Biological insight

Here I keep track of bio facts that can be of use in my in silico explorations.

Apparently, this notebook will make much less sense since it will include pieces of information that do not necessarily lead somewhere :sweat_smile:

Pseudomonas aeruginosa: May rely on glutamine synthetase and nitrate/nitrite reduction for glutamine production.

Growth-yield trade-off

Harvey et al. (2014)

They compared a syntrophic consortia to a monoculture with equivalent metabolic capability. They found that consortia biomass is always lower than a monoculture with the same metabolic dynamics.

Increasing the growth rate or substrate affinity does not explain the observed consortial advantage. Increased metabolic pathway efficiency (yield) provides the observed increase in productivity.

Metabolic strategies

Bacteria can switch from sequential to co-utilization of the available resources especially when the concentrations of those are low Okano et al. [10].

From D’Souza et al. (2014)

• the loss of essential biosynthetic genes was generally beneficial when the required metabolite was sufficiently present in the cells’ growth environment,

• the metabolite concentration an auxotroph required to attain WT growth levels differed significantly depending on the metabolite as well as the species analyzed,

• the loss of different genes from the same metabolic pathway resulted in differential fitness consequences for the corresponding mutants, and

• auxotrophs of two species that lacked the same biosynthetic gene responded very differently when exposed to the same concentrations of the required amino acid

Mycobacterium tuberculosis is a shikimate pathway specialist (22); this pathway is strongly related to aromatic amino acid biosynthesis.

Degenerate pathways

E.coli uses can produce tryptophan through the central metabolic pathway, the shikimic acid (SK) pathway, and the chorismate (CHO) pathways.