Figure 1.
Nutrients Exchanged between Plant and Bacteroid
Flow of molecules exchanged during symbiosis between plant and bacteroid. PM represents the peribacteroid membrane. The exchange of nutrients includes some amino acids whose evidence has been recently reported [6]. The presence of myo-inositol has been observed, but its source is unknown.
Figure 2.
Metabolic Pathways for Rhizobium etli
The metabolic reconstruction for R. etli includes 26 metabolic pathways involving 363 genes and 383 metabolic reactions.
Figure 3.
Experimental Validation with In Silico Gene Deletions
The effects that mutations have on symbiotic nitrogen fixation was evaluated using linear (FBA) and quadratic (MOMA) programming [35]. This table shows the predicted increases (+) or decreases (−) in the OF, nitrogenase flux, PHB flux, and glycogen synthase flux with respect to the wild-type strain. Each entry of the table contains a pair of signs representing the effects of the deleted reaction on the fluxes. The first sign is the effect predicted by FBA, the second is that obtained from MOMA. At the end of each row we report the references that give experimental support to the increase or decrease of nitrogen fixation after the corresponding gene deletion. A brief description of the experimental assessment is presented in each gene deletion. In silico prediction of the effects of the double gene deletion (PHB and glycogen) depends on the optimization method (FBA or MOMA).
Figure 4.
The phenotypic phase plane shows the dependence of symbiotic nitrogen fixation on succinate and oxygen uptake rates. Succinate and oxygen uptake rates are expressed in mmol/gDW/hr. The OF has the same units, and its magnitude is expressed by the color scale (A). Regions denoted by I, II, and III characterize qualitatively different phenotypes in the phase plane (C). The phase plane is shown in 2-D (A) and 3-D (B).