Dataset Information

Predictive evolution of metabolic phenotypes using model-designed environments.

ABSTRACT: Adaptive evolution under controlled laboratory conditions has been highly effective in selecting organisms with beneficial phenotypes such as stress tolerance. The evolution route is particularly attractive when the organisms are either difficult to engineer or the genetic basis of the phenotype is complex. However, many desired traits, like metabolite secretion, have been inaccessible to adaptive selection due to their trade-off with cell growth. Here, we utilize genome-scale metabolic models to design nutrient environments for selecting lineages with enhanced metabolite secretion. To overcome the growth-secretion trade-off, we identify environments wherein growth becomes correlated with a secondary trait termed tacking trait. The latter is selected to be coupled with the desired trait in the application environment where the trait manifestation is required. Thus, adaptive evolution in the model-designed selection environment and subsequent return to the application environment is predicted to enhance the desired trait. We experimentally validate this strategy by evolving Saccharomyces cerevisiae for increased secretion of aroma compounds, and confirm the predicted flux-rerouting using genomic, transcriptomic, and proteomic analyses. Overall, model-designed selection environments open new opportunities for predictive evolution.

SUBMITTER: Jouhten P

PROVIDER: S-EPMC9536503 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Predictive evolution of metabolic phenotypes using model-designed environments.

Jouhten Paula P Konstantinidis Dimitrios D Pereira Filipa F Andrejev Sergej S Grkovska Kristina K Castillo Sandra S Ghiachi Payam P Beltran Gemma G Almaas Eivind E Mas Albert A Warringer Jonas J Gonzalez Ramon R Morales Pilar P Patil Kiran R KR

Molecular systems biology 20221001 10

Adaptive evolution under controlled laboratory conditions has been highly effective in selecting organisms with beneficial phenotypes such as stress tolerance. The evolution route is particularly attractive when the organisms are either difficult to engineer or the genetic basis of the phenotype is complex. However, many desired traits, like metabolite secretion, have been inaccessible to adaptive selection due to their trade-off with cell growth. Here, we utilize genome-scale metabolic models t ...[more]

PMID: 36201279

Similar Datasets

Project description:BackgroundOsteosarcoma (OS) is the most common primary bone tumor affecting humans and it has extreme heterogeneity. Despite modern therapy, it recurs in approximately 30-40% of patients initially diagnosed with no metastatic disease, with the long-term survival rates of patients with recurrent OS being generally 20%. Thus, early prediction of metastases in OS management plans is crucial for better-adapted treatments and survival rates. In this study, a radiomics model for metastasis risk prediction in OS was developed and evaluated using metabolic imaging phenotypes.Methods and findingsThe subjects were eighty-three patients with OS, and all were treated with surgery and chemotherapy for local control. All patients underwent a pretreatment 18F-FDG-PET scan. Forty-five features were extracted from the tumor region. The incorporation of features into multivariable models was performed using logistic regression. The multivariable modeling strategy involved cross validation in the following four steps leading to final prediction model construction: (1) feature set reduction and selection; (2) model coefficients computation through train and validation processing; and (3) prediction performance estimation. The multivariable logistic regression model was developed using two radiomics features, SUVmax and GLZLM-SZLGE. The trained and validated multivariable logistic model based on probability of endpoint (P) = 1/ (1+exp (-Z)) was Z = -1.23 + 1.53*SUVmax + 1.68*GLZLM-SZLGE with significant p-values (SUVmax: 0.0462 and GLZLM_SZLGE: 0.0154). The final multivariable logistic model achieved an area under the curve (AUC) receiver operating characteristics (ROC) curve of 0.80, a sensitivity of 0.66, and a specificity of 0.88 in cross validation.ConclusionsThe SUVmax and GLZLM-SZLGE from metabolic imaging phenotypes are independent predictors of metastasis risk assessment. They show the association between 18F-FDG-PET and metastatic colonization knowledge. The multivariable model developed using them could improve patient outcomes by allowing aggressive treatment in patients with high metastasis risk.

Dataset Information

Predictive evolution of metabolic phenotypes using model-designed environments.

Publications

Predictive evolution of metabolic phenotypes using model-designed environments.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets