Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation.

The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5, 5, 8, and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed.

Computational models in plant-pathogen interactions: the case of Phytophthora infestans.

BACKGROUND: Phytophthora infestans is a devastating oomycete pathogen of potato production worldwide. This review explores the use of computational models for studying the molecular interactions between P. infestans and one of its hosts, Solanum tuberosum. MODELING AND CONCLUSION: Deterministic logistics models have been widely used to study pathogenicity mechanisms since the early 1950s, and have focused on processes at higher biological resolution levels. In recent years, owing to the availability of high throughput biological data and computational resources, interest in stochastic modeling of plant-pathogen interactions has grown. Stochastic models better reflect the behavior of biological systems. Most modern approaches to plant pathology modeling require molecular kinetics information. Unfortunately, this information is not available for many plant pathogens, including P. infestans. Boolean formalism has compensated for the lack of kinetics; this is especially the case where comparative genomics, protein-protein interactions and differential gene expression are the most common data resources.

Hha, YbaJ, and OmpA regulate Escherichia coli K12 biofilm formation and conjugation plasmids abolish motility.

Escherichia coli Hha is an environmental-response regulator of the pathogenic hemolysin operon, and Hha and the contiguous YbaJ are both induced 30-fold in E. coli biofilms (Appl. Microbiol. Biotechnol. 64:515, 2004). Here it is shown that Hha and YbaJ regulate biofilm formation since the hha/ybaJ deletion reduces biofilm mass in microtitre plates (81% in minimal medium, 50% in complex medium) and in flow cells (1,000-fold less surface coverage in minimal medium). The addition of the derepressed conjugative plasmid R1drd19, which increases significantly biofilm formation, eliminated motility completely in wild-type E. coli K12, promoted cell aggregation 27.18 +/- 0.05-fold, and produced a flatter biofilm. Deletion of hha/ybaJ or ybaJ restored motility (this motility phenotype may be complemented by providing hha(+)/ybaJ(+) or ybaJ(+) in trans) and reduced cell aggregation to that of the wild-type strain that lacks the conjugation plasmid. This increase in motility due to deleting hha/ybaJ was found to be due to 8-fold induction of fliA transcription. In addition, deletion of ompA reduced biofilm mass by 80% in both LB medium and LB medium with glucose. Also, Hha/YbaJ promotes conjugation since there was five-fold less conjugation in the hha/ybaJ mutant. It appears that conjugation plasmids promote biofilm formation by promoting cell aggregation, and that Hha and YbaJ increase biofilm formation by increasing conjugation and by decreasing motility when a conjugative plasmid (R1drd19) is present (YbaJ plays the most important role in this regulation of motility). When hha/ybaJ are deleted, there is less conjugation, less aggregation, more motility, and less biofilm.