TY  - JOUR
A1  - Botero, David
A1  - Monk, Jonathan
A1  - Rodriguez Cubillos, Maria Juliana
A1  - Rodriguez Cubillos, Andres Eduardo
A1  - Restrepo, Mariana
A1  - Bernal-Galeano, Vivian
A1  - Reyes, Alejandro
A1  - Gonzalez Barrios, Andres
A1  - Palsson, Bernhard O.
A1  - Restrepo, Silvia
A1  - Bernal, Adriana
T1  - Genome-scale metabolic model of Xanthomonas phaseoli pv. manihotis
BT  - an approach to elucidate pathogenicity at the metabolic level
JF  - Frontiers in genetics
N2  - Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)(+) balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
KW  - Xanthomonas
KW  - Xpm
KW  - cassava bacterial blight
KW  - genome-scale metabolic
KW  - model
KW  - quorum sensing
Y1  - 2020
U6  - https://doi.org/10.3389/fgene.2020.00837
SN  - 1664-8021
VL  - 11
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Fernandez-Nino, Miguel
A1  - Giraldo, Daniel
A1  - Lucia Gomez-Porras, Judith
A1  - Dreyer, Ingo
A1  - Gonzalez Barrios, Andres Fernando
A1  - Arevalo-Ferro, Catalina
T1  - A synthetic multi-cellular network of coupled self-sustained oscillators
JF  - PLoS one
N2  - Engineering artificial networks from modular components is a major challenge in synthetic biology. In the past years, single units, such as switches and oscillators, were successfully constructed and implemented. The effective integration of these parts into functional artificial self-regulated networks is currently on the verge of breakthrough. Here, we describe the design of a modular higher-order synthetic genetic network assembled from two independent self-sustained synthetic units: repressilators coupled via a modified quorum-sensing circuit. The isolated communication circuit and the network of coupled oscillators were analysed in mathematical modelling and experimental approaches. We monitored clustering of cells in groups of various sizes. Within each cluster of cells, cells oscillate synchronously, whereas the theoretical modelling predicts complete synchronization of the whole cellular population to be obtained approximately after 30 days. Our data suggest that self-regulated synchronization in biological systems can occur through an intermediate, long term clustering phase. The proposed artificial multicellular network provides a system framework for exploring how a given network generates a specific behaviour.
Y1  - 2017
U6  - https://doi.org/10.1371/journal.pone.0180155
SN  - 1932-6203
VL  - 12
PB  - PLoS
CY  - San Fransisco
ER  -