|
Author
|
Topic: The IHE and Beyond
|
Mike Gene
Member
Member # 149
|
posted 07. January 2003 14:59
In my previous essay, I used the paper from Singer and Hickey to demonstrate the plausibility of the IHE playing out in evolution. Singer and Hickey showed a strong relationship between nucleotide bias and the amino acid content of the proteome, such that AT-rich genomes contained proteins enriched with the residues, FYMINK. However, such analyses don't directly detect the IHE in that the authors used AT-enriched codons in their analysis rather than the codon pool tapped by cytosine deamination.
Another way to detect the IHE would be to analyze the effects of RNA editing that exploited cytosine deamination. During such editing processes, the synthesized RNA molecule is altered such that specific bases are changed through the use of cellular machinery. As a result, the RNA that is used by the cell is not directly encoded in the genome. A focus on RNA editing would allow us to see the effects of cytosine deamination all at once, rather than being spread out across time through incremental evolution.
So let me now discuss the second article: Philippe Giegé and Axel Brennicke. 1999. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. PNAS 96, 15324-15329
Giege and Brennicke (G&B) identified 456 instances of RNA editing. All of the edits were C-to-U changes and 441 occurred in open reading frames. The editing was rather extensive, where one of 15 cytosines was changed to uracil. Yet the editing was not evenly distributed, as genes coding for complex I (of the electron transport chain) and cytochrome c biogenesis were edited at a frequency higher than others.
The effects of the editing nicely illustrate the IHE. According to G&B:
quote:
RNA Editing Increases the Overall Hydrophobicity of Mitochondrial Proteins.
One of the potential consequences of RNA editing in mRNAs and the corresponding change of the specified amino acid could be a modification of the overall biochemical nature of the affected mitochondrial proteins. The general tendency of the effect of RNA editing in Arabidopsis mitochondria is to increase the proportion of hydrophobic amino acid codons. As an example, the three most frequent amino acid transitions (93 S to L, 80 P to L, and 47 S to F) all result in codons for hydrophobic amino acids. In the overall analysis of RNA editing in Arabidopsis mitochondria, 35% of the modifications are hydrophilic to hydrophobic, and 35% are hydrophobic to hydrophobic codon alterations. Only the 27 P to S codon transitions reverse the tendency by creating codons for hydrophilic amino acids from those for hydrophobic ones. In the 425 modified codons detected, 41.5% specify hydrophobic amino acids before editing and 84.9%, after editing (Fig. 1).Thus RNA editing increases the hydrophobicity of mitochondrial proteins.
Figure 1 from their study is shown below:
The interesting thing here is that the IHE may only be tweaking proteins and their function. For example, many of the subunits of NADH dehydrogenase are extensively edited, yet there is no reason to think any novel function has appeared. Instead, the effects of cytosine deamination may be utilized to accelerate the fine-tuning of any particular protein.
The effects of cytosine deamination not only are channeled into the IHE, but also may play a role in modifying RNA structure and function. G&B report:
quote:
The Arabidopsis mitochondrial intron population is exclusively composed of organellar group II introns with a well-conserved secondary structure, which has been shown to be important for splicing. Some of the editing sites affecting group II intron sequences are predicted to improve the quality of the intron folding (Fig. 2) and thus very likely to improve functional splicing.
The fact that cytosine deamination produces uracil is quite intriguing. Just as the hydrophobic amino acids play a crucial role in protein structure, thus function, uracil appears to play such a role in RNA structure and function.
In 1994, Stephen Holbrook, a chemist in the Structural Biology Division, determined that uracil had the ability to base pair with any of the bases in RNA. Here are some excerpts from Lynn Yarris' report on this [1]:
quote:
Holbrook subsequently determined the three-dimensional structure of an RNA molecule containing U-U base pairs. Unlike the U-G and U-C base pairs, the U-U partners formed two hydrogen bonds that were stable without the presence of tightly bound water molecules.
"Non-standard base pairs such as the U-G, U-C, and U-U partners we have observed are common in ribosomal RNA, viroids, messenger RNA, and retroviruses," says Holbrook. "Runs of these mismatched pairs in the middle of double helical RNA form internal loops."
"Uracil can now be called the universal partner in RNA structure," says Holbrook. "That it can pair with any other base helps explain why RNA is so flexible in terms of how it interacts with itself and why, unlike DNA, it can take on so many different shapes."
It is also worth noting that G·U is the most frequent non-canonical base-pair found in RNA [2]. And it also just happens to be the most stable mismatch (UU being the most flexible), although less stable than the canonical G-C pair. If we imagine a hairpin structure in RNA important for function, G-C pairs are most likely to be converted to G-U pairs because of cytosine deamination. This could, depending on the sequence context, slightly destabilize the hairpin allowing the RNA the flexibility to interact on a novel way. However, since G-U mismatches are the most stable, the search stays close to the original RNA structure.
SUMMARY
The Increasing Hydrophobicity Effect can be seen both through the genomic analyses of Singer and Hickey and the RNA Editing study of Giege and Brennicke. It thus clearly has played out in evolution. However, it still remains an open question as to exactly how it has played out. There are at least three possibilities:
1) The IHE works only to tweak and adjust protein function as may be the case with the mitochondrial proteins analyzed by Geige and Brennicke. It would be helpful to biochemically characterize some of these edited proteins and compare their properties to unedited versions.
2) In addition to 1), the IHE may have been coupled to carefully chosen intitial states to unlock front-loaded states as previously suggested. [3]
3) In addition to 1) and 2), the IHE has the ability to evolve novel proteins not front-loaded into the initial states. If this is true, how often has it occurred and what frequency of novel protein evolution was dependent on the IHE?
In addition to the IHE, cytosine deamination may also play a helpful role in RNA evolution. It is noteworthy that such a mutation would unleash uracil in a position originally housed by cytosine and uracil appears to play an important role increasing RNA flexibility, thus function.
It is also worth commenting on the apparent conceptual tie between the effects of cytosine deamination on protein and RNA structure/function. In both cases, the most common base substitution appears to have significant functional potential, as both hydrophobic amino acids and uracil seem to make the greatest impact of protein and RNA structure, respectively. It's as if an engineer is trying to get the "most bang from your buck" when it comes to utilizing a nitrogenous base poised to change.
1. Researchers unlock secret of RNA's versatility
2. Meroueh M, Chow CS. Thermodynamics of RNA hairpins containing single internal mismatches. Nucleic Acids Res 1999 Feb 15;27(4):1118-25
3. http://idthink.net/biot/deam/index.html
[ 09. January 2003, 20:59: Message edited by: Mike Gene ]
IP: Logged
|
|
Frances
Member
Member # 169
|
posted 07. January 2003 23:58
Thank you for links to very interesting papers. I have been collecting vaste amounts on papers on these topics and they surely are fascinating.
One thing I would like to point out is that you seem to have shown that non-teleological and teleological assumptions seem to have led to similar conclusions. I understand that your position is not to support front loading as evidence for ID perse but rathet use teleological thinking such as front loading to explore scientific issues. I have just read the Thread on Front Loading: A Research Program and notice that many unanswered questions remain. Do you think that it is reasonable to expect ID to find ways to distinguish between front loading and methodological naturalism or is such distinction even possible or relevant?
In my research I have found how a Reader, J.S. & Joyce, G.F. "Catalytic activity of a binary information macromolecule" Nature 420, 841-844 two base self catalytic macromolecule[/url], Rogers, J. & Joyce, G.F. "A ribozyme that lacks cytidine" Nature 402, 323-325 three base ribozyme all show how at least in principle natural selection could explain a possible route for the genetic code.
Cytodine free ribozymes:
quote:
Cytidine-free ribozymes show that evolution can cope with a very restricted set of chemical building blocks in generating macromolecules
that have a complex structure and function. Several biological RNAs have very low cytidine content, such as the dutA messenger RNA of Dictyostelium discoideum14, mitochondrial RNase P RNA of Candida glabrata15, and various introns from dicot plants16. Cytidine-free ribozymes can be studied as model systems, with catalysis as a measure of structural integrity, to understand how
naturally occurring cytidine-deÆcient RNAs adopt a well defined secondary and tertiary structure. How, for example, does an RNA molecule compensate for the lack of a stable G×C pair? How is a unique tertiary fold achieved when every pyrimidine (U) has the potential to pair with every purine (A and G)?
The original genetic material has been proposed to contain fewer than four different subunits, for example, a system involving only adenine and inosine17. Clearly, RNA folding and catalysis can be achieved in a three-nucleotide system. Perhaps guanosine could be eliminated as well. Biological evolution has developed an elegant solution to the problem of cytidine's chemical instability: organisms with large DNA genomes use 59-methyl deoxyuridine (thymidine) in place of deoxyuridine and rely on the enzyme uracil-DNA glycosylase to repair deoxyuridines that have resulted from the
deamination of deoxycytidine18. With or without cytidine, evolution manages to find an acceptable solution.
Another issue seems to be the repair mechanisms for cytodine deamination, was this repair mechanism also 'front loaded' or did it evolve ?
quote:
In addition to contributing to the full understanding of the dUTP specificity, the structures of the dUTPase complexes showed that very short polypeptides can specifically bind nucleotides by mimicking Watson-Crick DNA base pairing. Thus, the b hairpin in dUTPases seems to be an ancient nucleotide-binding motif that originated at the very beginning of evolution [5].
Let me also add the following
Rogers, J. & Joyce, G. F. The effect of cytidine on the structure and function of an RNA ligase ribozyme. RNA 7, 395-404 (2001).
And while I am feeling particularly sharing
Secret sharers in the immune system: a novel RNA editing activity
links switch recombination and somatic hypermutation, Nancy Maizels
quote:
A new mechanism for regulation in the immune system has been identified: a cytidine deaminase is critical for both class switch recombination and somatic hypermutation, revealing an unanticipated link between these two processes.
Btw RNA editing is not limited to C -> U transitions but also A -> U/I see Changing genetic information through RNA editing by Stefan Maas and Alexander Rich.
[ 08. January 2003, 00:12: Message edited by: Frances ]
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 08. January 2003 10:25
Frances,
You write: One thing I would like to point out is that you seem to have shown that non-teleological and teleological assumptions seem to have led to similar conclusions.
But what non-teleological assumptions are you talking about and what conclusion do you have in mind?
You also ask if it is reasonable to expect ID to find ways to distinguish between front loading and methodological naturalism or is such distinction even possible or relevant. Like I have said before, I just don't view this as an important question at this point in time. It's more important to flesh out some positive ID thinking. I can simply repeat myself:
You want ways to distinguish between front loading design and natural processes. Yet it's way too early in the investigation to provide such a definitive answer. At this stage in the game, FLE represents an alternative perspective. That is, if the two perspectives cannot be distinguished, there is no reason for me to ignore the FLE perspective and focus entirely on natural processes to the exclusion of their possible teleological use. Now, after the FLE perspective has been thoroughly fleshed out, to answer several of the questions I have posed, we can then return to your question. That is, let's first see what falls out from a more focused FLE perspective, okay?
There is no reason to be impatient. I have the patience to wait many years as I further develop this lines of thought. When you are dealing with an investigation sensitive to subtle clues (and thus at high risk of building on false positives), impatience is poison.
As for the repair mechanisms, there are two possibilities. 1) It was originally designed such that the original cells were endowed with it or 2) It evolved into existence. If the answer is 2), there are two further possibilities. a) It was actively front-loaded or b) is was passively front-loaded simply through the inclusion of cytosine. The very interesting paper you provided clearly indicates the repair mechanism is quite ancient. Do you have evidence that it did evolve (not to be confused with "could have evolved" claims)?
As for editing, I am well aware that it can involve other types of substitutions. I'll be talking about these in the future.
Thanks for the interesting article cites.
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 08. January 2003 10:29
Frances: three base ribozyme all show how at least in principle natural selection could explain a possible route for the genetic code.
Yes, but I'm not all that impressed with "could happen" alternative explanations (just as you aren't with mine). Yet even at this modest level, you'd need to establish cytosine-dependent primordial RNA functions.
IP: Logged
|
|
|
Printer-friendly view of this topic