Ran Kafri

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

More Glycine, Please To better characterize metabolic properties of cancer cells, Jain et al. (p. 1040; see the Perspective by Tomita and Kami) measured systematically the concentrations of hundreds of metabolites in cell culture medium in which 60 different cancer cell lines were growing. The fastest growing cancer cells tended to consume glycine, whereas more slowly growing cells excreted some glycine. The rapidly growing cancer cells appeared to need glycine for synthesis of purine nucleotides required for continued synthesis of DNA. Interfering with glycine metabolism slowed growth of the rapidly proliferating cancer cells. Thus, an increased dependence on glycine by rapidly growing cancer cells could potentially provide a target for therapeutic intervention. Rapidly growing cancer cells rely on the amino acid glycine to make nucleotides. Metabolic reprogramming has been proposed to be a hallmark of cancer, yet a systematic characterization of the metabolic pathways active in transformed cells is currently lacking. Using mass spectrometry, we measured the consumption and release (CORE) profiles of 219 metabolites from media across the NCI-60 cancer cell lines, and integrated these data with a preexisting atlas of gene expression. This analysis identified glycine consumption and expression of the mitochondrial glycine biosynthetic pathway as strongly correlated with rates of proliferation across cancer cells. Antagonizing glycine uptake and its mitochondrial biosynthesis preferentially impaired rapidly proliferating cells. Moreover, higher expression of this pathway was associated with greater mortality in breast cancer patients. Increased reliance on glycine may represent a metabolic vulnerability for selectively targeting rapid cancer cell proliferation.

Cell Growth and Size Homeostasis in Proliferating Animal Cells

Size Matters Cells of different types come in different sizes. Size is established by a trade-off of growth and division; as a result, the distribution of cell size in a population is held stable over time. A classic question in cell physiology is whether the growth rate of cells is constant over time or whether, as cells grow bigger during the cell cycle, they grow faster and faster. Using experimental and mathematical approaches, Tzur et al. (p. 167; see the Perspective by Edgar and Kim) show that the growth rate of mouse lymphoblastoid cells in culture is slow in the G1 phase and then increases to reach a constant exponential rate. Thus, there is an active size-control mechanism that limits size variation in animal cells. Lymphoblasts grow slowly after mitosis, then reach a constant exponential rate, indicating an active size-control mechanism. A long-standing question in biology is whether there is an intrinsic mechanism for coordinating growth and the cell cycle in metazoan cells. We examined cell size distributions in populations of lymphoblasts and applied a mathematical analysis to calculate how growth rates vary with both cell size and the cell cycle. Our results show that growth rate is size-dependent throughout the cell cycle. After initial growth suppression, there is a rapid increase in growth rate during the G1 phase, followed by a period of constant exponential growth. The probability of cell division varies independently with cell size and cell age. We conclude that proliferating mammalian cells have an intrinsic mechanism that maintains cell size.

Transcription control reprogramming in genetic backup circuits

A key question in molecular genetics is why severe mutations often do not result in a detectably abnormal phenotype. This robustness was partially ascribed to redundant paralogs that may provide backup for one another in case of mutation. Mining mutant viability and mRNA expression data in Saccharomyces cerevisiae, we found that backup was provided predominantly by paralogs that are expressed dissimilarly in most growth conditions. We considered that this apparent inconsistency might be resolved by a transcriptional reprogramming mechanism that allows the intact paralog to rescue the organism upon mutation of its counterpart. We found that in wild-type cells, partial coregulation across growth conditions predicted the ability of paralogs to alter their transcription patterns and to provide backup for one another. Notably, the sets of regulatory motifs that controlled the paralogs with the most efficient backup activity deliberately overlapped only partially; paralogs with highly similar or dissimilar sets of motifs had suboptimal backup activity. Such an arrangement of partially shared regulatory motifs reconciles the differential expression of paralogs with their ability to back each other up.

Quantitative Live Cell Imaging Reveals a Gradual Shift between DNA Repair Mechanisms and a Maximal Use of HR in Mid S Phase

DNA double-strand breaks are repaired by two main pathways: nonhomologous end joining (NHEJ) and homologous recombination (HR). The choice between these pathways depends on cell-cycle phase; however the continuous effect of cell cycle on the balance between them is still unclear. We used live cell imaging and fluorescent reporters for 53BP1, Rad52, and cell cycle to quantify the relative contribution of NHEJ and HR at different points of the cell cycle in single cells. We found that NHEJ is the dominant repair pathway in G1 and G2 even when both repair pathways are functional. The shift from NHEJ to HR is gradual, with the highest proportion of breaks repaired by HR in mid S, where the amount of DNA replication is highest. Higher proportions of HR also strongly correlate with slower rates of repair. Our study shows that the choice of repair mechanism is continuously adjusted throughout the cell cycle and suggests that the extent of active replication, rather than the presence of a sister chromatid influences the balance between the two repair pathways in human cells.

Genetic Redundancy: New Tricks for Old Genes

Many crucial components of signal transduction, developmental, and metabolic pathways have functionally redundant copies. Further, these redundancies show surprising evolutionary stability over prolonged time scales. We propose that redundancies are not just archeological leftovers of ancient gene duplications, but rather that synergy arising from feedback between redundant copies may serve as an information processing element that facilitates signal transduction and the control of gene expression.

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

Biologists have long been concerned about what constrains variation in cell size, but progress in this field has been slow and stymied by experimental limitations. Here we describe a new method, ergodic rate analysis (ERA), that uses single-cell measurements of fixed steady-state populations to accurately infer the rates of molecular events, including rates of cell growth. ERA exploits the fact that the number of cells in a particular state is related to the average transit time through that state. With this method, it is possible to calculate full time trajectories of any feature that can be labelled in fixed cells, for example levels of phosphoproteins or total cellular mass. Using ERA we find evidence for a size-discriminatory process at the G1/S transition that acts to decrease cell-to-cell size variation.

On being the right (cell) size

How cells know when they are the right size Biologists have long recognized that cells exist in a large range of sizes. Cell size is also flexible: Cells can differentiate into another cell type with a very different size. External factors can also influence cell size, but the consistent size of a given cell type shows that cells have mechanisms to measure their own size and adjust their growth rate or rate of cell division to maintain uniformity. Ginzberg et al. review recent advances in understanding how cells know when they are at the right size. Science, this issue 10.1126/science.1245075 BACKGROUND How do the different cell types in our bodies maintain their distinctive and characteristic sizes? Although much is known about the signaling networks that stimulate or suppress cell growth, such as the mammalian target of rapamycin (mTOR) pathway, this central question remains: How do a common set of pathways precisely specify the appropriate size for any given cell type and physiological condition? The precision with which size is controlled is demonstrated by the uniformity in cell size typically seen in tissues. Most epithelial tissues, for example, display a striking regularity in the size and morphology of cells, whereas size heterogeneity can be a sign of neoplastic growth. Most work on the subject of how cell size is regulated has explored the control of cell growth and proliferation by extracellular signals, such as growth factors and cytokines. However, although these signals can dictate the mean size of cells, individual cells will inevitably deviate from that mean. Variability in cell size can arise from variability in growth rate and cell-cycle length or asymmetry in cell division. These sources of variation raise the question of whether they are counteracted by cellular mechanisms that act to increase size homogeneity. Size variation can only be reduced with processes that differentially affect cells of different sizes, despite the fact that they share the same environment. This kind of control requires that individual cells measure their own size and adjust their behavior as necessary to achieve a common target size. ADVANCES In this Review, we present a growing body of evidence that suggests that animal cells autonomously measure and adjust their individual sizes to maintain uniformity within a population. We discuss possible mechanisms by which this can be achieved, including the size-dependent adjustment of cell-cycle length and/or growth rate, as well as the limitations of these strategies. We summarize the progress that has been made thus far in identifying the cell’s size control machinery and highlight important unanswered questions. The presence of mechanisms ensuring precise size specification suggests that there may be an optimal cell size for a particular cell’s function. Here, we address the question of whether cells function most efficiently when at the “right” size by examining cases in which cell size was altered naturally or experimentally. Some tissues seem to easily compensate for cell-size changes, whereas in others, cells appear to perform best at their appropriate size. We highlight examples of cell types, such as pancreatic β cells and adipocytes, in which a relationship between cell size and cell function has been observed. OUTLOOK We conclude by discussing the gaps in our understanding of how cell size is regulated, stressing the questions that have been most neglected. Throughout this Review, we point out the experimental challenges that have hindered progress in this field and emphasize recent technological advances that may allow us to overcome these obstacles. Last, we pose the questions that we anticipate will guide this field in the upcoming years. How is cell size specified? (Left) In populations of proliferating cells, size uniformity may be ensured by linking the processes of growth and cell-cycle progression. One way this can be accomplished is by restricting progress through a particular cell-cycle stage (for example, the G1/S transition) to cells that have reached a specific “target” size. (Right) Typical sizes of various human cell types. Cells are drawn to scale: pancreatic β cells, hepatocytes, keratinocytes, fibroblasts, and adipocytes. ILLUSTRATION CREDIT: K. SUTLIFF/SCIENCE Different animal cell types have distinctive and characteristic sizes. How a particular cell size is specified by differentiation programs and physiology remains one of the fundamental unknowns in cell biology. In this Review, we explore the evidence that individual cells autonomously sense and specify their own size. We discuss possible mechanisms by which size-sensing and size-specification may take place. Last, we explore the physiological implications of size control: Why is it important that particular cell types maintain a particular size? We develop these questions through examination of the current literature and pose the questions that we anticipate will guide this field in the upcoming years.

Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy

The widely observed dispensability of duplicate genes is typically interpreted to suggest that a proportion of the duplicate pairs are at least partially redundant in their functions, thus allowing for compensatory affects. However, because redundancy is expected to be evolutionarily short lived, there is currently debate on both the proportion of redundant duplicates and their functional importance. Here, we examined these compensatory interactions by relying on a genome wide data analysis, followed by experiments and literature mining in yeast. Our data, thus, strongly suggest that compensated duplicates are not randomly distributed within the protein interaction network but are rather strategically allocated to the most highly connected proteins. This design is appealing because it suggests that many of the potentially vulnerable nodes that would otherwise be highly sensitive to mutations are often protected by redundancy. Furthermore, divergence analyses show that this association between redundancy and protein connectivity becomes even more significant among the ancient duplicates, suggesting that these functional overlaps have undergone purifying selection. Our results suggest an intriguing conclusion—although redundancy is typically transient on evolutionary time scales, it tends to be preserved among some of the central proteins in the cellular interaction network.

Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly’ s composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a ‘monomer world’ towards polymer-based living entities.We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a ‘scaffold’ for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer ‘take-over’ – the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.

Spontaneous chiral symmetry breaking in early molecular networks

BackgroundAn important facet of early biological evolution is the selection of chiral enantiomers for molecules such as amino acids and sugars. The origin of this symmetry breaking is a long-standing question in molecular evolution. Previous models addressing this question include particular kinetic properties such as autocatalysis or negative cross catalysis.ResultsWe propose here a more general kinetic formalism for early enantioselection, based on our previously described Graded Autocatalysis Replication Domain (GARD) model for prebiotic evolution in molecular assemblies. This model is adapted here to the case of chiral molecules by applying symmetry constraints to mutual molecular recognition within the assembly. The ensuing dynamics shows spontaneous chiral symmetry breaking, with transitions towards stationary compositional states (composomes) enriched with one of the two enantiomers for some of the constituent molecule types. Furthermore, one or the other of the two antipodal compositional states of the assembly also shows time-dependent selection.ConclusionIt follows that chiral selection may be an emergent consequence of early catalytic molecular networks rather than a prerequisite for the initiation of primeval life processes. Elaborations of this model could help explain the prevalent chiral homogeneity in present-day living cells.ReviewersThis article was reviewed by Boris Rubinstein (nominated by Arcady Mushegian), Arcady Mushegian, Meir Lahav (nominated by Yitzhak Pilpel) and Sergei Maslov.