Published on June 3, 2008
Energ etic c in yea osts st Micha el Bar ton Unive rsity o Manc f heste r
cost of a new cell • protein • fats • nucleic acids • ...
cost selection hypothesis • cost of synthesis reﬂected in genome • evolve to minimise cost • selection prefers a bargain?
energy is currency? • ATP • NADPH
Craig and Weber his, tyr, Mol Biol Evol (1998)15:774–776 phe, trp amino acid gly, ser, biosynthetic cost cys via glycolysis and ala, lys TCA cycle leu, met, asp, val asn, thr, ile pro, glu, gln, arg
tryptophan • biosynthetically expensive • long branch • higher in glycolysis
serine • biosynthetically cheap • short branch • further into glycolysis
What price does the cell have to pay?
What price does the cell have to pay? at i s the e. g. wh ent inv estm en ergy ins? in p rote
£10 0m 42 illio goa n ls cost vs beneﬁt il lion 0 m als £8 go 16
cost decreases with predicted expression level Akashi & Gojobori PNAS (2002) 99:3695–3700
but, is there a single currency?
systems biology approach
yeast genome scale model • 750 metabolic reactions • can predict growth on different media • can predict mutant phenotypes
Duarte, Herrgård, and Palsson Genome Research (2004) 14:1298–1309 NH4 growth Glu supply distribution of demand resources
nutrient supply increasing amino acid demand
nutrient supply per s lope stee = eater cost gr increasing amino acid demand
trp arg gly glucose limited cost
trp arg gly nitrogen limited cost
cost selection • minimise cost • transcript levels • protein levels • amino acid levels
regression energetic cost atomic content expression level codon adaptation (CAI) tRNA count
regression energetic cost atomic content expression level codon adaptation (CAI) tRNA count depen dent c ost in apta tion o f cod on ad
importance cost carbon nitrogen sulphur tRNA CAI transcript level
trans latab ility importance over c mini ost misa tion cost carbon nitrogen sulphur tRNA CAI transcript level
importance cost carbon nitrogen sulphur tRNA CAI protein level
ility importance nsl atab tra ag ain cost carbon nitrogen sulphur tRNA CAI protein level
importance cost carbon nitrogen sulphur tRNA amino acid levels
transcripts 39% proteins 41% amino acids 78% variation explained (R2)
summary biosynthetic cost and genome evolution
summary biosynthetic cost and genome evolution estimate u sing systems bi ology
summary biosynthetic cost and genome evolution estimate u sing ated trends in systems bi cost rel ology ene expression g
acknowledgements • Casey Bergman • Ian Donaldson • Magnus Rattray • Raquel Linheiro • Balazs Papp • Paul Cartwright • Daniela Delneri • Steve Oliver
more information • preprint tinyurl.com/6c6xdb • website www.michaelbarton.me.uk
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