"Despite its beauty, Watson-Crick complementarity is absolutely insufficient to ensure an acceptable fidelity of replication, even with perfect raw materials. ... Fortunately, fidelity of nucleotide attachment depends not on complementarity, but on active involvement of DNA polymerases." Kondrashov [1]
These statements changed my thinking about DNA dramatically and definitively. More than Tomas Lindahl did. Perhaps because Kondrashov contrasts replication fidelity so clearly with the A:T and C:G base complementarity.
I always had the idea that A:T and C:G base pairing was the crucial
feature of DNA and that it was a necessary and sufficient condition for the
double-helix structure, replication, transcription and translation. In a
restricted sense this is still true, but it is certainly not the whole
story. It is a necessary component of life, but it needs help. Lots of
help! In the background hundreds of enzymes are constantly working to
correct base mis-pairings and replication errors. Kondrashov gives a
detailed description of the known enzymes that are involved.
Don't be mistaken, I still agree with the central importance of DNA in biology:
"The model of the DNA structure built by James Watson and Francis Crick certainly is one of the central discoveries in twentieth-century biology and the entire history of biology." Eugene Koonin [2].
Just as Mendeleev’s periodic table of elements created a foundation in the science of chemistry, so does the structure of DNA create the foundation of biology. DNA as a carrier of genetic information draws the line between living and non-living systems. With the invention of DNA, evolution took off and created millions of species from the most simple to the most complex. Bacteria are based on DNA. Humans are based on DNA. And everything between is based on DNA. DNA seems to have an unlimited potential.
But again, DNA cannot even 'self-replicate' without enzymes. DNA on its own is just a large non-living chemical macro-molecule. It becomes useful only when it is transcribed and translated into proteins ... with the help of enzymes. DNA needs help. Curiously, it created the help itself! Let me introduce the self-building crane as a metaphor for DNA creating its own helpers:
How to build a crane? A crane can be built by a second crane. But, how
to build that second crane? An ingenious solution is a self-building
crane which does away with the second crane requirement. It only needs
building blocks. The crane can pick them up, integrate them and it
grows. Gradually. Similarly, DNA does not need external help. DNA can
copy and repair itself with helper enzymes which are encoded in DNA itself.
Why are DNA polymerases needed anyway?
It is not immediately clear from Watson & Crick's model why special enzymes such as DNA-polymerases are needed, since the AT and CG base-pairs are formed naturally and spontaneously. Wrong base pairs are excluded by the base pairing rules. Wrong base pairing, for example A with C or T with G, does not fit in the double helix. So, the strong suggestion is that the base-pairing rules are enough for DNA replication. The fidelity of DNA-replication is completely based on the base pairing rules.
"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material " Watson & Crick
In 1953 Watson and Crick had absolutely no idea of the insufficiency of
the base-pairing for DNA-replication. Their double-helix DNA structure,
base pairing and replication were prime examples of beauty and
simplicity.
"The idea of errors and repair didn’t occur to them, because it wasn’t
thought to be necessary” ! [4]
The fact is that enzymes such a s DNA-polymerase are required. Without DNA-polymerases, DNA-replication would produce a 1000-fold higher error rate. Without DNA-polymerase, the error rate would be 1% (10-2). With DNA-polymerase the error rate is down to 1 in 100,000 bases (10-5) [1]. That is still too high. Several mechanisms bring the error rate down even further.
How could DNA have started life without enzymes?
Rolie Barth wrote in a comment to the previous post: "But still I think that physical and chemical mechanisms might play an important role in keeping DNA-structure and information stable, because DNA storage functioned before repair systems were operational. Logically the latter evolved using functioning genes, isn't it?"
Exactly! Good thinking! If the error rate of DNA replication is so high, how could DNA have been replicated reliably without all those enzymes? A chicken and egg problem:
- DNA needs a lot of proofreading and repair enzymes
- these enzymes are encoded in DNA
-
this makes DNA longer (more complex, more genes, more information)
-
that means more DNA must be maintained
- this requires better and/or more enzymes
-
etc ...
In other words: Eigen paradox
[3]:
The error threshold (or critical mutation rate) is a limit on the number of base pairs a self-replicating molecule may have before mutation will destroy the information in subsequent generations of the molecule.
So, it seems you need a long DNA molecule with many high fidelity replication enzymes encoded in its DNA to produce high fidelity DNA replication. A vicious circle. What came first? But I see no reason why copying fidelity could not be improved in a gradual way step by step. It need not have increased a thousandfold in one step! Under favorable environmental conditions (climate, food) natural selection could improve the proofreading and repair machinery step by step. Furthermore, one doesn't need a separate proofreading enzyme, because DNA polymerase has also proofreading activity [5]. Ultimately, it all depends how many genes and how much junk is in your genome. A genome of 1 million functional base pairs can tolerate an error rate of 1:1,000,000 but a genome of 1 billion functional base pairs will degenerate quickly with the same error rate.
Conclusion: the above statement of Kondrashov about the insufficiency of base
complementarity was an absolute eye-opener for me. My view of DNA as the
perfect solution to the problem of heredity was shattered. Lindahl gave
the first blow. But I was only really blown away by Kondrashov's
statement. For me it is nothing less than a paradigm change.
Yes, DNA is the biggest revolution in biology, and yes,
Watson & Crick got it right, but: (1) despite Watson & Crick, DNA
replication fidelity is too low without the help of enzymes, (2) this
requirement immediately creates a problem for the evolution of complex
life based on DNA. In a future blog a will deal with that!
Notes
- Chapter 5 'Struggle for Fidelity', in: Kondrashov, 2017, Crumbling Genome.
-
Eugene Koonin (2011) The Logic of Chance, p.21 hardback.
-
Geen leven zonder DNA-repair. De Lindahl paradox en de Eigen
paradox. (blog 21 October 2015) (Dutch). See Wikipedia article:
Error threshold.
- According to Phil Hanawaltin in the New Scientist: Running repair keeps DNA in order, 15 March 2003.
- see wikipedia article DNA polymerase: DNA polymerase with proofreading ability.
Further Reading
- DNA repair – providing chemical stability for life, The Noble Prize in chemistry 2015:
"Besides base excision repair, nucleotide excision repair, and mismatch repair, there are several other mechanisms that maintain our DNA. Every day, they fix thousands of occurrences of DNA damage caused by the sun, cigarette smoke or other genotoxic substances; they continuously counteract spontaneous alterations to DNA and, for each cell division, mismatch repair corrects some thousand mismatches. Our genome would collapse without these repair mechanisms."
- Rais A. Ganai, Erik Johansson (2016) DNA Replication—A Matter of Fidelity (overview).
-
De Nobelprijs Chemie 2015 is gegaan naar een drietal pioniers op het
gebied van DNA reparatie ('DNA-repair'), my blog (in Dutch)
In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible.
- See complete video: How Tower Cranes Build Themselves on youtube.
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