Co-Evolution%20of%20the%20Genetic%20Code%20and%20Amino%20Acid%20BioSynthesis

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Co-Evolution ofthe Genetic Code andAmino Acid
BioSynthesis
An hypothesis from 1975 by Jeffrey Tze-Fei Wong

• Anna Battenhouse

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Universal Phylogenetic Tree
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Translation the Players

• Ribosome
• large subunit 23S rRNA, many proteins
• peptidyl transferase reaction,tRNA sites
• small subunit 16S rRNA, many proteins
• messenger RNA (mRNA) contacts
• 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

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Chicken or Egg?
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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

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Science 256 (1992)
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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)
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Whats Left to Explain?
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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

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PNAS 55 (1966)
7.5
9.1
Woese et al., Microbio. Mol. Bio. Rev., 641
(2000)
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(No Transcript)
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Yarus 2009 Results

• RNA can bind wide variety of AAs specifically
• polar, charged, aromatic
• even aliphatic
• Several AA/RNA binding sites showed anticodon
  enrichment
• Ile, Phe, Arg, His, Trp, (Tyr)
• However 80 of triplets not found

7.5
9.1
Woese, PNAS 55 (1966)
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Direct RNA Template Model
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Error Minimization
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Amino Acid Biosynthesis Co-Evolution
Wong, J.T., Trends Bio. Sci., Feb. 1981
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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

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Not all amino acids would initially be
available/abundant
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(No Transcript)
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Genetic Code by Biosynthetic Families
Wong, J.T., Coevolution theory of the genetic
code at age 30, BioEssays, 27.4 (2005)
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Amino Acyl tRNA Synthetases (aaRSs) tRNA
charging enzymes
Direct Charging
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Pre-translation Biosynthesis
Wong, J.T.,BioEssays 27.4 (2005)
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Distribution of Genes forPre-trans biosynthesis
Glu ? Gln
Asp ? Asn
Wong, J.T., Coevolution theory of the genetic
code at age 30, BioEssays 27.4 (2005)
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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 10017
(2003) Doring, et al., Scienece 292501 (2001)
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Pyrrolysine

• 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.
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Synthetic Code Expansion
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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
  message-reading translocation

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Blind men feeling an Elephant
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Transfer RNA (tRNA)
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Class I aaRSs
Class II aaRSs

• Beta sheet active site
• 3 OH attachment
• interacts with major groove of tRNA acceptor stem

• Rossman fold active site
• 2 OH attachment first
• interacts with minor groove of tRNA acceptor stem

Schimmel et al., in The RNA World, Third Edition,
Cold Spring Harbor Laboratory Press (2006)
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tRNA Identity Elements
Giege, R. et al., Nucleic Acids Res. 26 (1998)
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Class I aaRS
Class II aaRS
Giege, R. et al., Nucleic Acids Res. 26 (1998)
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tRNA phylogeny
Xue, H., Tong, K., Marck, C., Grosjean, H., Wong,
J.T., Transfer RNA paralogs, Gene 310 (2003)
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Universal Phylogenetic Tree
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Wobble
I (inosine) can pair with C,U,A
Watson/Crick A-U pair
Non-Watson/Crick G-U pair
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Wobble Usage
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Tong, K., Wong, J.T., Anticodon and wobble
evolution, Gene 333 (2004)