A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life.
Most genomes are much more complex than required for the minimum chemistry of life. Evolution has selected sophistication more than life itself. Could this also apply to bioenergetics? We first examine mechanisms through which bioenergetics could deliver sophistication. We illustrate possible benefits of the turbo-charging of catabolic pathways, of loose coupling, low-gear catabolism, automatic transmission in energy coupling, and of homeostasis. Mechanisms for such phenomena may reside at the level of individual proton pumps, or consist of rerouting of electrons over parallel pathways. The mechanisms may be confined to preexisting components, or involve the plasticity of gene expression that is so characteristic of most living organisms. These possible benefits lead us to the conjecture that also bioenergetics has evolved more for sophistication than for necessity. We next discuss a hitherto unresolved enigma, i.e. that bioenergetics does not seem to be critical for the physiological state. To decide on how critical bioenergetics is, we quantified the control exerted by catabolism on important physiological functions such as growth rate and growth yield. We also determined whether a growth inhibition mostly affected bioenergetics (catabolism) or anabolism; if ATP increases with growth rate, then growth should be considered energy (catabolism) limited. The experimental results for Escherichia coli pinpoint the enigma: its energy metabolism (catabolism) is not critical for growth rate. These results might suggest that because it has no direct control over cell function, bioenergetics is unimportant. Paradoxically however, in biology, highly important mechanisms tend to have little control on cell function, precisely because of that importance. Sophistication in terms of homeostatic mechanisms has evolved to guarantee robustness of the most important functions: The most important mechanisms are redundant in biology. Bioenergetics may be an excellent example of this paradox, in line with the above conjecture. It may be highly important and sophisticated. We then discuss work that has begun to focus on the sophistication of bioenergetics. Homeostasis of the energetics of DNA structure in E. coli is extensive. It relies both on preexisting components and on responsive gene expression. The vastly parallel electron-transfer network of Paracoccus denitrificans engages in sophisticated dynamic and hierarchical regulation. The growth yield of the organism can depend on which terminal oxidases are active. Effective proton translocation may vary due to rerouting of electrons. We conclude that much sophistication of bioenergetics will be discovered in this era of functional genomics.
BioCentrum Amsterdam, Amsterdam, The Netherlands
Sarah
S
Koefoed
Marijke
M
Otten
Brian
B
Koebmann
Frank
F
Bruggeman
Barbara
B
Bakker
Jacky
J
Snoep
Klaas
K
Krab
Rob
R
van Spanning
Henk
H
van Verseveld
Peter
P
Jensen
Johanna
J
Koster
Hans
H
Westerhoff
D000255:Adenosine Triphosphate / Q000096:biosynthesis; D004269:DNA, Bacterial / Q000378:metabolism; D004734:Energy Metabolism; D004926:Escherichia coli; D023281:Genomics; D006019:Glycolysis; D006128:Growth; D006706:Homeostasis; D010084:Oxidation-Reduction; D013816:Thermodynamics
D004269:DNA, Bacterial; D000255:Adenosine Triphosphate