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Author Topic:   Wright et al. on the Process of Mutation
herebedragons
Member (Idle past 120 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


(3)
Message 224 of 296 (645065)
12-22-2011 7:58 PM
Reply to: Message 218 by zi ko
12-14-2011 12:02 PM


Re: Are there RANDOM MUTATIONS?
Hi Zi Co,

In my opinion random mutations exist but they are less important in relation to those, which are environment information guided

It seems you are having difficulty understanding this issue of random mutations. I can relate. I had some difficulty with it for a while too. I will share some of the things that helped me understand this issue better and maybe it will help you too.

First, I don’t like the term “random” mutations. Not that its wrong or incorrect, I just think it lends some confusion when first trying to understand this subject. I think the term “spontaneous mutations” works better. I think it removed my preconceived notions of what random meant and made it more clear that it is more about “why” mutations occur that makes them “random”. Mutations arise primarily from mistakes in the replication processes (it may even be exclusively because of mistakes – I don’t know of any situation that would not be considered a mistake). A wrong base substitution, aberrant pairing during crossing over, non-disjunction during meiosis, deletions, inversions etc... mistakes in replication.

This paper discusses another source of mutations – single stranded DNA, which may at first seem as though this could be a directed process. Open the DNA, switch some base pairs and off you go. But it is just not that easy. In order for the cell to make the proper substitutions it would need to know what substitutions would produce what effects. There is no know mechanism that could account for that.

One possible mechanism is a type of DNA editing similar to what some eukaryotes use to process mRNA. Starvation could induce production of an RNA template that could be used to edit the sequence in the single stranded DNA being transcribed. But even if such a mechanism did exist, why do only 2 out of 1 billion get the proper mutation? And there was no mention of the number of harmful mutations or neutral mutations (although Taq alluded to it) because those mutations were not the subject of this study. How many harmful or neutral mutations do you suppose there were in that population of 1 billion? A lot more than 2 maybe?

This may not be intuitive in bacteria since any effects of mutations are almost immediately expressed in novel environments. Also, the effects of a mutation affect not only the offspring but the parent cell too. However, you could think of this in a different way. You have in your body right now millions of sperm cells (I assume you are male, if not substitute egg for sperm ). Each of those sperm probably contains at least one mutation. How could your sperm possibly know what mutation your offspring will need to deal with the environment they will be subjected to? There is also no way to specify which sperm will get to fertilize the egg – the first one to the egg wins, essentially a random process too.

Bottom line... mutations are “random” with respect to fitness. They occur spontaneously without respect to whether the organism needs it or not. Of course, organisms have mechanisms that help them deal with their environment, such as the one discussed in this paper – hypermutation of a specific region. There is no known mechanism that allows the bacteria to specify the specific mutation that happens but it does allow them to “try” many different mutations and the end result is the population gets “just the right mutation” they need to survive.

Hope this helps

HBD


This message is a reply to:
 Message 218 by zi ko, posted 12-14-2011 12:02 PM zi ko has responded

Replies to this message:
 Message 231 by zi ko, posted 12-23-2011 11:59 AM herebedragons has not yet responded

  
herebedragons
Member (Idle past 120 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 225 of 296 (645066)
12-22-2011 8:12 PM
Reply to: Message 1 by Taq
08-01-2011 6:23 PM


Hi Taq,

Its been a while since I have posted on this forum, but I have a break for about a month and thought I would spend a little time here.

I do not disagree with the major premise of the thread that mutations are random with respect to fitness. I do, however, have some questions about the Wright et al. paper and would like to discuss them.

1. The authors do seem to be arguing for at least a form of directed mutation.

quote:
RNA polymerase pausing is thought to be a mechanism that could determine the site of mutagenesis

Specifying the site of a mutation would certainly increase the likelihood of getting the “needed” mutation. Wouldn’t you consider this a type of directed mutation? I realize that even at a specified site the exact mutation would be random, but directing a mutagen to a specific site would definitely improve the odds.

quote:
In our view, these studies demonstrating enhanced mutation rates as a result of artificially induced transcription are all examples of specifically induced mutations.

I realize that “specifically induced mutations” is not the same thing as directed mutations. But perhaps this has caused some confusion with those in this thread that have trouble with mutations being random. I am unclear as to what their actual hypothesis was in this paper. It seems to be derepression-induced hypermutation being the link between mutations and environmental stress. Is that a fair summary of their position?

2. The authors state that

quote:
ssDNA is more vulnerable to mutagenesis than double-stranded DNA.

I guess I fail to see how this would be. While transcription is going on wouldn’t the template strand be shielded from mutations? Perhaps the non-template strand would be vulnerable but this would have little or no effect. When transcription ended, the DNA would zip back up, polymerase would detect the misplaced bases and repair (at least the majority). Perhaps they would “repair” the wrong strand and end up with a mutation, but I don’t really see that as hypermutation. In addition, when DNA opens up into single strand, it adds proteins (I don’t recall the name for them) to stabilize and protect the ssDNA. So I don’t really see how transcription alone is cause for hypermutation. I did not see where they gave anymore explanation for increased mutation rate besides increased transcription.

3. In the OP you stated:

With respect to the paper, I will attempt to demonstrate that the same mechanisms that produce reversions in leuB- organisms will also cause deleterious mutations in very important and vital genes as well as mutations which do not change the fitness of offspring.

I did not see where you did this. Not that I doubt that the premise would be true, but I don’t think the data in the paper supports rates of deleterious or neutral mutations. It seems that leu- or reversion mutations were all that were distinguish. How were you going to accomplish this statement in your OP? Is there data I missed? It would seem that the total rate of mutation would have been important to this study. It would help establish hypermutation. It looks as if mutation (reversions) rates doubled, maybe quadrupled? Is that right? Not exactly “hyper” IMHO. So could it could be only reversions that increased and not total mutation rate? If so, it could indicate that something was indeed directing mutations to a specific site (the reversion site).

I guess that’s it for now.

HBD


This message is a reply to:
 Message 1 by Taq, posted 08-01-2011 6:23 PM Taq has responded

Replies to this message:
 Message 226 by Taq, posted 12-23-2011 1:50 AM herebedragons has responded

  
herebedragons
Member (Idle past 120 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 250 of 296 (645471)
12-27-2011 8:07 AM
Reply to: Message 226 by Taq
12-23-2011 1:50 AM


They are arguing just that. However, they fail miserably IMHO.

I’m not sure I agree that they have failed miserably. Maybe overstated the significance of their findings.

I do agree that only 1 reversion in 500 million is not really suggestive of a “directed” mutation. But I am also not sure at what level it could be considered “directed”. Would it need to be 50%? Or 25%, 10%? Seems kind of arbitrary. It may be a subjective rather than objective observation.

At the end of the day this is no different than a beggar on the corner getting an extra ten dollars to spend on the lottery. The non-random increase in the purchase of tickets in no way makes the actual lottery drawing non-random with respect to financial need.

But, if I sought out only those beggars who were starving and close to starving to death and gave 500 million of them each a lottery ticket, it would surely increase the likelihood that I would save the life and improve the lifestyle of several beggars. That would be targeted. So, while the drawing itself may still be random, the distribution of the “chances” would not be but would be specifically targeted to those that needed it most.

I cited DNA gyrase as one of those genes, and it serves as a good example ... So, the very mechanism that increases the rate of beneficial mutations in the lueB gene also increases the neutral and lethal mutations in vital housekeeping genes. By definition, this is random mutation. It is an increase in changes that are random with respect to fitness.

There was no data regarding the mutation rate of any housekeeping genes in this paper (and as I said, I think that would be good data to have) So it is difficult to interpret what is going on in other areas of the genome. Does mutation rate increase in all genes or merely in the targeted genes? It is at least implied by the authors that the increase is targeted to specific genes. There is no product being made that is a mutagen that would increase overall mutation rate.

The only mechanism mentioned for increasing mutation rate is increased transcription (and in fact, the lueB gene seems to be stuck in the “on” position). Would transcription of DNA gyrase (for example) increase? In fact, Wright says that during starvation ppGpp inhibits the synthesis of DNA, rRNA, nucleotides and phospholipids and therefore arrests cell division. So many of the housekeeping genes would actually be down regulated. She also states that

quote:
ppGpp activates only those genes that are specifically derepressed by the type of starvation imposed

So the target of increased transcription is specific and should not affect other genes operating at constituent levels. There would continue to be mutations in other genes, but only at background levels. I think the whole point is that the genes that needed the mutation became the most likely targets while the others were somewhat protected from mutation. A balance between getting the needed mutation and preventing deleterious mutations.

Another thing I found interesting was the amount of mRNA transcribed by the leuB gene during starvation. LeuB mRNA was about 6 times more abundant when starved for leucine than when grown to log phase. (fig 2.) Since mRNA can be translated at the same time it is being transcribed, and by several ribosomes simultaneously it appears to be “fishing”. Generate large amounts of mRNA until something works. What are the mRNA levels in a leuB+ strain when starving? Another key piece of evidence to show that this is indeed increased transcription and hypermutation, I believe.

Finally, I had trouble understanding how the mechanisms the authors proposed in this paper, ssDNA vulnerability and RNA polymerase stalling, could induce hypermutability. Wright discusses the mechanisms here that may account for targeted mutations and increased mutation rates. (You may have already seen this, WK pointed it out earlier in this thread) I think they are quite plausible. The vulnerability of ssDNA comes from secondary structures and the resultant unpaired and mispaired bases in the stem-loop system. The second mechanism described is localized supercoiling and, again, the secondary structures that form (RNAP stalling may be a consequence of supercoiling, but is not really discussed in detail).

I would say that based on this paper and supporting literature, there is evidence that some mutations are directed as they apply to fitness. Maybe it is just a matter of semantics, but perhaps directed is inappropriate. Perhaps “guided” would be a better term. While the mutations themselves are random, they are “guided” to some genes or areas that are more likely to provide a benefit to the organism. Difficult to draw a solid conclusion based on one study, but more work could be done on this; I would think it could have considerable implications in human disease.

HBD


This message is a reply to:
 Message 226 by Taq, posted 12-23-2011 1:50 AM Taq has not yet responded

  
herebedragons
Member (Idle past 120 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 251 of 296 (645472)
12-27-2011 8:18 AM
Reply to: Message 236 by Wounded King
12-23-2011 3:40 PM


It just so happens that in the specific experimental setup in the paper there is a very limited repertoire of potential mutations that will rescue the leuB- mutant. Whether Wright would actually see it this way I don't know, I've said before that I think she exaggerates a number of things, and one of them is the specificity of the response.

I believe she is claiming that the leuB- mutation is characterized as a C-to-T transition at aa286 resulting in a serine-to-leucine substitution. So a very specific mutation. She also claims that 80% of revertants were true revertants, which I take to mean they undid the aforementioned mutation. So, as you said, a very limited repertoire of potential mutations that rescue the leuB- mutant.

In her follow up paper, A Biochemical Mechanism for Nonrandom Mutations ..., she asserts that unpaired and mispaired bases in stem-loop structures are more likely to undergo mutation. Fig 1C shows such a structure, but I don’t think it is specific to leuB but merely illustrative of her hypothesis. However, mutation (1) supposedly represents the C-to-T mutation of interest.

So, why is it you think the specificity of the response is exaggerated?

I would say her claims of upsetting neo-Darwinism and going against the established paradigm are exaggerated. And maybe she has jumped the gun on claims of “directed mutations” based on these limited studies. But this particular response does seem to be quite specific. It remains to be seen if this applies to other operons as well.

HBD

BTW, I am just trying to clarify your objections, not argue my particular point.


This message is a reply to:
 Message 236 by Wounded King, posted 12-23-2011 3:40 PM Wounded King has responded

Replies to this message:
 Message 252 by Wounded King, posted 12-27-2011 11:59 AM herebedragons has responded

  
herebedragons
Member (Idle past 120 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 253 of 296 (645546)
12-27-2011 7:56 PM
Reply to: Message 252 by Wounded King
12-27-2011 11:59 AM


I don't think it is quite as restrictive as you make out.

Yea, I didn't realize they were defining true revertants to even include those that substituted valine or methionine. I assumed true revertants were exact reversals. My misunderstanding or perhaps an exaggeration on the part of the author

By focussing on such a specific target and ignoring the possibility of any other elevated mutation rates in the rest of the responsive genome Wright effectively exaggerates the specificity of the response. The reverting mutation may be highly specific, but without a better characterisation of the change in mutation rates at a wider sample of upregulated loci we can't really say how specific the response was.

Agreed. This was basically my criticism . Not enough information regarding background and responses at other genes. She only reported the data that supported her hypothesis.

Thanks

HBD


This message is a reply to:
 Message 252 by Wounded King, posted 12-27-2011 11:59 AM Wounded King has acknowledged this reply

  
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