Maps for when the living gets tough: Maneuvering through a hostile energyCitation formats

TY - JOUR

T1 - Maps for when the living gets tough: Maneuvering through a hostile energy

AU - Mondeel, Thierry D.G.A

AU - Rehman, Samrina

AU - Zhang, Yanfei

AU - Verma, Malkhey

AU - Duerre, Peter

AU - Barberis, Matteo

AU - Westerhoff, Hans V.

PY - 2016

Y1 - 2016

N2 - With genome sequencing of thousands of organisms, a scaffold has become available for data integration: molecular information can now be organized by attaching it to the genes and their gene-expression products. It is however, the genome that is selfish not the gene, making it necessary to organize the information into maps that enable functional interpretation of the fitness of the genome. Using flux balance analysis one can calculate the theoretical capabilities of the living organism. Here we examine whether according to this genome organized information, organisms such as the ones present when life on Earth began, are able to assimilate the Gibbs energy and carbon that life needs for its reproduction and maintenance, from a relatively poor Gibbs-energy environment. We shall address how Clostridium ljungdahlii may use at least two special features and one special pathway to this end: gear-shifting, electron bifurcation and the Wood-Ljungdahl pathway. Additionally, we examined whether the C. ljungdahlii map can also help solve the problem of waste management. We find that there is a definite effect of the choices of redox equivalents in the Wood-Ljungdahl pathway and the hydrogenase on the yield of interesting products like hydroxybutyrate. We provide a drawing of a subset of the metabolic network that may be utilized to project flux distributions onto by the community in future works. Furthermore, we make all the code leading to the results discussed here publicly available for the benefit of future work.

AB - With genome sequencing of thousands of organisms, a scaffold has become available for data integration: molecular information can now be organized by attaching it to the genes and their gene-expression products. It is however, the genome that is selfish not the gene, making it necessary to organize the information into maps that enable functional interpretation of the fitness of the genome. Using flux balance analysis one can calculate the theoretical capabilities of the living organism. Here we examine whether according to this genome organized information, organisms such as the ones present when life on Earth began, are able to assimilate the Gibbs energy and carbon that life needs for its reproduction and maintenance, from a relatively poor Gibbs-energy environment. We shall address how Clostridium ljungdahlii may use at least two special features and one special pathway to this end: gear-shifting, electron bifurcation and the Wood-Ljungdahl pathway. Additionally, we examined whether the C. ljungdahlii map can also help solve the problem of waste management. We find that there is a definite effect of the choices of redox equivalents in the Wood-Ljungdahl pathway and the hydrogenase on the yield of interesting products like hydroxybutyrate. We provide a drawing of a subset of the metabolic network that may be utilized to project flux distributions onto by the community in future works. Furthermore, we make all the code leading to the results discussed here publicly available for the benefit of future work.

KW - Wood-Ljungdahl pathway

KW - Clostridium ljungdahlii

KW - genome-wide metabolic map

KW - flux balance analysis

KW - electron bifurcation

KW - gear-shifting

KW - syngas

KW - biodegradable plastics

U2 - 10.1016/j.iflacol.2017.03.002

DO - 10.1016/j.iflacol.2017.03.002

M3 - Article

VL - 49

SP - 364

EP - 370

JO - IFAC-PapersOnLine

JF - IFAC-PapersOnLine

SN - 2405-8963

IS - 26

ER -