Transcript tRNA

Co-Evolution of
the Genetic Code and
Amino Acid BioSynthesis
An hypothesis from 1975
by Jeffrey Tze-Fei Wong
Anna Battenhouse
Universal Phylogenetic Tree
Translation – the Players
• large subunit: 23S rRNA,
many proteins
– peptidyl transferase reaction,
tRNA sites
small subunit: 16S rRNA,
many proteins
– messenger RNA
Translation factors
• EF-Tu, EF-G proteins, GTP
tRNA (transfer RNA)
• acceptor arm holds amino acid
• anticodon arm “reads” mRNA,
implements Genetic Code
aaRS (aminoacyl tRNA synthetase)
• “charge” tRNAs with the
appropriate amino acid
22 “coded” amino acids
Chicken or Egg?
excellent information storage,
poor catalysis
poor information storage,
excellent catalysis
adequate information storage,
adequate catalysis
Simplifying Assumptions
• Ribosome proteins serve as scaffold
• Small PTC RNA core with 2-fold symmetry
– A, P sites
• Translation factors not required
– EF-Tu, EF-G, GTP
• “Proto-genes” were RNA molecules
– copied by an RNA replicase ribozyme
• tRNA charging enzymes were ribozymes
– left imprint on modern aaRSs
Science 256 (1992)
The Pre-translation
RNA world was
metabolically complex
Diverse RNA enzymes
(ribozymes), using cofactors
and small random peptides
Benner, S.A., Ellington, A.D., Tauer, A.,
Modern metabolism as a palimpset of the RNA world
PNAS 86 (1989)
What’s Left to Explain?
What drove code evolution?
• Sterochemical interactions
– Codon assignments arose from Physical/chemical
interactions between AAs and RNA
• Error minimization
– Adjacency of codons minimizes potential damage
due to mutations/translation errors
• Expanding codons
– Not all codon triplets used at first. Usage
expanded over time to modern 64.
• Amino acid biosynthesis
– Formation/extension of AA biosynthetic pathways
Woese et al., Microbio.
Mol. Bio. Rev., 64:1
Yarus 2009 Results
• RNA can bind wide variety
of AAs specifically
– polar, charged, aromatic
– even aliphatic
• Several AA/RNA binding
sites showed anticodon
– Ile, Phe, Arg,
His, Trp, (Tyr)
– However ~80% of triplets
not found
Woese, PNAS 55 (1966)
Direct RNA Template Model
Error Minimization
Amino Acid Biosynthesis Co-Evolution
Wong, J.T.,
Trends Bio. Sci.,
Feb. 1981
Wong, J.T., PNAS 73 (1976)
BioSynthesis Co-Evo Predictions
• AA biosynthesis is essential
– phase 1 AA abundancy
– phase 2 AA non-abundancy
• Biosynthetic evolutionary trace
should still be discernable for
precursor  product pairs
– codon allocation
– “pre-translation” synthesis
• Set of encoded AAs is, in theory,
(slightly) mutable
Not all amino acids would initially be available/abundant
Cys, Met, Trp, Phe, His
 UV labile
Asn, Gln 
thermally unstable
Gly, Ala, Val, Leu Ile,
Ser, Asp, Glu,
 initially most abundant
Genetic Code by Biosynthetic Families
Wong, J.T., Coevolution theory of the genetic code at age 30, BioEssays, 27.4 (2005)
Amino Acyl tRNA Synthetases (“aaRSs”)
tRNA charging enzymes
Direct Charging
Indirect Charging
(“pre-translation” biosynthesis)
Pre-translation Biosynthesis
Wong, J.T.,
BioEssays 27.4 (2005)
Sep-tRNA  Cys-tRNA
(Sep = O-phosphoserine)
Lack of CysRS
O’Donoghue et al.,
PNAS 102:52 (2005)
Distribution of Genes for
Pre-trans biosynthesis
Glu  Gln
neither precursor nor product aaRS
precursor aaRS only
both precursor and product aaRS
Asp  Asn
Wong, J.T., Coevolution theory of the genetic code at age 30, BioEssays 27.4 (2005)
Additional Evidence
• Phylogeny of aaRS genes
– product aaRSs are often related to their
precursor aaRSs (and precursors more ancient)
• Enzyme for de novo Asn synthesis in many
archaea was once an AspRS
– pre-trans  de novo biosynthesis via aaRS paralog
• Natural and synthetic modifications to the
Genetic code exist
– pyrrolysine – 22nd amino acid
– engineered AA additions in E. coli
Roy et al., and Francklyn, C., PNAS 100:17 (2003); Doring, et al., Scienece 292:501 (2001)
• Incorporated in only a few prokaryotic proteins
– has its own tRNA, (codon UAG, normally “stop”), aaRS
• Found in only a few species
– Archaea
• 3 Methanosarcina
• Methanococcoides
– Eubacteria
• Desulfitobacterium hafniense (HGT)
• All species live off methylamine (fishy smell)
– Pyl used in monomethylamine methyltransferase enzyme
Lehninger, Principles of Biochemistry, Fifth Ed.
Synthetic Code Expansion
BioSynth Co-Evo Theory Limitations
• Long on correlations, short on mechanisms
• Does not address the important questions
surrounding tRNA
– how did it arise?
– did the anticodon arm develop independently of
the acceptor stem?
– how did aaRSs come to be?
• and the Class I/Class II aaRS division
– role of the extensive AA base modifications
• What about the co-evolution of tRNAs and
the 23S and 16S RNAs?
– and the fascinating questions around messagereading translocation
Blind men feeling an Elephant
Transfer RNA (tRNA)
wobble position
Maizels, N. et al., Biol. Bull. 196 (1999)
Class I aaRSs
Rossman fold active site
2’ –OH attachment first
interacts with minor
groove of tRNA acceptor
Class II aaRSs
Beta sheet active site
3’ –OH attachment
interacts with major
groove of tRNA
acceptor stem
Schimmel et al., in The RNA World, Third Edition, Cold Spring Harbor Laboratory Press (2006)
tRNA Identity Elements
Giege, R. et al., Nucleic Acids Res. 26 (1998)
Class I aaRS
Class II aaRS
Giege, R. et al., Nucleic Acids Res. 26 (1998)
Xue, H., Tong, K., Marck, C., Grosjean, H., Wong, J.T., Transfer RNA paralogs, Gene 310 (2003)
Universal Phylogenetic Tree
I (inosine) can pair with C,U,A
Watson/Crick A-U pair
Non-Watson/Crick G-U pair
Wobble Usage
Tong, K., Wong, J.T., Anticodon and wobble evolution, Gene 333 (2004)