RESUMEN
Carbon concentrating mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO2 around the carbon-fixing enzyme rubisco, thereby increasing CO2 assimilatory flux and reducing photorespiration. Biophysical CCMs, like the pyrenoid-based CCM of Chlamydomonas reinhardtii or carboxysome systems of cyanobacteria, are common in aquatic photosynthetic microbes, but in land plants appear only among the hornworts. To predict the likely efficiency of biophysical CCMs in C3 plants, we used spatially resolved reaction-diffusion models to predict rubisco saturation and light use efficiency. We found that the energy efficiency of adding individual CCM components to a C3 land plant is highly dependent on the permeability of lipid membranes to CO2, with values in the range reported in the literature that are higher than used in previous modeling studies resulting in low light use efficiency. Adding a complete pyrenoid-based CCM into the leaf cells of a C3 land plant was predicted to boost net CO2 fixation, but at higher energetic costs than those incurred by photorespiratory losses without a CCM. Two notable exceptions were when substomatal CO2 levels are as low as those found in land plants that already employ biochemical CCMs and when gas exchange is limited, such as with hornworts, making the use of a biophysical CCM necessary to achieve net positive CO2 fixation under atmospheric CO2 levels. This provides an explanation for the uniqueness of hornworts' CCM among land plants and evolution of pyrenoids multiple times.
RESUMEN
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827. We find that ZNF827 accumulates at stalled forks and DNA damage sites, where it activates ATR and promotes the engagement of homologous recombination-mediated DNA repair. Additionally, we demonstrate that ZNF827 depletion inhibits replication initiation and sensitizes cancer cells to the topoisomerase inhibitor topotecan, revealing ZNF827 as a therapeutic target within the DNA damage response pathway.
Asunto(s)
Proteínas Quinasas , Transducción de Señal , Proteínas Quinasas/metabolismo , Fosforilación , Proteína de Replicación A/metabolismo , Proteínas de la Ataxia Telangiectasia Mutada/metabolismo , Proteínas de Unión al ADN/metabolismo , Replicación del ADN , Daño del ADN , ADN de Cadena Simple , Reparación del ADNRESUMEN
Carbon Concentrating Mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO2 around the carbon-fixing enzyme rubisco, thereby increasing CO2 assimilatory flux and reducing photorespiration. Biophysical CCMs, like the pyrenoid-based CCM of Chlamydomonas reinhardtii or carboxysome systems of cyanobacteria, are common in aquatic photosynthetic microbes, but in land plants appear only among the hornworts. To predict the likely efficiency of biophysical CCMs in C3 plants, we used spatially resolved reaction-diffusion models to predict rubisco saturation and light use efficiency. We find that the energy efficiency of adding individual CCM components to a C3 land plant is highly dependent on the permeability of lipid membranes to CO2, with values in the range reported in the literature that are higher than used in previous modeling studies resulting in low light use efficiency. Adding a complete pyrenoid-based CCM into the leaf cells of a C3 land plant is predicted to boost net CO2 fixation, but at higher energetic costs than those incurred by photorespiratory losses without a CCM. Two notable exceptions are when substomatal CO2 levels are as low as those found in land plants that already employ biochemical CCMs and when gas exchange is limited such as with hornworts, making the use of a biophysical CCM necessary to achieve net positive CO2 fixation under atmospheric CO2 levels. This provides an explanation for the uniqueness of hornworts' CCM among land plants and evolution of pyrenoids multiple times.
RESUMEN
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ2 -test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.
Asunto(s)
Análisis de Flujos Metabólicos , Modelos Biológicos , Análisis de Flujos Metabólicos/métodos , Reproducibilidad de los Resultados , Ingeniería Metabólica/métodos , Redes y Vías Metabólicas , Isótopos de CarbonoRESUMEN
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.
Asunto(s)
Magnoliopsida , Magnoliopsida/genética , Plantas/genética , Estrés Fisiológico/genética , Hojas de la Planta/genética , Expresión Génica , Regulación de la Expresión Génica de las Plantas/genéticaRESUMEN
The modeling of rates of biochemical reactions-fluxes-in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint-based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to-date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C-metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands-on computer laboratory component of a four-day metabolic modeling workshop and participant survey results showed improvements in learners' self-assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.
Asunto(s)
Análisis de Flujos Metabólicos , Redes y Vías Metabólicas , Humanos , Análisis de Flujos Metabólicos/métodos , Cinética , Modelos BiológicosRESUMEN
MOTIVATION: The accurate prediction of complex phenotypes such as metabolic fluxes in living systems is a grand challenge for systems biology and central to efficiently identifying biotechnological interventions that can address pressing industrial needs. The application of gene expression data to improve the accuracy of metabolic flux predictions using mechanistic modeling methods such as flux balance analysis (FBA) has not been previously demonstrated in multi-tissue systems, despite their biotechnological importance. We hypothesized that a method for generating metabolic flux predictions informed by relative expression levels between tissues would improve prediction accuracy. RESULTS: Relative gene expression levels derived from multiple transcriptomic and proteomic datasets were integrated into FBA predictions of a multi-tissue, diel model of Arabidopsis thaliana's central metabolism. This integration dramatically improved the agreement of flux predictions with experimentally based flux maps from 13C metabolic flux analysis compared with a standard parsimonious FBA approach. Disagreement between FBA predictions and MFA flux maps was measured using weighted averaged percent error values, and for parsimonious FBA this was169%-180% for high light conditions and 94%-103% for low light conditions, depending on the gene expression dataset used. This fell to 10%-13% and 9%-11% upon incorporating expression data into the modeling process, which also substantially altered the predicted carbon and energy economy of the plant. AVAILABILITY AND IMPLEMENTATION: Code and data generated as part of this study are available from https://github.com/Gibberella/ArabidopsisGeneExpressionWeights.
Asunto(s)
Análisis de Flujos Metabólicos , Proteómica , Análisis de Flujos Metabólicos/métodos , Biología de Sistemas , Perfilación de la Expresión Génica , Redes y Vías Metabólicas , Transcriptoma , Modelos BiológicosRESUMEN
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction network models of metabolism operating at steady state, so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. A number of approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to decide on and/or discriminate between alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ2-test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how the adoption of robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology in particular.
RESUMEN
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.
Asunto(s)
Genes Esenciales , Shewanella , Dióxido de Carbono/metabolismo , Ribulosa-Bifosfato Carboxilasa/genética , Shewanella/genética , Shewanella/metabolismo , Eliminación de GenRESUMEN
SignificancePhotosynthesis metabolites are quickly labeled when 13CO2 is fed to leaves, but the time course of labeling reveals additional contributing processes involved in the metabolic dynamics of photosynthesis. The existence of three such processes is demonstrated, and a metabolic flux model is developed to explore and characterize them. The model is consistent with a slow return of carbon from cytosolic and vacuolar sugars into the Calvin-Benson cycle through the oxidative pentose phosphate pathway. Our results provide insight into how carbon assimilation is integrated into the metabolic network of photosynthetic cells with implications for global carbon fluxes.
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Carbono/metabolismo , Redes y Vías Metabólicas , Fotosíntesis , Azúcares/metabolismo , Ciclo del Carbono , Dióxido de Carbono/metabolismo , Citosol/metabolismo , Modelos Biológicos , Hojas de la Planta/metabolismo , Fenómenos Fisiológicos de las PlantasRESUMEN
Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism. It is active in approximately 10-15% of cancers. We present a DNA-fiber protocol, combining YOYO-1 staining of genomic DNA, telomere fluorescence in situ hybridization (FISH), and EdU labeling of nascent DNA, to measure telomere extension events in ALT cancer cells. The protocol can be used to delineate ALT-mediated telomere extension. For complete details on the use and execution of this protocol, please refer to Barroso-Gonzalez et al. (2021).
Asunto(s)
Neoplasias , Imagen Individual de Molécula , ADN/genética , Hibridación Fluorescente in Situ/métodos , Neoplasias/genética , Telómero/genética , Homeostasis del Telómero/genéticaRESUMEN
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in â¼15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT.
Asunto(s)
ADN de Neoplasias/metabolismo , Proteínas de Unión al ADN/metabolismo , Proteína 2 Homóloga a MutS/metabolismo , Neoplasias/enzimología , Ácidos Nucleicos Heterodúplex/metabolismo , Homeostasis del Telómero , Telómero/metabolismo , Línea Celular Tumoral , Reparación de la Incompatibilidad de ADN , ADN de Neoplasias/genética , Proteínas de Unión al ADN/genética , Inestabilidad Genómica , Células HeLa , Humanos , Modelos Genéticos , Proteína 2 Homóloga a MutS/genética , Neoplasias/genética , Neoplasias/patología , Conformación de Ácido Nucleico , Ácidos Nucleicos Heterodúplex/genética , RecQ Helicasas/genética , RecQ Helicasas/metabolismo , Telómero/genéticaRESUMEN
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson-Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
Asunto(s)
Cromatina/ultraestructura , Desoxirribonucleótidos/metabolismo , Lamina Tipo A/fisiología , Lámina Nuclear/patología , Progeria/genética , Homeostasis del Telómero/genética , Telómero/patología , Adulto , Animales , Células Cultivadas , Senescencia Celular/genética , Daño del ADN , Replicación del ADN , Fibroblastos , Genes Reporteros , Proteínas Fluorescentes Verdes , Código de Histonas , Humanos , Recién Nacido , Lamina Tipo A/análisis , Lamina Tipo A/deficiencia , Lamina Tipo A/genética , Lamina Tipo B/análisis , Ratones , Ratones Noqueados , Progeria/patología , Proteínas Recombinantes de Fusión/metabolismo , Piel/patologíaRESUMEN
BACKGROUND: Prostate cancer (PC) and its treatments lead to significant acute, chronic, or latent adverse effects that result in declines in patients' physical functions, quality of life and reduced sense of masculinities. Robust evidence shows that physical activity (PA) can improve many health outcomes in men with PC; however, less is known about the facilitators, preferences, and barriers to PA engagement in this population. The purpose of this scoping review is to document the nature and extent of literature related to these aspects of PA participation among men with PC. METHODS: We conducted a scoping review of PA among men with PC. Databases searched included Medline, CINAHL, Embase, Rehabilitation & Sports Medicine Source, and SportDiscus from inception to June 30, 2020. Multiple reviewers were used in all screening and data abstractions. RESULTS: The search yielded 2788 individual citations after duplicates were removed. Following title and abstract screening, 129 underwent full-text review, and 46 articles were included. Quantitative data related to our research question showed that structured group exercise was the most commonly reported facilitator/preference among men with PC, whereas treatment-related effects and lack of time are the most common barriers. In terms of qualitative data, the most prominent theme noted related to masculinities and gender-specific needs within the context of having PC. CONCLUSION: Men with PC have unique facilitators and barriers concerning PA. More work is needed from the research and clinical practice perspectives to enable this population to engage and remain in regular PA.
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Ejercicio Físico , Neoplasias de la Próstata/fisiopatología , Neoplasias de la Próstata/psicología , Calidad de Vida , Humanos , MasculinoRESUMEN
Sarcoidosis is a non-infective granulomatous disorder of unknown aetiology, with cutaneous involvement affecting up to 30% of patients. Drug-induced sarcoidosis has been reported secondary to modern melanoma therapies including immune-checkpoint inhibitors and first generation BRAF inhibitors such as vemurafenib and dabrafenib. Herein, we report a case of cutaneous micropapular sarcoidosis that first developed on immune-checkpoint inhibition with ipilimumab and nivolumab for metastatic melanoma, which was exacerbated and further complicated by pityriasis rubra pilaris-like palmar plaques upon transition to a next-generation BRAF-dimerisation inhibitor. Both the micropapular eruption and palmar plaques rapidly resolved after cessation of the novel BRAF-inhibitor and concurrent commencement of hydroxychloroquine. It is unclear how inhibition of BRAF-dimerisation results in granuloma formation, though upregulation of TH1/TH17 T-cells and impairment of T-reg cells may be responsible. Clinicians should be aware of the potential for exacerbation of sarcoidosis when transitioning from immune-checkpoint inhibitors to these novel BRAF-dimerisation inhibitors, particularly as their uptake in treating cancers increases beyond clinical trials. Further studies are required to assess whether these next-generation agents can trigger sarcoidosis de-novo, or simply exacerbate pre-existing sarcoidosis.