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Allotopic Expression & the "Mitochondrial Problem"


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#1

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Posted 20 March 2005 - 02:25 AM


In virtually a formalized recapitulation of the debate that occurred here recently on the feasibility of allotopic expression (AE), Aubrey's most recent paper (1) places a defensible cornerstone on the rationale for scientists to investigate the feasibility of AE in mammalian cells. His central argument, as the title suggests, is that AE merely faces two technologically solvable hurdles, hydrophobicity and genetic code disparity, for which he has offered theoretical solutions (2, 3). Aubrey's paper is counter-weighed in the same Bioessays issue by a contrary view that argues for the functional need of mitochondrial genes to be localized in organelles, a premise that should it be found to be strongly supported by experimental evidence, would pose a presently insurmountable hurdle and thus require an alternative strategy to be considered for addressing the "mitochondrial problem".

(1) BioEssays 27:436–446, 2005
Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity?
Aubrey D.N.J. de Grey

(2) Trends Biotechnol. 2000 Sep;18(9):394-9.
Mitochondrial gene therapy: an arena for the biomedical use of inteins.
Aubrey D.N.J. de Grey

(3) Rejuvenation Res. 2004 Summer;7(2):95-8.
Inter-species therapeutic cloning: the looming problem of mitochondrial DNA and two possible solutions.
Aubrey D.N.J. de Grey

(4) BioEssays 27:426–435, 2005
Energy transduction anchors genes in organelles
John F. Allen, Sujith Puthiyaveetil, Jorgen Strom and Carol A. Allen

#2

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Posted 20 March 2005 - 02:28 AM

... and the attachment on the contrary view.

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#3 John Schloendorn

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Posted 20 March 2005 - 06:27 AM

From the energy transduction paper:

There are clues, and the beginnings of experimental support, for the theory that expression of mitochondrial and chloroplast genes is regulated by the function of their gene products. For safe and efficient energy transduction, genes in organelles are in the right place at the right time.

When the same point was rised in the earlier debate here, Aubrey countered that all mitochondrially encoded proteins can only function and exist only in 1:1 complexes with nuclear encoded genes. Thus, exactly the same regulation pattern must be achievable in the nucleus, or we would see deviations from the 1:1 stochiometry. The new paper here does nothing to address this idea.

#4 ag24

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Posted 20 March 2005 - 11:26 AM

John Allen has recently returned to London after spending most of his career in Sweden, and is having a sort of "welcome symposium" on April 13th. I have corresponded with him quite a bit but never met him, so I am very much looking forward to this; you can be sure that the stoichiometry question will be among the topics we discuss. A couple of other points:

- Allen surveys the alternative hypotheses for why organelles retain genomes but dismisses the hydrophobicity one only on the basis that there are too many counterexamples to it. My paper's main thust is the demonstration that these alleged counterexamples are in fact not.

- Even if Allen's hypothesis were the correct reason why organelles retain genomes during evolution, allotopic expression may well still work fine: we must remember that something that has a very mild deleterious effect on fitness, far milder than would be biomedically relevant, will still be rapidly selected against by evolution.

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Posted 20 March 2005 - 12:09 PM

The point of contention is in the existence of a regulatory mechanism that couples gene expression to redox state, what the authors call the CORR (CO-location for Redox Regulation) hypothesis (1). This is the reason, claimed by the authors and others (2), that the rest of the mitochondrial genome has not entirely migrated to the nucleus. Should such a regulatory mechanism be proven to exist it would compromise the prospects of AE, in its current incarnation, as a strategy of protecting the mitochondrial genome.

It is a hypothesis that has not been refuted, however and aside from the seemingly obvious logic of the 1:1 stoichiometry between nuclear and mitochondrial encoded proteins, it deserves consideration, particularly in the context of SENS and especially because there is no alternative strategy for mitochondrial DNA damage should it be experimentally validated.

As Aubrey expressed in the previous post, he believes that even if CORR is proven to be true it is likely not to impact greatly on AE. On this I have my doubts - we have never seen a single example in nature of such a phenomenon as the entire mitochondrial genome existing in the nucleus and it may well be, according to CORR, for physiological reasons that could well prove to be more challenging than presently being conceived.

So I suggest that an alternative mitochondrial DNA damage strategy be considered.


(1) BioEssays 27:426–435, 2005
Energy transduction anchors genes in organelles
John F. Allen, Sujith Puthiyaveetil, Jorgen Strom and Carol A. Allen

(2) Trends Genet. 1999 Sep;15(9):364-70
Why have organelles retained genomes?
Race HL, Herrmann RG, Martin W.

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#6 DJS

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Posted 20 March 2005 - 09:21 PM

Allen surveys the alternative hypotheses for why organelles retain genomes but dismisses the hydrophobicity one only on the basis that there are too many counterexamples to it. My paper's main thust is the demonstration that these alleged counterexamples are in fact not.


The big misconception, I believe, is to consider nuclear-coded hydrophobic proteins as counter examples to the hydrophobicity hypothesis (HH), rather than exceptions. Or as Aubrey put it, the viability of HH depends on robust arguments that the exceptions "do not count".

The key point is that hydrophobicity can not be viewed as some insurmountable biological law, but as a finite force capable of being over come by an adequate level of selection pressure. I'm not surprised at all that there are a nunber of exceptions to the rule.

#7 DJS

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Posted 20 March 2005 - 09:30 PM

The point of contention is in the existence of a regulatory mechanism that couples gene expression to redox state, what the authors call the CORR (CO-location for Redox Regulation) hypothesis (1). This is the reason, claimed by the authors and others (2), that the rest of the mitochondrial genome has not entirely migrated to the nucleus. Should such a regulatory mechanism be proven to exist it would compromise the prospects of AE, in its current incarnation, as a strategy of protecting the mitochondrial genome.

It is a hypothesis that has not been refuted, however and aside from the seemingly obvious logic of the 1:1 stoichiometry between nuclear and mitochondrial encoded proteins, it deserves consideration, particularly in the context of SENS and especially because there is no alternative strategy for mitochondrial DNA damage should it be experimentally validated.


I guess it is possible for the HH/CDH & CORR to exist in tandem. Let's hope this is not the case because it would make the job of allotopic expression all the more complex.

I am curious. How "significant" of an issue is the 1:1 stoichiometry? (Note: I understand what 1:1 stoichiometry is, just not how it relates the merits of CORR) Would someone mind explaining this issue to me, or pointing me in the direction of some resources on it? It would be most appreciated.

Thanks

DonS

Edited by DonSpanton, 20 March 2005 - 09:49 PM.


#8 John Schloendorn

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Posted 21 March 2005 - 01:26 AM

Should such a regulatory mechanism be proven to exist it would compromise the prospects of AE, in its current incarnation, as a strategy of protecting the mitochondrial genome.

Please explain how so. The plan is to completely ignore any form of regulation that may exist in the mito, whatever it is, and use the regulation from the nucleus instead that can demonstrably accomplish the same results. How often do we have to repeat this?!

(Note to Don: That's what the 1:1 stochiometry demonstrates. There is no deep relation to CORR or whatever mitochondiral regulatory phenomenon)

#9 jaydfox

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Posted 21 March 2005 - 12:57 PM

The plan is to completely ignore any form of regulation that may exist in the mito, whatever it is, and use the regulation from the nucleus instead that can demonstrably accomplish the same results.

If the CORR mechanism for regulation, dependent upon the organellor DNA, in part influences or drives the nuclear expression of the nuclear-coded subcomplexes, then the removal of the organellor DNA could disrupt this system. 1:1 stoichiometry ensures that the subcomplexes are produced in the correct amount, relative to each other, but it only works provided the overall quantity produced is appropriate to begin with.

I'm not saying that I think that the CORR mechanism has any significant influence on the expression of nuclear-coded genes; it's just speculation. But for those who keep repeating "how often do we have to repeat this?!", as if it were obvious that there might not be a simple wrench the monkies might throw in, you may want to factor in this possibility.

It would be a shame to spend 6-10 years and $20-$50 million trying to get this to work, only to realize that the mtDNA must remain in the mitochondria for the regulatory mechanisms to work. Which is why other options must be considered, especially when so many promising alternatives seem to be available.

On the other hand, I still think that, should the technical hurdles be overcome, allotopic expression will give us the most bang for the buck, especially since improving upon it would be a simple matter of improving nuclear genomic stability, another SENSworthy task which I hope to see on the table eventually.

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Posted 21 March 2005 - 01:41 PM

Please explain how so. The plan is to completely ignore any form of regulation that may exist in the mito, whatever it is, and use the regulation from the nucleus instead that can demonstrably accomplish the same results. How often do we have to repeat this?!


You may repeat it as a litany and as often as makes you comfortable since it appears that you are attempting to convince yourself of something that may well defy biology dogma (i.e. lets just ignore regulation and it will go away).

The CORR theory implicitly states, and reiterates on concerns I have expressed on previous occasions, that the mitochondrial genome including its transcription, translation and replication is likely to be regulated by the extreme oxidative environment unique to mitochondria. Extrapolating from this premise it is therefore highly probable that *if* the CORR hypothesis turns out to be correct, that the mitochondrial genome and the proteins and enzymes it encodes could behave unpredictably in the dramatically different biochemistry in the nucleus.

Ignoring any form of regulation that may exist in mitochondria could have catastrophic consequences in light of the fact that mitochondria are pivotal to the initiation and execution of apoptosis.

You state above. "...use the regulation from the nucleus instead that can demonstrably accomplish the same results." What evidence do you have that allows you to say "demonstrably" in such an authoritative fashion?

Ultimately, only bench work is going to determine who is right. What is indisputable, however, is that the possibility exists, no matter how much you may try to convince yourself otherwise, that AE may not work, either for those reasons stated above or for other as yet unexplored factors.

For as long as such a possibility exists, it means that the mitochondrial DNA damage problem may not be addressed by SENS.

#11 jaydfox

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Posted 21 March 2005 - 02:00 PM

For as long as such a possibility exists, it means that the mitochondrial DNA damage problem may not be addressed by SENS.

I am becoming increasingly concerned that SENS—as de Grey has formulated it—is not the swiss army knife of anti-aging treatments I once thought. While I am reasonably sure he has isolated the main types of damage that need to be addressed, I am less and less convinced that the plans on the table will be sufficient.

Based on pessimistic assumptions about the interplay of the seven items of SENS, it's reasonable to assume that solving only 5 of 7 items might only get us an extra couple decades, and that 6 of 7 might only provide one or two decades more, depending on which 5 or 6 we're talking about. In my mind, it's critical that all seven targets be addressed, and that, from a scientific and pragmatic standpoint, we have backup options in the plan, even if they aren't the focus of the first round of funding.

In other words, if we can get enough funding to get started, perhaps a few million a year, I wouldn't want to split it necessarily, but focus it on a prime target. But as more funding becomes available, those backups must be on the table and receive their share. More importantly, by giving them recogntion, we know where our priorities lie. Also, by having the other options on the table, we can see where the scientific community at large will be focussing their efforts so that we can watch the changing information landscape with the correct perspective.

DNA damage (nuclear or mitochondrial) is the most critical aspect of SENS. The other items are cleanup, but you can't just "clean up" damaged DNA. You either have to ablate low quality cells (or mitochondria), or prevent the damage in the first place. Until it becomes possiblt to perform WGRT (Whole-body Genome Replacement Therapy), these are our two choices: ablate, or repair.

So the nuDNA and mtDNA problems are the ones that we most desparately need backup plans for.

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Posted 21 March 2005 - 02:11 PM

I am curious. How "significant" of an issue is the 1:1 stoichiometry? (Note: I understand what 1:1 stoichiometry is, just not how it relates the merits of CORR) Would someone mind explaining this issue to me, or pointing me in the direction of some resources on it? It would be most appreciated.


Each mitochondrion contains several hundreds of proteins and 2 - 10 copies of mitochondrial (mt) DNA. Even though mitochondria have their own genome, most of their proteins and enzymes are encoded in the nucleus. Considering that a single cell may harbor as many as a few thousand mitochondria at any one time and that mitochondria are turned over independently of cell division suggests a complex interplay of communications between the nucleus and mitochondria in order that the nucleus produce sufficient transcripts to meet the needs of vast mitochondrial numbers. When Aubrey refers to 1:1 stoichiometry he is referring to the ability of the nucleus to match mitochondrial encoded proteins with nuclear encoded proteins, interpreting this as evidence that there is no cryptic, mitochondrially exclusive regulatory mechanism that needs to be accounted for in AE. It is a reasonable assumption, but like CORR, it has not been experimentally validated. Nevertheless, this observed stoichiometric equivalence does not repudiate the CORR theory, since it does not disprove the existence of a mitochodriocentric regulatory mechanism. It is possible for the nucleus to accommodate the needs of the cell's mitochondrial population for nuclear encoded genes whilst the behavior of mitochondrially encoded genes is influenced by the redox biochemistry of mitochondria.

#13 jaydfox

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Posted 21 March 2005 - 02:58 PM

It is possible for the nucleus to accommodate the needs of the cell's mitochondrial population for nuclear encoded genes whilst the behavior of mitochondrially encoded genes is influenced by the redox biochemistry of mitochondria.

Prometheus,

That the nuclear-coded subcomplexes are produced in sufficient quantities to match the mt-coded subcomplexes is evidence enough that allotopic expression will preserve the 1:1 stoichiometry, and this is the point which you seem to deflect whenever it is raised. It is a strong point, on face value, so I'm curious how you feel about it.

That said, the 1:1 stoichiometry is sufficient for AE, provided that the changes made to effect allotopic expression do not alter any underlying components of the nuclear expression regulatory mechanism. Such changes might include (but are not limited to) silencing or deleting mtDNA from the organelles, or otherwise accounting for the altered stoichiometry that will result from having allotopicaly and mitochondrially expressed copies of the same genes.

For example, if the nuclear regulatory mechanism is in part driven by the mitochondrial regulatory mechanism, and if we perturb that mt-regulatory mechanism (e.g. by silencing mtDNA), then the nuclear regulatory mechanism may also be perturbed. So the success of AE depends not only on overcoming the technical hurdles of moving the genes out of and getting the proteins back into the mitochondria (while avoiding toxicity issues which have been experimentally observed), it also depends on accomplishing this feat without disrupting a very complex regulatory process.

In other words, if we can delete the genes from the mitochondria, without affecting the nuclear expression regulatory mechanism, then AE should be fine, assuming we overcome the other technical hurdles.

Alternatively, if we can deactivate (e.g. silence) the mt-coded genes, without affecting the nuclear regulatory mechanism, then AE should be fine, assuming we overcome the other technical hurdles.

Alternatively, if we can produce proteins via nuclear-coded genes, thus disrupting the 1:1 stoichiometry, without disrupting the effectiveness or efficiency of the complexes, then AE should be fine (assuming we overcome...). In theory, this would give a 2:1 stoichiometry, if the mt-coded gene expression rates remain unaltered in the face of the imported AE subcomplexes, and if such a screwy stoichometry isn't a problem, then we should be fine.

Alternatively, we can take the regulatory regions that code for the nuclear subcomplexes, and add a full copy of the each subcomplex for that complex, thus preserving the 1:1 stoichiometry (one mt-coded copy mitochondrially expressed, one mt-coded copy and two nuclear-coded copies allotopically expressed), but only so long as the mitos continue to work fine, after which the stoichiometry drops to 1:2, which is still better than 0:1... Which, er, doesn't buy us a lot, so I'm mainly throwing it out there for the comic relief value (if you can picture what I'm picturing... If not, the "comic" part might not seem to apply...).

#14 ag24

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Posted 21 March 2005 - 03:44 PM

You're absolutely right, Jay: in theory, the signals that regulate the expression of nuclear genes for mitochondrial proteins could involve the mitochondrial DNA and/or mRNAs themselves. On a scale of biological plausibility, however, this is a long way below plenty of other things that might frustrate other aspects of SENS. Nonetheless, as I've said, alternative solutions to each of the seven deadly things (including this one) are always welcome, and that's why I'll have not only Merril but also Lightowlers, Yagi and Smigrodzki at SENS 2.

#15 John Schloendorn

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Posted 22 March 2005 - 08:40 AM

Prometheus, the formal argument was this:
(1) If we express the mitochondrial genes in the nucleus under the same promoters / regulatory elements that their nuclear 1:1 complex partners naturally use, we would get the proteins in their normal concentrations in the mito.

(2) If all mitochondrial proteins are present in their normal concentrations, with their DNA scrambled, then the behavior of the mito could not be distinguished from a mito that expressed the proteins by itself.

(3) Therefore, allotopic expression should be able to successfully emulate any mitochondiral regulatory mechanism.

A hard as I try, in nothing of what you say can I detect any challenge to 1, 2 or the reasoning that 1+2=3.

The CORR theory implicitly states, and reiterates on concerns I have expressed on previous occasions, that the mitochondrial genome including its transcription, translation and replication is likely to be regulated by the extreme oxidative environment unique to mitochondria.

The "extreme oxidative environment unique to mitochondria" would be preserved according to (1) and (2).

Extrapolating from this premise it is therefore highly probable that *if* the CORR hypothesis turns out to be correct, that the mitochondrial genome and the proteins and enzymes it encodes could behave unpredictably in the dramatically different biochemistry in the nucleus.

Because of (1) and (2) it seems unlikely that, "proteins and enzymes" inside the mito would behave differently. The mitochondrial DNA would, because of being scrambled. Every gene expression-related function would be rescued from the nucleus by (1) and (2). So as Aubrey pointed out, the only way in that the DNA could cause trouble, is if its sequence information acted as a signalling molecule that impacts other things than the expression of its own genes. Despite such functions of genomic DNA sequences being as rare as not known to me, Jay used this argument to challenge (2):

dependent upon the organellor DNA, in part influences or drives the nuclear expression of the nuclear-coded subcomplexes, then the removal of the organellor DNA could disrupt this system

To be precise, dependent on the organellar DNA sequence information (because it could be scrambled). If this were the case, then there would have been no salient evolutionary point in moving the genes of these subcomplexes to the nucleus in the first place. The theory is that this happened precisely because it would protect the genes from the high mutation envionment of the mito. If they had retained regulatory ties in the mitochondrial DNA, that would compromise their expression if mutated, then this protection would never have occured. Therefore the regulation of the nuclear subunits can be expected to be independent from mitochondrial DNA, i.e. (1) should hold.

Aubrey also challenged (2), calling in mRNAs, a signalling function of which seems to me mechanistically more plausible than of the DNA. But since mRNA sequence directly derives from DNA sequence, the same evolutionary counter argument would hold.

Ignoring any form of regulation that may exist in mitochondria could have catastrophic consequences in light of the fact that mitochondria are pivotal to the initiation and execution of apoptosis.

This is a statement, no explanation. Aside, all apoptosis related functions are mediated by nuclear encoded proteins, which according to (2) could function properly.

You state above. "...use the regulation from the nucleus instead that can demonstrably accomplish the same results." What evidence do you have that allows you to say "demonstrably" in such an authoritative fashion?

As I also stated in that post, the evidence is the expression of nuclear genes at levels that would be just right for the mitochondrial genes in every wild-type organism.

What is indisputable, however, is that the possibility exists, no matter how much you may try to convince yourself otherwise, that AE may not work, either for those reasons stated above or for other as yet unexplored factors. For as long as such a possibility exists, it means that the mitochondrial DNA damage problem may not be addressed by SENS.

Indeed, I fully agree. Why don't we find out by trying allotopic expression, instead of faffing about here.

Jay,

I'm not saying that I think that the CORR mechanism has any significant influence on the expression of nuclear-coded genes; it's just speculation. But for those who keep repeating "how often do we have to repeat this?!", as if it were obvious that there might not be a simple wrench the monkies might throw in, you may want to factor in this possibility.

I apologize for the provocation, but this is really the first time I am aware of that you actually appreciate and respond to this objection. So being provocative had its use, sorry if it hurt.

In other words, if we can delete the genes from the mitochondria, without affecting the nuclear expression regulatory mechanism, then AE should be fine, assuming we overcome the other technical hurdles.

And without affecting anything else that might rely on any hypothetical mito-DNA sequence dependent signalling pathways that cannot be short-circuited otherwise. I can't help it, this sounds to me safe enough to be worth a shot.

It would be a shame to spend 6-10 years and $20-$50 million trying to get this to work, only to realize that the mtDNA must remain in the mitochondria for the regulatory mechanisms to work

Clever experimental design can get us that answer MUCH cheaper. I.e. cell culture work only, use of reporter genes in mito-ablated cells, ect...

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Posted 22 March 2005 - 11:15 AM

That the nuclear-coded subcomplexes are produced in sufficient quantities to match the mt-coded subcomplexes is evidence enough that allotopic expression will preserve the 1:1 stoichiometry, and this is the point which you seem to deflect whenever it is raised. It is a strong point, on face value, so I'm curious how you feel about it.


Let's look at what is encoded by the mitochondrial genome:

a) 13 polypeptide genes:
- 7 of 43 subunits of complex I (NADH dehydrogenase 1, 2, 3, 4, 4L, 5, 6)
- 1 of 11 subunits of complex III (cytochrome b)
- 3 of 13 subunits of complex IV (cytochrome oxidase 1, 2, 3)
- 2 of 17 subunits of complex V (ATP synthase 6, 8)

b) 12S and 16S ribose RNA genes

c) 22 tRNA genes

I must admit, that on first examination, (a) makes a pretty compelling case for AE feasibility in respect to regulatory concerns and one may be justified to question my issue with it.

So I should I explain my concerns: whilst there are documented cases of AE being successfully implemented for some mitochondrially encoded genes, due to the hydrophobicity problem it will take a certain amount of clever engineering (e.g. using Aubrey's intein solution or molecular chaperones) to convince the more resistant allotypically expressed proteins to enter and localize themselves into mitochondria without any cytoplasmic mischief. The technical challenge becomes more apparent when considering that cytochrome oxidase I and cytochrome b have never been observed to be expressed in the nucleus of any known species. Furthermore, there appear to be regulatory circuits associated with the unusual redox biochemistry of the mitochondrion.

Why don't we find out by trying allotopic expression, instead of faffing about here.


That would be the optimal solution, if we had a suitably equipped lab at our disposal. :) Unfortunately I am at the mercy of other's data (here is an article on some recent attempts at AE I posted that if you have not already read you may find of relevance).

Nevertheless, I have little doubt that given enough time and resources that AE will become technologically feasible and that if any critical mitochondriocentric regulatory mechanisms emerge they will be accounted for. By the time this happens however, it may be possible to engineer an organelle that converts pyruvate to ATP by an entirely different enzymology and biochemistry, so that ROS are not the major byproduct, or it may be possible to satisfy the cell's need for ATP in an entirely different way.

Thus my concern is ultimately not one of feasibility but of timescale. How long would it take to develop such technologies that enable AE to be implemented and would AE by then become redundant due to superior solutions?

This is why I maintain that it is of vital importance that we identify and pursue alternative escape velocity bridging strategies. One of these is increased rate of mitochondrial DNA repair, another which I will discuss in greater detail shortly is increased rate of mitochondrial turnover.

#17 jaydfox

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Posted 22 March 2005 - 01:04 PM

I'm not saying that I think that the CORR mechanism has any significant influence on the expression of nuclear-coded genes; it's just speculation. But for those who keep repeating "how often do we have to repeat this?!", as if it were obvious that there might not be a simple wrench the monkies might throw in, you may want to factor in this possibility.

I apologize for the provocation, but this is really the first time I am aware of that you actually appreciate and respond to this objection. So being provocative had its use, sorry if it hurt.

(my emphasis)

Au contraire!

From the Mitochondrial DNA damage:

First, expressing the genes in the correct amounts in the first place. Dr. de Grey has covered this:

Regulation: we're lucky there, because every one of the 13 mt-coded proteins is a subunit of a complex that also has nuclear-coded ones in 1:1 stoichiometry. So even if it turns out to be necessary to mimic existing expression patterns really well (and in fact there is some evidence that this is not actually very crucial, e.g. heterozygous deletion of nuclear-coded OXPHOS complex subunits never has a phenotype in flies), we can just slap our coding region into the regulatory DNA of such a nuclear gene.

There was some disagreement over this point at first, but eventually all sides agreed, so I'm satisfied.

I did both appreciate and respond to that objection long ago, and sided with de Grey. In fact, I tried to sum up the stoichiometry argument in my own words.

In layman's terms, if Complex Q has three genes, Qa, Qb, and Qc, then for each Qa that gets produced, there should be 1 Qb and 1 Qc. If I'm interpreting this wrong, then de Grey needs to be more clear.

Okay, with this as a given, if we know that the right amounts of Qa are already being transcribed in the nucleus and transported to where they are needed, then we can assume that all we need to do is transcribe Qb and Qc at the same time. Hence, de Grey assumes that we can insert the coding regions for Qb and Qc, from the mtDNA, into the coding region for Qa in the nuclear genome. When the region coding Qa is transcribed, a copy of Qb and Qc will be transcribed as well. (If I am reading this wrong, then a better explanation is required, at least for us laymen.)

The same logic would hold for the other complexes.


In fact, in that same post, I covered how Prometheus partially yielded on the issue: partially, because he still maintained that there was some signalling system involved that would be disrupted in the process:

However, would you agree that permeability to transcription factors and other signaling molecules is different between the mitochondrial membrane and the nuclear membrane?

And if such permeability is different then it would imply that the regulation of the mitochondrial genome in terms of gene expression activity resulting from said transcription factors and other signaling molecules would also be altered if it were transferred to the nucleus.

Therefore if regulation is altered due to allotopic expression then it has to be accounted for (more work).

(emphasis original)

However, I didn't particularly like his objection, because it related to the expression of mt-coded genes, and we've already covered that the nuclear-coded subunits are already expressed in the correct quantities, and AE would piggyback the mt-coded genes onto those regulatory regions. So if the purpose of the regulatory mechanism within the mitochondria is solely for the regulation of mt-coded genes, then his objection does not pose a problem for your points (1) and (2) adding up to point (3).

This is why I brought up the possibility that the CORR, the regulatory mechanism Prometheus is concerned about, might be influencing nuclear expression (since how else would the nucleus have any reasonable clue as to how many subunits of each complex to produce?)

You say such a system is probably rare:

So as Aubrey pointed out, the only way in that the DNA could cause trouble, is if its sequence information acted as a signalling molecule that impacts other things than the expression of its own genes. Despite such functions of genomic DNA sequences being as rare as not known to me, Jay used this argument to challenge (2)


But we're talking about communication of needed proteins through two semi-impermeable membranes, so such a signalling system is hardly far-fetched. As I said, the nucleus must have some signalling method to have any remotely reasonable clue about how many subunits to produce, so until the nuclear regulatory system is understood, or a signalling system from the mitochondria is experimentally ruled out, it remains a valid and, in my opinion, not exceedingly improbable objection.

That said, I still don't think that the stoichiometry thing is a problem, nor do I really believe that the CORR will turn out to be important enough to screw with AE's success. BUT, I brought up my objection to your "how often ..." remark because you were completely ignoring the possibility that CORR might affect nuclear expression (via mRNAs, or some other unforeseen signalling pathway dependent upon mtDNA information).

Sure, it's a weak argument, and we can break it down, but until it's broken down, it is not obvious that there aren't any monkeys waiting in the periphery to throw in wrenches when you're not looking. Besides, since I didn't object to stoichiometry in the first place, you weren't patronizing me, so I didn't take offense for my own sake. But you were patronizing Prometheus, and I took offense for his sake.

You'll notice that, while it may seem like I'm attacking de Grey's every theory, I'm actually playing both sides. Admittedly more on Prometheus's side, mainly because I agree with him on the nuDNA issue, but also because for anything positive to come out of this, I need to play more to his side when the water's muddy (to make sure de Grey's crossed his t's and dotted his i's), and point out his faults when the water clears. Go back through all my posts, and you'll see I've criticized Prometheus from time to time, or at the least taken de Grey's side and moved on to the next point.

#18 jaydfox

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Posted 22 March 2005 - 01:11 PM

Prometheus posted a broken link. Rather than edit his entry to fix it, I'll just post the correct link.

That would be the optimal solution, if we had a suitably equipped lab at our disposal. :) Unfortunately I am at the mercy of other's data (here is an article on some recent attempts at AE I posted that if you have not already read you may find of relevance).

The link by itself:
http://www.imminst.o...t=20#entry50824

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Posted 23 March 2005 - 02:26 PM

Personally, I am not particular to gambling - and at this stage AE feels like a gamble - and genetic regulation is a mystery that continues to unfold (see Laz's story on the RNA backup genome found in Arabidopsis). I am convinced that it will not be easy to get AE to work, and once we do get it working, we will probably know enough about cell biology and genetic regulation that another solution may present itself. Until I can identify more evidence, that's all I'll say on that topic for the moment.

#20 Lazarus Long

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Posted 23 March 2005 - 06:06 PM

Since you mention the article Prometheus here is the link.

http://www.imminst.o...4&t=5740&hl=&s=

#21

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Posted 26 March 2005 - 06:10 AM

The next important neoSENS and proposed SENS target is the rate of mitochondrial autophagy.

The following leads on from discussion in a thread initiated by Manofsan, titled mitochondrial remediation associated with mitochondrial turnover rates.

Autophagy involves subcellular membrane rearrangements that direct sequestered cell components to become degraded via lysosomal or vacuolar processes. Periodic protein and organelle turnover by autophagy is a vital recycling function in the cell, mitochondria in particular, being turned over approximately every 2 weeks - a process that ensures that mtDNA is being replicated (hence diluted) at a rate that is faster than the rate of damage due to ROS and thus ensures that the number of dysfunctional mitochondria is prevented from accumulating. It has been observed that the rate of autophagy declines with aging and results in dramatic mitochondrial changes including increased variability in morphology and size which can swell to gigantic proportions whilst experiencing a reduction in the number of christae or even complete destruction of the inner membrane. The physiological result invariably leads to reduced ATP and increased ROS production. With the decrease in aerobic capacity, it is likely that the cell becomes increasingly challenged and attempts to compensate by inducing the biogenesis of more mitochondria that in time may also become increasingly dysfunctional in the setting of a reduced rate of autophagy. In contrast, the biogenesis of mitochondria does not seem to be affected by aging the way autophagy is, with mitochondria continuing to proliferate in older cells. The consequence of increased mitochondrial numbers is more ROS byproduct causing oxidative damage to the mitochondria themselves, as well as other cell components including nuclear DNA leading into an escalating cycle that culminates in irreversible cellular damage.

What causes this decrease in the housekeeping role of autophagy? Lysosomal lipofuscin accumulation interferes with lysosomal autophagy and Lon protease, a mitochondrial protease that degrades damaged mitochondrial proteins also becomes less abundant in aged cells. Factors associated with the induction of mitochondrial fission are also reduced, driving the increase of mitochondrial swelling. These down-modulating effects appear to be conserved but manifest at different rates according to the lifespan and developmental stage of the cell.

Not surprisingly, the rate of autophagy becomes increased by caloric restriction (1). In fact some investigators have recently suggested pharmaceutical modulation of metabolism as a stimulator of autophagy to treat aging (2).

Strangely, the merit of increasing the rate of autophagy has been questioned by some members. It is my view that the rate of autophagy could be increased to youthful levels, and that this process would be beneficial so long as it targeted the entire mitochondrial population uniformly and irregardless of functional status (Aubrey hypothesized that the selective advantage that malfunctioning mitochondria gain is via evading autophagy (3)). Admittedly this would not be as efficient as tagging faulty mitochondria but it would substantially lower the levels of mitochondrially produced ROS without needing to discover tagging targets - a process that would require added R&D. Putative mechanisms for increasing autophagy in a non-targeted fashion include RNAi mediated inhibition of TOR (a repressor of autophagosome formation in mammalian cells) and overexpression of Belcin 1 (an autophagosome inducer). TOR is a particularly promising target because it is associated with the nutrient sensing regulatory mechanisms of autophagosome formation (4). Interestingly, TOR knockout mutants in C. elegans increase lifespan (5). UTH1, a mitochondrial protein that appears to be responsible for mitochondrial protein biogenesis, when deleted has been shown to increase cell lifespan (6), thus suggesting an alternative approach of dealing with age-related autophagy reduction: retarding the rate of mitochondrial protein biogenesis.

Consequently there is abundant research scope for conducting relatively simple experiments to test the hypothesis that the rate of mitochondrial autophagy can be increased in order to reduce the quantity of dysfunctional mitochondria and the concentration of ROS, and extend functional cell lifespan. In the context of an alternative to AE, we must be reminded that mitochondria, despite their inherent instability due to their energy producing biochemistry, are the only known cellular component that, due to what is observed from maternal inheritance, can be demonstrated to be potentially immortal whilst maintaining normal function. It is my contention that the health of such virtually immortal mitochondria is maintained in large by a rate of autophagy that more than compensates for mtDNA damage and that since this rate of autophagy already exists in nature it represents the least amount of R&D investment to reproduce it therapeutically.




(1) Experimental Gerontology 38 (2003) 519–527
Ageing-related changes in the in vivo function of rat liver macroautophagy and proteolysis

(2) The International Journal of Biochemistry & Cell Biology 36 (2004) 2392–2404
The role of macroautophagy in the ageing process, anti-ageing intervention and age-associated diseases (attached)

(3) Bioessays, 19, (1997) 161–166
A proposed refinement of the mitochondrial free radical theory of aging.

(4) The International Journal of Biochemistry & Cell Biology 36 (2004) 2445–2462
Regulation and role of autophagy in mammalian cells

(5) Current Opinion in Cell Biology (2005) 17:158–166
The expanding TOR signaling network

(6) FEMS Yeast Research 5 (2004) 133–140
Uth1p: a yeast mitochondrial protein at the crossroads of stress, degradation and cell death FEMS Yeast Research 5 (2004) 133–140

#22 manofsan

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Posted 27 March 2005 - 02:16 AM

In the context of an alternative to AE, we must be reminded that mitochondria, despite their inherent instability due to their energy producing biochemistry, are the only known cellular component that, due to what is observed from maternal inheritance, can be demonstrated to be potentially immortal whilst maintaining normal function. It is my contention that the health of such virtually immortal mitochondria is maintained in large by a rate of autophagy that more than compensates for mtDNA damage


Aha! I was gradually coming to a similar conclusion, although as a result of thinking on a different topic. It was from that previous debate we had on the "immortality" of protozoa/bacteria and how they don't suffer from any limit on number of generations, as our own human cells do, due to the effect of Darwinistic natural selection pressure that weeds out the defective protozoa instead of allowing them survive as duds. I was pondering how the contrastingly sheltered environment within the multicellular organism allows dud cells and dud mitochondria to survive and accumulate, resulting in progressively reduced efficiency of the population as a whole. In the case of mitochondrial autophagy and biogenesis, this would have to be the equivalent of a managed/orchestrated Darwinist selection, just like how a rancher may deliberately cull a herd by killing weak members.

and that since this rate of autophagy already exists in nature it represents the least amount of R&D investment to reproduce it therapeutically


Okay, if you're saying that natural autophagy will eliminate the dud mitos, then great. I'm not familiar with how biogenesis of mitos works, but I always thought existing mitos divide and reproduce copies of themselves, which allows dud mitos to continue their role as spoilers.

But if you've said that lipofuscin buildup eventually interferes with autophagy, and if this buildup is itself at least partially the result of mutation defects (ie. loss of ability by mutant mitos to metabolize routine metabolites), then your prescription of increased rate of autophagy to knock off defects sounds like the simplest solution.

So how much of an increase in the rate of autophagy is necessary? From turnover time of 2 weeks down to 1 week? Why did Mother Nature decide to make it 2 weeks to begin with, instead of 2 days? Is it because overly frequent autophagy uses up too much cellular resources?

#23 manofsan

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Posted 27 March 2005 - 02:19 AM

Is there any way to mathematically model the lifespan of a cell, based on rates of lipofuscin accumulation, and using rate of autophagy as a variable parameter?

#24

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Posted 27 March 2005 - 11:14 AM

I was pondering how the contrastingly sheltered environment within the multicellular organism allows dud cells and dud mitochondria to survive and accumulate, resulting in progressively reduced efficiency of the population as a whole.



"Dud" cells can escape regulatory mechanisms and turn into cancer cells which is a well known and comprehensively characterized process. "Dud" mitochondria according to the theory that Aubrey proposed in his modified version of the mitochondrial free radical theory of aging (see reference in my previous post) manage to survive their functional siblings by merit of their reduced ROS generation. If this is indeed the case, and it may well be the case for at least a subset of zombie (my term for dud) mitochondria, then it would tie in with autophagy being triggered by ROS concentration which is why such mito's manage to evade autophagy. On the other hand we must not discount the general underlying drop in autophagy and ubiquitin associated proteolysis that is occurring in aging cells because the most important factor immediately after genomic stability of a post-mitotic cell is its ability to recycle used proteins and enzymes and remove waste and debris.

So how much of an increase in the rate of autophagy is necessary? From turnover time of 2 weeks down to 1 week? Why did Mother Nature decide to make it 2 weeks to begin with, instead of 2 days? Is it because overly frequent autophagy uses up too much cellular resources?



In my view a return to youthful rates would provide substantial reduction of ROS proportional to how far the cell is gone in being overrun by zombie mitochondria. Remember, we do not know yet whether zombies are being clonaly selected by evading autophagy or are thriving by some other mechanism such as accelerated fission, so the extent of benefits provided to an old cell by an increased rate of autophagy cannot be predicted until we know more about zombie proliferation and the mechanism of selecting a mitochondrion for autophagy.

Another point to bear in mind is that the rate of autophagy must be coupled by the rate of biogenesis (as Kevin pointed out). So if we accelerate the rate of autophagy beyond biogenesis capacity then very soon the cell would run out of mitochondria and ATP production would plummet. I would agree with you that overly frequent autophagy would be selected against due to the excess energy requirements.

Is there any way to mathematically model the lifespan of a cell, based on rates of lipofuscin accumulation, and using rate of autophagy as a variable parameter?



I would say yes and also factor in the number of healthy mitochondria versus zombies, the concentration of ROS and ATP production. I would also invite Jay to do the modeling having shown that he is quite adept at these things ;)

#25 manofsan

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Posted 27 March 2005 - 07:50 PM

You guys have said that rate of autophagy declines with age. Is there any graph of autophagy rate vs age? How does the autophagy rate of a 40-yr-old compare with that of a 10-yr-old, or an infant?

I'm just trying to get a vague idea of the correlation of autophagy rate with overall general health.

Measurements have been taken of old people, showing how those who exercise and eat balanced diets have better muscle tone and overall health than those who don't. Measurements have also been taken showing that those practicing caloric intake restriction are in better health during the latter years of life, as compared to those who don't. You've pointed out that the CR may be stimulating more aggressive recycling within cells. Has anybody then ever measured autophagy rates on people/organisms undergoing caloric restriction?

Does autophagy rate change dynamically or oscillate, perhaps as part of circadian rhythms? Or is it a more steady thing?








Has anybody ever taken any measurements of autophagy rate

#26 Michael

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Posted 29 March 2005 - 12:39 AM

All:

prometheus:The next important neoSENS and proposed SENS target is the rate of mitochondrial autophagy.

What causes this decrease in the housekeeping role of autophagy? Lysosomal lipofuscin accumulation interferes with lysosomal autophagy and Lon protease, a mitochondrial protease that degrades damaged mitochondrial proteins also becomes less abundant in aged cells.

Consequently there is abundant research scope for conducting relatively simple experiments to test the hypothesis that the rate of mitochondrial autophagy can be increased in order to reduce the quantity of dysfunctional mitochondria and the concentration of ROS, and extend functional cell lifespan.

You're bang on here on several fronts, IMO. The key point is that part of the existing SENS platform is to clear out the lipofuscin from lysosomes via targeting xenobiotic lipofuscin-degrading enzymes to the lysosome; as you note, lifofuscin accumulation interferes with lysosomal autophagy and Lon protease, so clearing them out should rejuvenate autophagy.

We have pretty direct experimental evidence of this, as clearing out Abeta restores proteasomal degradation of early tau pathology (4) (NB that Abeta immunization clears out intraneuronal Abeta & that this has now been shown to itself induce cognitive deficits (5)); from the opposite end, inhibition of the proteasoome enhances lipofuscin formatioin (6), implying that a dysfuncional proteasome winds up having it and its targets sent to the lysosome so that a the effects of a dysfunctional proteasome could be partly obviated by a "souped-up" lysosome.

Several other studies similarly show that secondary lysosome or inclusion body formation is increased by proteasome inhibition, again suggesting that lysosomal enhancement will clear out the whole system: polyglutamine tracts in polyQ diseases wind up in the lysosome even though their main degradation pathway is proteasomal (7); early Alzheimer's pathology is characterized by a failure of autophagosome degradation, suggesting that proteasomal autophagy occurs but then autophagosomes fail to fuse with lysosomes (8), also observed when the latter are full of lipofuscin-type gak; the erecent finding of ubiquilin polymorphisms being associated w/AD risk (9) could just be effects on presenilin degradation, but "ubiquilin proteins colocalize with ubiquitin-immunoreactive structures in cells and ... are present within the inner core of aggresomes, which are structures associated with accumulation 3 of misfolded proteins in cells." (10)

prometheus:In the context of an alternative to AE, we must be reminded that mitochondria, despite their inherent instability due to their energy producing biochemistry, are the only known cellular component that, due to what is observed from maternal inheritance, can be demonstrated to be potentially immortal whilst maintaining normal function.


See previous comments on this:

Michael:
Careful. Individual oocyte mt are not necessarily terribly robust, nor are oocytes themselves. The immortality and agelessness of the germ line has been rather misrepresented. One of the main reasons that the germ line is retained intact is that the body is so much more rigorous in apoptosing (neologism!) defective cells in the line -- not that the cells themselves are individually retained pristine. The body selects for healthy ova using atresia, keeping ova quiescent until ovulation, and even more rigorous selection of teh fittest during oogenesis. Also, defective mitochondria in the germ line (I seem to recall -- but perhaps others can provide either documentation or correction) are more likely to lead to flat-out cell death than the same phenomenon in somatic cells.

Result: a woman is born with 1-2 million ovarian follicles; by puberty she has only 300,000 & despite the fact that ovulation per se only leads to the "wastage" of 1 (or a few) eggs per month, only a few hundred remain at menopause.

Really, then, the germline is only immortal/ageless in the sense that the species is: individuals die, but the line passes forward, from generation unto generation.

I now see that Aubrey has elsewhere  given reasons why mt in oocytes also have less damage -- but again, not because the mt are actually, individually more robust:

Aubrey:
It's complicated. (a) When the germ line is rapidly dividing (in early embryogenesis) there may be selection against mutant mitochondria (see below). (b) When it's not dividing (in the oocyte during the mother's life until fertilisation) the host cell has very low energy requirements so is respiring very little, so is producing few mutagenic free radicals. © The mitochondria that get into the oocyte are apparently put through a population bottleneck, which means that if any mutant mitochondria get into a given oocyte then it is virtually guaranteed that lots will; this is good because it will cause that oocyte to fail to ovulate (or to abort very early in embryogenesis) whereas a small number of mutants may not kill the offspring until much later. Kearns-Sayre syndrome is likely to be a case of this last trick not working.


The other thing is that, in Aubrey's MiFRA, the problem with lack of autophagy of "evil" mt is not a failure of autophagy per se, but that they elude teh autophagic machinery by not damaging their membranes ("Survival of the Slowest"). (3, 11-13). Thus, even rejuvenated autophagy will still leave RHH intact as a source of systemic oxidative stress.

Likewise, per RHH, the "evil" mt could be quite immortal and still cause the exact same problem they already do.

-Michael

(1) Experimental Gerontology 38 (2003) 519–527
Ageing-related changes in the in vivo function of rat liver macroautophagy and proteolysis

(2) The International Journal of Biochemistry & Cell Biology 36 (2004) 2392–2404
The role of macroautophagy in the ageing process, anti-ageing intervention and age-associated diseases (attached)

(3) de Grey AD. A proposed refinement of the mitochondrial free radical theory of aging. Bioessays. 1997 Feb;19(2):161-6. Review. PMID: 9046246 [PubMed - indexed for MEDLINE]
http://www.gen.cam.a.../sens/manu7.pdf

4. Oddo S, Billings L, Kesslak JP, Cribbs DH, LaFerla FM.
Abeta immunotherapy leads to clearance of early, but not late,
hyperphosphorylated tau aggregates via the proteasome.
Neuron. 2004 Aug 5;43(3):321-32.
PMID: 15294141 [PubMed - indexed for MEDLINE]

5. Billings LM, Oddo S, Green KN, McGaugh JL, Laferla FM.
Intraneuronal Abeta causes the onset of early Alzheimer's disease-related
cognitive deficits in transgenic mice.
Neuron. 2005 Mar 3;45(5):675-88.
PMID: 15748844 [PubMed - in process]

6. Terman A, Sandberg S.
Proteasome inhibition enhances lipofuscin formation.
Ann N Y Acad Sci. 2002 Nov;973:309-12.
PMID: 12485885 [PubMed - indexed for MEDLINE]

7. Yamada M, Tsuji S, Takahashi H.
Involvement of lysosomes in the pathogenesis of CAG repeat diseases.
Ann Neurol. 2002 Oct;52(4):498-503.
PMID: 12325080 [PubMed - indexed for MEDLINE]

8: Nixon RA, Wegiel J, Kumar A, Yu WH, Peterhoff C, Cataldo A, Cuervo AM.
Extensive involvement of autophagy in Alzheimer disease: an immuno-electron
microscopy study.
J Neuropathol Exp Neurol. 2005 Feb;64(2):113-22.
PMID: 15751225 [PubMed - in process]

9. Bertram L, Hiltunen M, Parkinson M,
Family-based association between Alzheimer's disease and variants in UBQLN1.
N Engl J Med. 2005 Mar 3;352(9):884-94.
PMID: 15745979 [PubMed - indexed for MEDLINE]

10: Massey LK, Mah AL, Ford DL, Miller J, Liang J, Doong H, Monteiro MJ.
Overexpression of ubiquilin decreases ubiquitination and degradation of
presenilin proteins.
J Alzheimers Dis. 2004 Feb;6(1):79-92.
PMID: 15004330 [PubMed - indexed for MEDLINE]

11. de Grey AD. The reductive hotspot hypothesis of mammalian aging: membrane metabolism magnifies mutant mitochondrial mischief. Eur J Biochem. 2002 Apr;269(8):2003-9. Review. PMID: 11985576 [PubMed - indexed for MEDLINE]
http://www.gen.cam.a...sens/mmmmmm.pdf

12. de Grey AD. The mitochondrial free radical theory of aging. 1999; Austin, TX: Landes Bioscience. (ISBN 1-57059-564-X).


13. de Grey ADNJ. A mechanism proposed to explain the rise in oxidative stress during aging. J Anti-Aging Med 1998; 1(1):53-66.
http://www.gen.cam.ac.uk/sens/pmor.pdf v

#27

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Posted 02 April 2005 - 01:53 PM

The key point is that part of the existing SENS platform is to clear out the lipofuscin from lysosomes via targeting xenobiotic lipofuscin-degrading enzymes to the lysosome; as you note, lifofuscin accumulation interferes with lysosomal autophagy and Lon protease, so clearing them out should rejuvenate autophagy



It may be that an endogenous mechanism for reversing lipofuscin accumulation already exists for post-mitotic cells and is inducible (!) as the authors of the attached paper suggest from their studies in crayfish. If that is the case, rather than investigating the expression and efficacy of intracellularly targeted xenobiotic enzymes we should be looking towards stimulating the exocytosis of lipofuscinosomes. Once out of the cell, lipofuscin may be easier to metabolize or target for enzymatic degradation.


(1) Neurobiology of Aging 26 (2005) 69–76
Reversal of a hallmark of brain ageing: lipofuscin accumulation
D.B. Fonseca, M.R.J. Sheehy, N. Blackman, P.M.J. Shelton, A.E.Prior

Attached Files



#28 manofsan

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Posted 02 April 2005 - 07:38 PM

Hiya,
So without having read this crayfish paper yet, it sounds like you're saying that we can more easily expel the lipofuscin without having to go to the trouble of breaking it down locally inside the cell. Hmm, so the only reason why evolution hasn't sharpened our cellular abilities more in this direction is because we already have our kids before the lipofuscin builds up enough?

What is the mechanism by which cells expel chunks/pellets/blobs of stuff? I always thought they had to break stuff down to molecular level and expel out the molecules. I remember from highschool how amoebae surround and evelope their prey and bring them in as a vacuole. Would this expulsion process be sort of the opposite of that? (ie. move the lipofuscin vacuole to the edge of the cell, and then expel it out.)

Is there anything we can take in our diet to assist lysosome formation? Any vitamins or supplementary substances?

#29

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Posted 03 April 2005 - 03:45 AM

What is the mechanism by which cells expel chunks/pellets/blobs of stuff?



The mechanism of vesicle formation and exocytosis is a complex one involving various proteins associated with the assembly, transport and fusion of vesicles with the plasma membrane. Consequently there exist plenty of opportunities for any exocytosis-associated rate-limiting component which, due to age related transcriptional alteration, has been down-regulated resulting in impaired lysosomal activity. If there is a mechanism of lipofuscin removal from the cell, as the "crayfish" (1) paper suggests may exist, then what we perceive as an accumulation of lipofuscin could be attributable to the well characterized decline in lysosomal and proteasome function that occurs with aging (2).

If the regulation of organelle turnover is associated with proteolytic mechanisms, then inducing an overall increase of the rate of these mechanisms to youthful levels may have the doubly beneficial effect of lowering intracellular lipofuscin levels in parallel to decreasing the rate of mitochondrial genome damage and consequent mitochondrial dysfunction.

(1) Neurobiology of Aging 26 (2005) 69–76
Reversal of a hallmark of brain ageing: lipofuscin accumulation
D.B. Fonseca, M.R.J. Sheehy, N. Blackman, P.M.J. Shelton, A.E.Prior

(2) Proteolysis, free radicals, and aging (Attached)
Free Radical Biology and Medicine, Volume 33, Issue 1, 1 July 2002, Pages 29-36
Pamela A. Szweda, Bertrand Friguet and Luke I. Szweda

Attached Files



#30

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Posted 03 April 2005 - 04:01 AM

Thus, even rejuvenated autophagy will still leave RHH intact as a source of systemic oxidative stress.


Yes, provided autophagy is coupled to damaged membranes. However, if this is the case, then it is likely that such mitochondria may not be contributing to oxidative stress directly since they are not extensive ROS producers (if they were they would be damaging their membranes). Therefore, even if these SOS-types continue to propagate in the cell they should not overtly affect the benefits that increased autophagy of normal mitochondria would provide.




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