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Evolution of the Genetic Evolution of the Genetic CodeCode

Adi SternAdi Stern

30/3/0530/3/05

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OutlineOutline

1.1. Introduction – the translation Introduction – the translation mechanismmechanism

2.2. Cracking the codeCracking the code

3.3. Genetic code(s)Genetic code(s)

4.4. The 3 theories of evolutionThe 3 theories of evolution

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Introduction - translationIntroduction - translation

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tRNAtRNA

Matches amino acids Matches amino acids to codons in mRNAto codons in mRNA

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Aminoacyl-tRNA synthetaseAminoacyl-tRNA synthetase

Attach amino acids to tRNA Attach amino acids to tRNA Most cells: 20 aminoacyl synthetasesMost cells: 20 aminoacyl synthetasesBacteria: less than 20, some “incorrectly” Bacteria: less than 20, some “incorrectly”

attached tRNAs are modifiedattached tRNAs are modifiedHigh-accuracy defining stageHigh-accuracy defining stage

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tRNAtRNA

61 codons → < 61 different tRNAs:61 codons → < 61 different tRNAs:human: 48 different tRNAs (anticodons)human: 48 different tRNAs (anticodons)bacteria: 31 different tRNAs (anticodons)bacteria: 31 different tRNAs (anticodons)

Wobble (codon Wobble (codon base 3)base 3)

(anticodon base 1)(anticodon base 1)

UUG or IG or I

CCG or IG or I

AAUU

GGCC

Wobble (codon Wobble (codon base 3)base 3)

(anticodon base 1)(anticodon base 1)

UUA,G or IA,G or I

CCG or IG or I

AAU or IU or I

GGC or UC or U

BACTERIA EUKARYOTES

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CRACKING THE CODECRACKING THE CODE

1953: DNA structure 1953: DNA structure (Watson and Crick)(Watson and Crick)

1961: the genetic code 1961: the genetic code (Matthaei and Nirenberg)(Matthaei and Nirenberg)

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……in betweenin between… …

George Gamow – a Russian physicist, is excited George Gamow – a Russian physicist, is excited by the double helixby the double helix

The “RNA tie club”The “RNA tie club”

Watson (Proline)

Crick (Tyrosine)

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The Diamond code (Gamow,1954)The Diamond code (Gamow,1954)

Problems:(1) overlapping code, restricts aa neighbours.(2) translation in ctyoplasm

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Comaless code (Crick, 1958)Comaless code (Crick, 1958)

No commas (proved correct)No commas (proved correct)Only 20 of 64 codons are meaningful – all Only 20 of 64 codons are meaningful – all

other are skipped.other are skipped.No frameshift!No frameshift! a codon such as a codon such as

AAA is meaninglessAAA is meaningless ABA ABB ACA BCC

aa1 aa2 aa3 aa4

? Does not exist!

“The most genius theory proved wrong…”

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CrackedCracked!!

A Cell-free system was devisedA Cell-free system was devisedin which in which UUUUUUUUUUUU was translated UUUUUUUUUUUU was translated (=FFFFFFF) (=FFFFFFF) CCCCCCCCCCCC was translatedCCCCCCCCCCCC was translated(=PPPPPPP)(=PPPPPPP)and so on…and so on…

““Almost disappointing…”Almost disappointing…”

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The standard genetic codeThe standard genetic code

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The Universal Genetic CodeThe Universal Genetic Code??

Found in “all” organismsFound in “all” organismsChange in the genetic code would affect Change in the genetic code would affect

all coding proteins all coding proteins lethal. lethal. ““The frozen accident” (Crick, 1968)The frozen accident” (Crick, 1968)

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But … there isn’t only 1 code, but 16But … there isn’t only 1 code, but 16!!

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The code can evolve.The code can evolve. Codon assignments are non-randomCodon assignments are non-random

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AdaptationAdaptation

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Reduces the effect of translation errorReduces the effect of translation errorReduces the effect of point mutationReduces the effect of point mutation

… … but – these are chemical considerationsbut – these are chemical considerations

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Code optimalityCode optimality

Compare the code(s) with random alternativesCompare the code(s) with random alternatives

Standard genetic code

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BUTBUT… …

This works when the criteria is:This works when the criteria is:- polarity- polarity- PAM distance- PAM distance

But it doesn’t work with:But it doesn’t work with:- size- size

+ there is a lot of debate on the validness of + there is a lot of debate on the validness of these methods (e.g. DeGulio 2000)these methods (e.g. DeGulio 2000)

HOW IS CHANGE POSSIBLE?HOW IS CHANGE POSSIBLE?

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Codon CaptureCodon Capture

The ‘codon capture’ theory The ‘codon capture’ theory (Osawa-Jukes 1988):(Osawa-Jukes 1988):

FollowingFollowing GC content pressure on the GC content pressure on the genome, tRNAs disappear and reappear genome, tRNAs disappear and reappear with a different recognition.with a different recognition.

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Codon-Capture Model Codon-Capture Model

Supposed model in Supposed model in Mycoplasma capricolum:

1. TGG (Trp), TGA (Stop)

2. TGG (Trp), TGA → disappears, replaced for instance by TAA (Stop)

AT pressure

3. release factor (TGA) disappears (no selective pressure)

AT pressure reduced

4. TGA reappears, unrecognized

5. tRNA (TGG) for Trp duplicates, and mutates to recognize TGA. Now TGA codes for Trp

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Evidence in favourEvidence in favour

In In Mycoplasma capricolum, tRNA (TGG) tRNA (TGG) and tRNA (TGA) are on the same operon.and tRNA (TGA) are on the same operon.

In related bacteria – the codon TGG has In related bacteria – the codon TGG has entirely disappeared…(replaced entirely entirely disappeared…(replaced entirely by TGA)by TGA)

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The ambiguous intermediateThe ambiguous intermediate

Codons did not disappear – tRNAs which are Codons did not disappear – tRNAs which are ambiguous, led to fixation of one tRNA + codon ambiguous, led to fixation of one tRNA + codon in one species an to another in another speciesin one species an to another in another species

Supporting evidence: E.Coli UAG translates to Supporting evidence: E.Coli UAG translates to stop, Trp or selenocysteine.stop, Trp or selenocysteine.

Replacements of all codons by another a.a. are Replacements of all codons by another a.a. are not necessarily lethal!not necessarily lethal!Experiment: partial replacement of Ile by Cys in Experiment: partial replacement of Ile by Cys in E.ColiE.Coli resulted in only low loss in fitness! resulted in only low loss in fitness! (Doring (Doring and Marliere, 1998)and Marliere, 1998)

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Genome streamlining hypothesisGenome streamlining hypothesis

Pressure to minimize the genome of Pressure to minimize the genome of mitochondria (or other) obligatory mitochondria (or other) obligatory parasites leads to reassignment of parasites leads to reassignment of codons.codons.

Transfer of genes to nuclear genomes → Transfer of genes to nuclear genomes → less constraint on the mitochondria less constraint on the mitochondria genome.genome.

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History – a slowly growing codeHistory – a slowly growing code

Initial, limited set of amino acids.Initial, limited set of amino acids.Newly introduced amino acids according Newly introduced amino acids according

to similar biosynthetic path.to similar biosynthetic path.New amino acids did not make drastic New amino acids did not make drastic

change in the protein.change in the protein.Theory:Theory:

First base – similar biosynthetic pathwayFirst base – similar biosynthetic pathwaySecond base – similar aa propertiesSecond base – similar aa properties

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tRNA, aa-tRNA-Synthetase tRNA, aa-tRNA-Synthetase phylogeniesphylogenies

aa-tRNA-Synthetases phylogeny supports aa-tRNA-Synthetases phylogeny supports the ‘biosynthetic theory’the ‘biosynthetic theory’

Phylogenies of tRNA and aa-tRNA-Phylogenies of tRNA and aa-tRNA-Synthetases are non-congruent…Synthetases are non-congruent…

So maybe all this happened within the So maybe all this happened within the Last Common Ancestor of all organismsLast Common Ancestor of all organisms

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Summary-change in genetic codeSummary-change in genetic code

Primordial code: expansion of code from Primordial code: expansion of code from few to 20 a.a.’sfew to 20 a.a.’s

tRNA and aa-tRNA-Synthetases are tRNA and aa-tRNA-Synthetases are invented invented → this enables codon swapping and code → this enables codon swapping and code optimizationoptimization

Ambiguity enables changeAmbiguity enables changeMost of these changes – in relatively Most of these changes – in relatively

‘simple’ organisms.‘simple’ organisms.