Principles
Lichens have long been known to be a symbiosis between a fungus, usually an ascomycete, and a photosynthesizing alga and/or cyanobacterium. However, a growing list of morphologically dissimilar lichen species are formed by identical pairs of ascomycete fungi and algae. Using a metatranscriptomics approach, we recently showed that a second fungus, a basidiomycete yeast, occurs in many of the world’s most common macrolichens and correlates with previously unaccounted-for phenotype differences (Spribille et al., Science 353, 488–492). Living yeast cells range from highly abundant to sparse in the outer polysacchariderich cortex layer. The newly discovered fungus is ubiquitous and likely an integral and heretofore unknown part of the symbiosis. Our results challenge the widespread notion that the lichen body plan is solely the outcome of a single ascomycete fungus and its photosynthesizing partner.
Quantitative measurements of all human proteins, their modifications, and spatial arrangements in human cells and tissues has been a long held goal in life sciences and an essential basis to understand systems-level properties of the proteome in physiology and disease. Due to the paucity of information on the human proteome and its immense complexity, proteomic measurements have lacked comprehensiveness and accurate quantification. We developed a comprehensive proteome map of essentially all human proteins through the use of an expansive synthetic peptide library representing multiple unique peptides for each protein and some of its variants. The data are freely accessible as a resource at http://www.srmatlas.org/ (Kusebauch et al., Cell 166, 766–778). Each peptide was associated with high-resolution fragment ion spectra and additional information thus providing the information required to identify and quantify 99.7% of the 20,277 annotated proteins of the human proteome by selected reaction monitoring. In essence the resource makes any protein in the human proteome reliably and reproducibly measurable.
‘‘Using a metatranscriptomics approach, we recently showed that a second fungus, a basidiomycete yeast, occurs in many of the world’s most common macrolichens and correlates with previously unaccounted-for phenotype differences.’’ What’s Next? Lichens are self-assembling, self-replicating microbial communities and lack a structural scaffold. How a lichen achieves dorsiventrality, radial symmetry, and distinct motifs in the absence of true meristematic tissue is a mystery. We are studying the polysaccharide composition of the cortex extracellular matrix and both fungal genomes to determine the drivers of thallus architecture in the lichen symbiosis.
‘‘The Human SRMAtlas resource enables researchers to perform direct measurements of proteins of interest and provides confidence of correct identification through the availability of reference peptide fragment spectra.’’ What’s Next? The Human SRMAtlas resource enables researchers to perform direct measurements of proteins of interest and provides confidence of correct identification through the availability of reference peptide fragment spectra. For example, applying this resource of molecular assays to studies in biomarker evaluation, perturbation of the proteome through drug response, and quantification of the transcriptional/translational interplay will deliver on the promise of understanding biological systems at the proteome level.
Parallel Screening of Computationally Engineered Proteins Mark G.F. Sun, Moon-Hyeong Seo, and Philip M. Kim, Department of Computer Science and Department of Molecular Genetics, Terrence Donnelly Centre, University of Toronto
Principles The ability to engineer a protein’s interface for tight binding toward a desired target is a long-standing protein-engineering goal. While combinatorial selection approaches have been successful, they are inherently limited. First, the exponential number of possible amino acid combinations results in vast undersampling of possible protein variants even with modern techniques that screen very large libraries. Second, the random nature of conventional libraries makes it difficult to specify the binders’ properties (e.g., the interface or conformation of binding). We overcome this limitation by applying computational protein design methods to systematically identify thousands of protein variants likely to bind a target, creating the protein variants using custom microarray oligonucleotide synthesis and identifying tight binding protein variants using highthroughput in vitro and in vivo selection systems (Sun, et al., Sci. Adv. 2, e1600692). Using this approach, we identified hundreds of nanomolar binding variants while retaining full control over their biochemical properties.
‘‘We expect that the integration of design and screening will be crucial and that computational methods that take specific advantage of the subsequent screening strategy will be particularly successful.’’ What’s Next? Having established this integrated protein engineering strategy, we are now developing both new computational methods and screening systems. We expect that the integration of design and screening will be crucial and that computational methods that take specific advantage of the subsequent screening strategy will be particularly successful. Since our method can be used in principle for any target, we hope to develop protein binders to a variety of crucial cellular proteins.
Cell Systems 3, August 24, 2016 111
Cell Systems
Cell Systems Call The E. Coli Cell Cycle
How Cells Compute Logarithms
Johan Elf, Uppsala University
Noah Olsman and Lea Goentoro, California Institute of Technology
Principles Recent progress in microfluidics and image analysis has revealed that genetically identical bacteria growing under identical conditions display large variability in generation times and cell sizes. In a recent study (Wallden et al. Cell 166, 729–739), we used quantitative live-cell imaging of thousands of E. coli cells to test a mathematical model for how replication and division cycles are coupled and what causes the observed cell-to-cell variability. From a modeling perspective, the study exemplifies how it is possible to use the propagation of intrinsic fluctuation in the observed variables to identify checkpoints and determine causality in biological networks.
‘‘.the study exemplifies how it is possible to use the propagation of intrinsic fluctuation in the observed variables to identify checkpoints and determine causality in biological networks.’’ What’s Next? The model provides a framework for the E. coli cell cycle that needs to be satisfied by more detailed mechanistic models, if the relation between growth rate, DNA replication, and division should be correctly retained. As such, the model also defines the specific questions that should be answered to get a more detailed but still globally consistent understanding of the bacterial cell. These include: what makes replication initiate at a fixed volume, what causes the cell-to-cell variation in growth rate, and what makes DNA replication and septum formation slow-down in slowly growing cells?
112 Cell Systems 3, August 24, 2016
Principles Many biological sensory systems, from vision and hearing to biochemical signaling pathways, respond not to the absolute level of signal but to fold change in signal relative background, as a way to maintain sensitivity across a broad dynamic range. Fold-change detection requires the system to sense signal on a logarithmic scale. It is an ongoing search to understand the precise molecular mechanisms that encode logarithmic sensing. We show mathematically that logarithmic sensing can be encoded within a protein, through allosteric regulation (Olsman and Goentoro, PNAS 113, E4423–E4430). We present evidence from published measurements that allosteric proteins are indeed used as such. The ability to sense signal logarithmically does not depend on a specific biophysical mechanism, but rather comes from the basic property of allostery, having the ability to tune binding kinetics without directly interfering with it, which gives rise to the logarithmic dependence of the activation function.
‘‘.logarithmic sensing can be encoded within a protein, through allosteric regulation’’
Oncogenic MYC Regulates Specific Genes by Binding to Low-Affinity Promoters Francesca Lorenzin, Uwe Benary, Jana Wolf, Martin Eilers, Elmar Wolf, Max-Delbrueck-Center for Molecular Medicine and University of Wuerzburg
Principles The MYC oncoprotein is a transcription factor that, when deregulated, drives the development of many human tumors. MYC binds to thousands of genes and can generally enhance all gene expression. Surprisingly, MYC-driven tumors are characterized by relatively small sets of MYC regulated ‘‘target’’ genes that hold prognostic value. We were able to reconcile these two seemingly contradicting observations by genome-wide analyses of MYC binding and MYC-induced changes in gene expression in cells with titratable MYC levels (Lorenzin et al., eLife 5, e15161). We found that increasing MYC levels to those found in tumors did not uniformly increase MYC occupancy at all promoters. MYC binding was not altered at many promoters that are highly bound by endogenous MYC. Mathematical modeling using absolute concentration of MYC in normal and tumor cells suggested that these promoters are saturated by physiological MYC levels. In contrast, occupancy increased at genes that were weakly bound by endogenous MYC, and expression of only these target genes responded to increasing MYC levels to those found in tumors.
What’s Next? Allosteric proteins function in diverse processes such as metabolism, oxygen transport, and ubiquitination. It will be interesting to test whether the pervasive allosteric proteins, beyond their roles as enzymes or transporters, may act as quantitative logarithmic sensors, facilitating fold-change detection in broader processes than currently appreciated. Our approach illustrates the use of theoretical analysis to uncover a new systems-level function for a mechanism in biology.
‘‘.increasing MYC levels to those found in tumors did not uniformly increase MYC occupancy at all promoters’’ What’s Next? Our results suggest that physiological and oncogenic MYC levels regulate only partially overlapping sets of target genes. We propose that systematically altering MYC levels in relevant tumor models in vivo will enable the identification of new druggable targets opening up therapeutic windows to treat MYC-driven tumors.
Cell Systems
Cell Systems Call A Network Approach to Analyze Untargeted Metabolomics Leila Pirhaji, Pamela Milani, and Ernest Fraenkel, Department of Biological Engineering, Massachusetts Institute of Technology
Principles Genome-wide and proteome-wide techniques are taken for granted, but measuring global changes in small molecules remains challenging. Targeted metabolomics assays analyze only a few hundred of the tens of thousands of cellular molecules, a situation similar to the state of transcriptional studies before the microarray. While untargeted metabolomics can measure many more molecules, the detected masses are not sufficient to identify them uniquely. We developed a network-based approach to analyze untargeted metabolomics data. Acknowledging the ambiguity of assigning a detected mass to a molecule, we created a graph in which the mass is represented as a node with edges to each potentially matching molecule. We then built an interactome that links tens of thousands of small molecules and proteins through over one million interactions. Searching for subgraphs with a high density of detected metabolites identifies altered pathways and resolves ambiguous assignments. Adding proteomics data to the analysis boosts the scope of the results (Pirhaji et al., Nat. Methods, published online August 1, 2016, http://dx. doi.org/10.1038/nmeth.3940).
‘‘Searching for subgraphs with a high density of detected metabolites identifies altered pathways and resolves ambiguous assignments.’’ What’s Next? The method has great potential for precision medicine. We plan to integrate more diverse omic data, create patient-specific networks using tumor samples and iPSCs, and search for compounds and drugs that target the pathways.
Cell Systems 3, August 24, 2016 113
Cell Systems Call Principles of Systems Biology, No. 8 Advances in biological engineering headline this month’s Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. Synthetic Bacterial Lysis for Cancer Therapy
Batteries Not Included
Omar Din and Jeff Hasty Hasty, University of California, San Diego; Tal Danino, Massachusetts Institute of Technology
Giovanni Salvatore, Swiss Federal Institute of Technology; Ungyu Paik, Hanyang University; John Rogers, University of Illinois at Urbana-Champaign
Principles
Principles
Given the landscape of interactions between microbes and the human body, the use of engineered bacteria as possible therapies to address certain diseases is an emerging prospect. Here, we develop a genetic circuit to control the population dynamics of bacteria via lysis. The circuit causes bacteria to collectively lyse at a threshold density using quorum sensing machinery, allowing them to limit growth while releasing therapeutic proteins. A small group of bacteria survive and re-populate the colony to repeat the process, leading to oscillatory population dynamics where lysis events are punctuated in time. We apply this as an in vivo delivery approach on cancer, using bacteria to produce therapeutic proteins inside tumors, and then release them upon synchronized lysis. We successfully demonstrate reduced growth of grafted tumors in mice before moving to a mouse model of liver metastases. We find a survival benefit when the engineered bacteria are delivered in combination with standard chemotherapy over either therapy alone (Din et al., Nature 536, 81–85).
‘‘Electronic skin,’’ or ‘‘epidermal electronics,’’ represents an emerging class of technology with thin, soft characteristics that enable direct lamination onto the surface of the skin as a measurement interface for its rich variety of bio-signals in an accurate and unobtrusive manner. Most existing embodiments, however, require wires for power and communication with the external world. In many cases, batteries do not offer an acceptable option due to difficulties in rendering them in thin, ‘‘epidermal’’ formats. In recent work (Kim et al., Sci. Adv. 2, e1600418) we demonstrated ultra-thin, stretchable optoelectronic circuits that adhere onto the skin like a temporary tattoo and are entirely battery-free and wireless in their operation. Power and data transfer exploit resonant inductive coupling and near field communication schemes, similar to those used for wireless payments (such as Apple and Android Pay), making the devices compatible with smartphones and tablets. We demonstrated integration of multicolor and miniaturized LEDs and photodetectors that enable the monitoring of heart rate, tissue oxygenation for peripheral vascular disease assess, UV dosimetry, and four-color spectroscopic evaluation of the skin.
‘‘.bacteria. produce therapeutic proteins inside tumors, and then release them upon synchronized lysis.’’ What’s Next? We hope this approach highlights the usefulness of synthetic biology tools in the context of the microbiota and cancer immunotherapy. We plan to investigate new strategies to prolong the therapeutic lifetime of the bacteria as well as novel combinations of strains and therapeutics.
‘‘.we demonstrated ultrathin, stretchable optoelectronic circuits that adhere onto the skin like a temporary tattoo and are entirely battery-free and wireless in their operation.’’ What’s Next? Next steps consist of broadening the array of sensors based on this platform and testing the devices on hospital patients.
110 Cell Systems 3, August 24, 2016 ª 2016 Published by Elsevier Inc.
Microfluidic Stepping Stone to Therapeutics for Neuromuscular Pathologies Sebastien Uzel, Harvard University; Roger Kamm, Massachusetts Institute of Technology
Principles Engineering in vitro neuromuscular tissues is crucial to expand our understanding of the formation and function of neuromuscular junctions and to identify the mechanisms responsible for disorders such as amyotrophic lateral sclerosis (ALS) or spinal muscular atrophy (SMA). In our recent paper, we present a microfluidic device recapitulating aspects of the motor units as they are found in vivo. Specifically, our device allows for the three-dimensional and physically separated culture of motor neurons and muscle fibers (Uzel et al., Sci. Adv. published online August 3, 2016. http://dx.doi. org/10.1126/sciadv.1501429). The presence of force sensors within the culture chamber allows for quantitative measurement of the muscle contraction. In addition, optogenetic modification of the stem cells from which the motor neurons are derived provides a wellcontrolled and non-invasive way of stimulating the tissue.
‘‘.our device allows for the three-dimensional and physically separated culture of motor neurons and muscle fibers.’’ What’s Next? The immediate next step will be to demonstrate the ability for the platform to reproduce phenotypic differences between healthy and patient-derived neuromuscular tissue, the overarching goal being to use a high-throughput version of this device to identify therapeutics capable of rescuing neuromuscular junction pathologies.
Cell Systems
Cell Systems Call Inferring the Microbial Building Blocks of the Lichen Symbiosis
A Molecular Measurement Atlas for the Human Proteome
Toby Spribille, Institute of Plant Sciences, University of Graz; and John P. McCutcheon, Division of Biological Sciences, University of Montana
Ulrike Kusebauch and Robert L. Moritz, Institute for Systems Biology; Ruedi Aebersold, Institute of Molecular Systems Biology, ETH Zurich, and University of Zurich
Principles
Principles
Lichens have long been known to be a symbiosis between a fungus, usually an ascomycete, and a photosynthesizing alga and/or cyanobacterium. However, a growing list of morphologically dissimilar lichen species are formed by identical pairs of ascomycete fungi and algae. Using a metatranscriptomics approach, we recently showed that a second fungus, a basidiomycete yeast, occurs in many of the world’s most common macrolichens and correlates with previously unaccounted-for phenotype differences (Spribille et al., Science 353, 488–492). Living yeast cells range from highly abundant to sparse in the outer polysacchariderich cortex layer. The newly discovered fungus is ubiquitous and likely an integral and heretofore unknown part of the symbiosis. Our results challenge the widespread notion that the lichen body plan is solely the outcome of a single ascomycete fungus and its photosynthesizing partner.
Quantitative measurements of all human proteins, their modifications, and spatial arrangements in human cells and tissues has been a long held goal in life sciences and an essential basis to understand systems-level properties of the proteome in physiology and disease. Due to the paucity of information on the human proteome and its immense complexity, proteomic measurements have lacked comprehensiveness and accurate quantification. We developed a comprehensive proteome map of essentially all human proteins through the use of an expansive synthetic peptide library representing multiple unique peptides for each protein and some of its variants. The data are freely accessible as a resource at http://www.srmatlas.org/ (Kusebauch et al., Cell 166, 766–778). Each peptide was associated with high-resolution fragment ion spectra and additional information thus providing the information required to identify and quantify 99.7% of the 20,277 annotated proteins of the human proteome by selected reaction monitoring. In essence the resource makes any protein in the human proteome reliably and reproducibly measurable.
‘‘Using a metatranscriptomics approach, we recently showed that a second fungus, a basidiomycete yeast, occurs in many of the world’s most common macrolichens and correlates with previously unaccounted-for phenotype differences.’’ What’s Next? Lichens are self-assembling, self-replicating microbial communities and lack a structural scaffold. How a lichen achieves dorsiventrality, radial symmetry, and distinct motifs in the absence of true meristematic tissue is a mystery. We are studying the polysaccharide composition of the cortex extracellular matrix and both fungal genomes to determine the drivers of thallus architecture in the lichen symbiosis.
‘‘The Human SRMAtlas resource enables researchers to perform direct measurements of proteins of interest and provides confidence of correct identification through the availability of reference peptide fragment spectra.’’ What’s Next? The Human SRMAtlas resource enables researchers to perform direct measurements of proteins of interest and provides confidence of correct identification through the availability of reference peptide fragment spectra. For example, applying this resource of molecular assays to studies in biomarker evaluation, perturbation of the proteome through drug response, and quantification of the transcriptional/translational interplay will deliver on the promise of understanding biological systems at the proteome level.
Parallel Screening of Computationally Engineered Proteins Mark G.F. Sun, Moon-Hyeong Seo, and Philip M. Kim, Department of Computer Science and Department of Molecular Genetics, Terrence Donnelly Centre, University of Toronto
Principles The ability to engineer a protein’s interface for tight binding toward a desired target is a long-standing protein-engineering goal. While combinatorial selection approaches have been successful, they are inherently limited. First, the exponential number of possible amino acid combinations results in vast undersampling of possible protein variants even with modern techniques that screen very large libraries. Second, the random nature of conventional libraries makes it difficult to specify the binders’ properties (e.g., the interface or conformation of binding). We overcome this limitation by applying computational protein design methods to systematically identify thousands of protein variants likely to bind a target, creating the protein variants using custom microarray oligonucleotide synthesis and identifying tight binding protein variants using highthroughput in vitro and in vivo selection systems (Sun, et al., Sci. Adv. 2, e1600692). Using this approach, we identified hundreds of nanomolar binding variants while retaining full control over their biochemical properties.
‘‘We expect that the integration of design and screening will be crucial and that computational methods that take specific advantage of the subsequent screening strategy will be particularly successful.’’ What’s Next? Having established this integrated protein engineering strategy, we are now developing both new computational methods and screening systems. We expect that the integration of design and screening will be crucial and that computational methods that take specific advantage of the subsequent screening strategy will be particularly successful. Since our method can be used in principle for any target, we hope to develop protein binders to a variety of crucial cellular proteins.
Cell Systems 3, August 24, 2016 111
Cell Systems
Cell Systems Call The E. Coli Cell Cycle
How Cells Compute Logarithms
Johan Elf, Uppsala University
Noah Olsman and Lea Goentoro, California Institute of Technology
Principles Recent progress in microfluidics and image analysis has revealed that genetically identical bacteria growing under identical conditions display large variability in generation times and cell sizes. In a recent study (Wallden et al. Cell 166, 729–739), we used quantitative live-cell imaging of thousands of E. coli cells to test a mathematical model for how replication and division cycles are coupled and what causes the observed cell-to-cell variability. From a modeling perspective, the study exemplifies how it is possible to use the propagation of intrinsic fluctuation in the observed variables to identify checkpoints and determine causality in biological networks.
‘‘.the study exemplifies how it is possible to use the propagation of intrinsic fluctuation in the observed variables to identify checkpoints and determine causality in biological networks.’’ What’s Next? The model provides a framework for the E. coli cell cycle that needs to be satisfied by more detailed mechanistic models, if the relation between growth rate, DNA replication, and division should be correctly retained. As such, the model also defines the specific questions that should be answered to get a more detailed but still globally consistent understanding of the bacterial cell. These include: what makes replication initiate at a fixed volume, what causes the cell-to-cell variation in growth rate, and what makes DNA replication and septum formation slow-down in slowly growing cells?
112 Cell Systems 3, August 24, 2016
Principles Many biological sensory systems, from vision and hearing to biochemical signaling pathways, respond not to the absolute level of signal but to fold change in signal relative background, as a way to maintain sensitivity across a broad dynamic range. Fold-change detection requires the system to sense signal on a logarithmic scale. It is an ongoing search to understand the precise molecular mechanisms that encode logarithmic sensing. We show mathematically that logarithmic sensing can be encoded within a protein, through allosteric regulation (Olsman and Goentoro, PNAS 113, E4423–E4430). We present evidence from published measurements that allosteric proteins are indeed used as such. The ability to sense signal logarithmically does not depend on a specific biophysical mechanism, but rather comes from the basic property of allostery, having the ability to tune binding kinetics without directly interfering with it, which gives rise to the logarithmic dependence of the activation function.
‘‘.logarithmic sensing can be encoded within a protein, through allosteric regulation’’
Oncogenic MYC Regulates Specific Genes by Binding to Low-Affinity Promoters Francesca Lorenzin, Uwe Benary, Jana Wolf, Martin Eilers, Elmar Wolf, Max-Delbrueck-Center for Molecular Medicine and University of Wuerzburg
Principles The MYC oncoprotein is a transcription factor that, when deregulated, drives the development of many human tumors. MYC binds to thousands of genes and can generally enhance all gene expression. Surprisingly, MYC-driven tumors are characterized by relatively small sets of MYC regulated ‘‘target’’ genes that hold prognostic value. We were able to reconcile these two seemingly contradicting observations by genome-wide analyses of MYC binding and MYC-induced changes in gene expression in cells with titratable MYC levels (Lorenzin et al., eLife 5, e15161). We found that increasing MYC levels to those found in tumors did not uniformly increase MYC occupancy at all promoters. MYC binding was not altered at many promoters that are highly bound by endogenous MYC. Mathematical modeling using absolute concentration of MYC in normal and tumor cells suggested that these promoters are saturated by physiological MYC levels. In contrast, occupancy increased at genes that were weakly bound by endogenous MYC, and expression of only these target genes responded to increasing MYC levels to those found in tumors.
What’s Next? Allosteric proteins function in diverse processes such as metabolism, oxygen transport, and ubiquitination. It will be interesting to test whether the pervasive allosteric proteins, beyond their roles as enzymes or transporters, may act as quantitative logarithmic sensors, facilitating fold-change detection in broader processes than currently appreciated. Our approach illustrates the use of theoretical analysis to uncover a new systems-level function for a mechanism in biology.
‘‘.increasing MYC levels to those found in tumors did not uniformly increase MYC occupancy at all promoters’’ What’s Next? Our results suggest that physiological and oncogenic MYC levels regulate only partially overlapping sets of target genes. We propose that systematically altering MYC levels in relevant tumor models in vivo will enable the identification of new druggable targets opening up therapeutic windows to treat MYC-driven tumors.
Cell Systems
Cell Systems Call A Network Approach to Analyze Untargeted Metabolomics Leila Pirhaji, Pamela Milani, and Ernest Fraenkel, Department of Biological Engineering, Massachusetts Institute of Technology
Principles Genome-wide and proteome-wide techniques are taken for granted, but measuring global changes in small molecules remains challenging. Targeted metabolomics assays analyze only a few hundred of the tens of thousands of cellular molecules, a situation similar to the state of transcriptional studies before the microarray. While untargeted metabolomics can measure many more molecules, the detected masses are not sufficient to identify them uniquely. We developed a network-based approach to analyze untargeted metabolomics data. Acknowledging the ambiguity of assigning a detected mass to a molecule, we created a graph in which the mass is represented as a node with edges to each potentially matching molecule. We then built an interactome that links tens of thousands of small molecules and proteins through over one million interactions. Searching for subgraphs with a high density of detected metabolites identifies altered pathways and resolves ambiguous assignments. Adding proteomics data to the analysis boosts the scope of the results (Pirhaji et al., Nat. Methods, published online August 1, 2016, http://dx. doi.org/10.1038/nmeth.3940).
‘‘Searching for subgraphs with a high density of detected metabolites identifies altered pathways and resolves ambiguous assignments.’’ What’s Next? The method has great potential for precision medicine. We plan to integrate more diverse omic data, create patient-specific networks using tumor samples and iPSCs, and search for compounds and drugs that target the pathways.
Cell Systems 3, August 24, 2016 113