livescience

Gordian knot conundrum

2008-08-19T01:04:00.010+01:00

The basic question that I try to find an answer to is this:
Is it pure chance that methionine is the universal start amino acid in protein synthesis or is there a logical explanation why this amino acid and not any other (formyl-methionine doesn't count and glutamine or isoleucine are much less efficient at initiation of translation than methionine) is used.

Francis Crick wrote:

"Discussion of the actual amino acids used in the code may not be very profitable. Some less common amino acids, such as cysteine and histidine, would clearly seem to have an advantage because of their chemical reactivity; but whether, say, methionine could be justified in this way seems less obvious."
Crick FH. The origin of the genetic code. J Mol Biol. 1968 Dec;38(3):367-79.

That may very well be true, but I think just opting for the "accident" solution is not a very satisfying answer and to have a logical explanation is better than not having any at all. Of course the structure of the initiator tRNA is the deciding factor in this, but it might have been conceivable that other initiator tRNAs might have been successful. If methionine is nearly always the first amino acid in a protein sequence, but often cleaved off with other N-terminal amino acids, then it might not be essential for the structure/function relation of the protein but still play an important role outside protein synthesis, which is where S-adenosylmethionine (AdoMet) comes in. S-adenosylmethionine is used in transmethylation (of DNA, rRNA, tRNA, mRNA-caps, proteins and lipids), transsulfuration, and aminopropylation (polyamine synthesis of spermidine and spermine). Could the fundamental processes of translation, transmethylation and polyamine synthesis be tethered or is it merely an interesting coincidence, a correlation in the absence of a "cause-and-effect" relation? How could one adress this question? How do you untangle a Gordian knot without using brute force that would wreck the whole system?

Mindgames with SAM-analogs

2008-08-15T19:24:00.018+01:00

I keep on wondering what different S-adenosylmethionine analogs would do to the cellular metabolism and if such molecules might prove useful for investigating experimental leishmaniasis. Obviously, these molecules are likely to be toxic to the host as well as the parasite, but perhaps there might be a way to limit their exposure to macrophages, targeting amstigotes, and thereby reducing the expected undersired side effects to a minimum.

Compared to S-adenosylmethionine:

The following molecule would not be expected to act as a substrate in methylation (of DNA, rRNA, mRNA caps, tRNA, proteins, and phospholipids) or the transfer of propylamine, but not interfere with putrescine synthesis directly as sinefungin might:

This one could be able to catalyse the formation of spermidine and spermine, but lead to ethylation instead of methylation:

Whilst this molecule, if accepted by the respective enzymes as a substrate, could only be used for the transfer of propylamine but not for methylation/ethylation:

On the other hand, the following molecule would only act as a substrate for methylation and not for polyamine synthesis:

Whilst tubericidin is a SAM-analog that has been shown to affect L. donovani promastigotes but treatment has also led to tubericidin-resistant strains emerging:

In addition, attention should be paid to the stereoisomeric form of S-adenosylmethionine (AdoMet), the (Sc, Ss) isomer being the biologically active form, the (Sc, Rs) isomer being a potent inhibitor. (See review by Ronald Bentley).

Another idea that crossed my mind was whether methyl donor supplementation during pregnancy might render C57BL/6 or CBA mice more susceptible to leishmaniasis (similar to the results obtained for agouti mice regarding coat colour [Waterland RA, Jirtle RL. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol. 2003 Aug;23(15):5293-300.]).

S-adenosylmethionine and sinefungin

2008-08-10T02:34:00.024+01:00

There is always the possibility that I am only seeing what I want to see, which is in itself slightly unnerving and the reason why I repeatedly ask for feedback from anyone out there. Whether or not anyone who stumbles across these pages is actually involved in science and could potentially use these ideas is another matter. For the time being, all I can do is to write down my thoughts and hope that some day someone will know what to do with them.

I recently came across an old paper on antileishmanial properties of the S-adenosylmethionine-analog sinefungin:

Nolan LL. Molecular target of the antileishmanial action of sinefungin. Antimicrob Agents Chemother. 1987 Oct;31(10):1542-8.

We'll see if and how things may fit together, but sinefungin-mediated inhibition of polyamine synthesis or DNA methylation/ epigenetics might be possible mechanisms worth considering... In fact, sinefungin looks especially cool because it combines being a SAM/SAH-homologue as well as an ornithine derivative...

S-adenosylmethionine

(taken from "http://www.freepatentsonline.com/7048948-0-large.jpg")

Sinefungin

(taken from "http://www.sigmaaldrich.com/thumb/structureimages/59/s______s8559.gif")

Leishmania donovani was shown to be very sensitive to treatment with sinefungin, with even promastigotes being affected by the treatment. Which makes me start to wonder what might have happened to sinefungin in the pipeline to becoming a widely used antileishmanial drug? Is it possible to devise a delivery method for sinefungin which would target macrophages specifically, either by liposomes or linked to peptides that bind to macrophage receptors?

Bachrach U, Schnur LF, El-On J, Greenblatt CL, Pearlman E, Robert-Gero M, Lederer E. Inhibitory activity of sinefungin and SIBA (5'-deoxy-5'-S-isobutylthio-adenosine) on the growth of promastigotes and amastigotes of different species of Leishmania. FEBS Lett. 1980 Dec 1;121(2):287-91.

Phelouzat MA, Basselin M, Lawrence F, Robert-Gero M. Sinefungin shares AdoMet-uptake system to enter Leishmania donovani promastigotes. Biochem J. 1995 Jan 1;305 (Pt 1):133-7.

This is a tRNA's world, but it would nothing, not one little thing, without an amino acid or a peptide...

2008-08-07T18:18:00.010+01:00

With the print version of my contribution to the Journal of Theoretical Biology made available today, here's a question that has been on my mind for quite some time.

I keep on wondering, in what way the basic components of the genetic code may have evolved in the absence of any translational machinery. In other words, is it possible that precursors to today's tRNAs simply bound to amino acids thus enabling them to accumulate in higher concentrations than would have been possible in the absence of such interactions? tRNA-like molecules that bound to hydrophobic amino acids may have been able to interact with lipids at the liquid/air or at the liquid/solid interphase. With an accumulation of those tRNA-like molecules other tRNA-like molecules that bound to hydrophilic amino acids may have in turn formed aggregates with the hydrophobic amino acid-binding tRNAs via the codon-equivalent regions, leading to the basic dichotomy between N-U-N and N'-A-N' codons and to a microenvironment with favourable conditions for interactions between different species of nucleic and amino acids. The hydrophilic amino acids would have to balance the charge inequalities leading to basic and acidic amino acids landing close codon proximity. The next step would be that RNA molecules with catalytic activity bound these adaptor RNAs at strategic positions and the attached amino acids started to be a part if the catalytic process. Finally, the translational machinery would have evolved and the code would have continued to change with it. Some RNA-amino acid pairings would have been thrown out of the race and new ones joined the process at this stage. A drive to reduce codon ambiguity and to minimize errors in translation are likely to be two important factors in the evolution of the code, but some initial rules laid down by the pre-translation system were already in place before the era of large-scale protein synthesis.

I am thankful for any comments you might care to send my way.

If you are interested in more literature on the genetic code, I can recommend:

Nirenberg, MW, Matthaei, JH, Jones, OW. An intermediate in the biosynthesis of polyphenylalanine directed by synthetic template RNA. Proc Natl Acad Sci U S A. 1962 Jan 15;48:104-9.

Woese, CR. On the evolution of the genetic code. Proc Natl Acad Sci U S A. 1965 Dec;54(6):1546-52.

Crick, FH. The origin of the genetic code. J Mol Biol. 1968 Dec;38(3):367-79.

Orgel, LE. Evolution of the genetic apparatus. J Mol Biol. 1968 Dec;38(3):381-93.

Wong, JT. A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A. 1975 May;72(5):1909-12.

Taylor, FJ, Coates, D. The code within the codons. Biosystems. 1989;22(3):177-87.

Szathmáry, E. The origin of the genetic code: amino acids as cofactors in an RNA world. Trends in Genetics. 1999 June;15(6): 223-9.

Massey, SE. A sequential "2-1-3" model of genetic code evolution that explains codon constraints. J Mol Evol. 2006 Jun;62(6):809-10. Epub 2006 Apr 11.

SOCS3 expression in classically activated rat macrophages impairs arginase expression

2008-07-31T12:32:00.014+01:00

Well, after nearly dismissing my ideas on SOCS and leishmaniasis in my last post, I came across this interesting paper by Liu and colleagues that rekindled the old flame a bit. Published in the Journal of Immunology in May 2008, they show that SOCS3 knockdown by RNA interference in classically activated rat macrophages coincided with an upregulation of alternative activation makers such as arginase.

Liu Y, Stewart KN, Bishop E, Marek CJ, Kluth DC, Rees AJ, Wilson HM. Unique expression of suppressor of cytokine signaling 3 is essential for classical macrophage activation in rodents in vitro and in vivo. J Immunol. 2008 May 1;180(9):6270-8.

This brings me back to my question: would SOCS3 shut down STAT3 (IL-6-induced arginase) and IRS-2 signalling and SOCS5 shut down STAT6 (IL-4-induced arginase) signalling so that arginase activity would drop to levels below those able to support parasite proliferation? What role does S-adenosylmethionine play in all this - control of SOCS expression via DNA methylation versus polyamine synthesis of spermine and spermidine? Untangling all this experimentally will no doubt be a bit tricky, because the effects of SOCS on macrophages should be kept separate from effects of SOCS on other cell types.

I would suggest to start in vitro and to compare the effects of RNAi mediated by siRNA against SOCS1, SOCS3, SOCS5, DNA (cytosine-5-)-methyltransferase 1, DNA (cytosine-5-)-methyltransferase 3 alpha, DNA (cytosine-5-)-methyltransferase 3 beta, S-adenosylmethionine synthetase, ornithine decarboxylase, S-adenosylmethionine decarboxylase, spermidine synthase and spermine synthase in respect to parasite development. An interesting side project would be to find out whether or not culturing macrophages in the presence of increased S-adenosylmethionine concentrations leads to higher parasite proliferation. The in vivo experiments that spring to mind are inducible macrophage-specific expression of transgenes: either SOCS-specific shRNA in resistant mice or SOCS in susceptible mice. Whilst it would be preferable if the gene expression was not leaky, I think my wish list is getting slightly too demanding, but if anyone out there thinks that some of these ideas are useful and has the means to set up the necessary experiments please feel welcome to do so. I believe that the sooner the scientific community can come up with new affordable drugs against this neglected tropical disease the better. I would argue the best way to achieve this is through cooperation rather than competition. As always, feedback is greatly appreciated.

Arginase and ageing - rethinking SAM

2008-05-26T18:14:00.006+01:00

Age-Related Alteration of Arginase Activity Impacts on Severity of Leishmaniasis
is a very exciting paper, so convincing in fact that it makes me question whether my hypothesis on SAM is of any use at all to explain susceptibility to leishmaniasis. Arginase activity has been shown time and time again to be crucial to parasite proliferation, but I always wondered whether there was some proverbial elephant standing in the room that no-one mentioned. The SAM story was meant to complement and expand the arginase part and I still believe that with its dual role in polyamine synthesis and regulation of gene expression amongst others, SAM might still be shown to play a role in this experimental system.

At first, I thought that by changes in DNA methylation SOCS expression would be altered affecting cell signalling and arginase activity in host macrophages. This may still be the case, but maybe it would be better to focus on the polyamine synthesis aspect at first. If antimony treatment should deplete SAM levels this could be investigated by incubating macrophage cultures with antimony and measure polyamine levels by thin layer chromatography as carried out by Modolell and colleagues.

Letting go - now back to Leishmania

2008-05-09T17:43:00.006+01:00

Letting go is hard to do, especially when you have fought tooth and nail to get your point across and went through some crazy times. I recently attended the "God Be in My Head" event at the Dana Centre, where a panel chaired by Colin Blakemore discussed the possibility of so-called "God spots" in the brain, and although epilepsy and schizzophrenia were mentioned as possible links to abstract thinking, creativity and spiritual experience, I was surprised to observe that no-one at the event mentioned mania, which seems to me to lie at the intersection between the two other states of mind. One of the best suggestions of the evening was the idea to analyse the brain activity of problem-solving scientists using functional MRI and to try to compare the results to the brain scans of nuns praying or monks meditating. I like it even though I am getting a bit tired of functional MRI papers, but somehow I don't see that experiment being carried out any time soon, the eureka experience and phenomena such as calculation-induced halucinations are science's dirty little secrets and I doubt whether scientists really are prepared to address these issues.

At any rate, I'm digressing, whilst it is fun to rejoin the scientific debate and to watch my representation of the genetic code climb the "google charts", I have to let go of certain ideas and redirect my focus on my PhD. Consequently, I find myself thinking more and more about Leishmania these days. Given that S-adenosyl methionine (SAM) is involved in a number of different cellular processes possibly affecting the replication of intracellular parasites, how would it be possible to differentiate the effects of the individual processes? The ones I am particularly interested in are polyamine synthesis and DNA methylation. Would it be enough to add radiolabelled SAM to infected cells and to try to see where the marked methyl group might end up? Is there radiolabelled SAM available in which the non-methyl carbon atoms are 14C, making the substance useful in tracking polyamines? Whilst I would try to focus on in vitro experiments at first keeping things as simple as possible, I also wonder what in vivo experiments might look like. What effect might adding or depleting SAM have in vivo? What about methylthioadenosine (MTA), a product of the SAM catabolism that arises after the polyamine synthesis step? How could the effect of SAM derivatives be untangled from possible changes to cytokine production?

Too many questions for me to answer...

Nearly there...

2008-05-02T13:27:00.022+01:00

Finally, the "Journal of Theoretical Biology" accepted my manuscript for publication as a letter to the editor. The unedited version of the article can be found ahead of print online at

http://dx.doi.org/10.1016/j.jtbi.2008.04.028.

What a relief. I know it's just one little paper and the impact factor of the journal could be higher, but for some reason this paper is incredibly important to me. I don't know if I have made a huge fool of myself or not, but it's too late anyway. I tried to keep the article as short as possible and did not include any acknowledgements, but of course I would not have been able to persevere in this ridiculous struggle had I not had the support of some incredible people along the way. I don't know whether mRNA-tRNA interaction occurs in a 2-1-2-3 way, but I find the sheer oddness of a language that starts with the middle instead of the beginning of an information unit exciting and cannot get the picture of tRNA-precursor molecules forming aggregates with the second codon base acting as an anchor out of my head. Imagine the message
"hteatsiksontosmcuhotseewahtonoenhsayteseenubtottihnwkhtanoonheaysetthuogthaobutthtawihcehvreyobdsyese."
being translated as "thetaskisnotsomuchtoseewhatnoonehasyetseenbuttothinkwhatnoonehasyetthoughtaboutthatwhicheverybodysees." and finally for the information to "fold" into the beautiful quote: "The task is not so much to see what no one has yet seen but to think what no one has yet thought, about that which everybody sees."

Of course if the interaction between mRNA and tRNA occurred in a 1-2-3-way, the importance of the second base might be explained by a longer interval spent reading the base, so the order would roughly be 1-2-2-3. If the binding of codon and anticodon happened in such a way that all three bases bound simultaneously, then the base in the middle might spend the longest time bound to its cognate because the bases 5' and 3' of it would act as a sort of buffer (like velcro, the middle bit usually the hardest to get off first).

With possible closure on the rearrangement of the genetic code in sight, I wonder if somebody else might pick up on the methionine story. Perhaps one group might try to engineer an organism that uses an initiator-tRNA charged with isoleucine, valine, threonine or homocysteine instead of methionine and report on what the resulting phenotype might be...

But all of this has merely been a side project, the biggest reward for me would be if my initial hypothesis about the involvement of S-adenosylmethionine in determining resistance or susceptibility in experimental leishmaniasis, might prove to be useful.

Early nerdcore

2008-04-27T12:35:00.012+01:00

Over at the excellent www.biology-blog.com I came across this wonderful video mixing free love and protein synthesis (trippy translation). I want more of this stuff: "The Knife" in charge of TLR signalling, "Roisin Murphy" could sing about MHC class I presentation whilst "Hot Chip" serenade MHC class II, cathepsins and lysosomes and "Portishead" would present apoptosis like no-one has ever done before...

Science classes would never be the same again...

Here's a brilliant clip I came across in 2009: Carl Sagan rocks!

SAM and polyamines

2007-11-14T13:13:00.007Z

Just to emphasise that methylation is not the only trick up SAM's sleeve, it's also involved in the production of the polyamines. Spermidine and spermine are synthesised using the putrescine backbone derived from arginine:

arginine -(arginase)-> ornithine -(ornithine decarboxylase)-> putrescine

S-adenosyl methionine -(S-adenosyl methionine decarboxylase)-> decarboxylated SAM

putrescine + decarboxylated SAM -(spermidine synthetase)-> spermidine

spermidine + decarboxylated SAM -(spermine synthetase)-> spermine

Polyamines are important for balancing the negative charge of nucleic acids amongst other things and are therefore essential in all cells and especially in cells undergoing proliferation. For instance, in my preferred animal model, polyamines have been shown to be key factors controlling Leishmania major proliferation.

Selenocysteine and Pyrrolysine

2007-09-23T23:16:00.001+01:00

More a postscriptum than a real post, but isn't it amazing, how selenocysteine and pyrrolysine, the 21st and 22nd proteinaceous amino acids, fit into the 2-1-3 genetic code scheme?

Selenocysteine (Sec / U): mRNA codon UGA. Related to cysteine, is in the same subgroup as tryptophane and cysteine and is in the same group as serine.

Pyrrolysine (Pyl / O): mRNA codon UAG. Consisting of a lysine backbone and a pyrrol ring containing a pi electron pair just as in tyrosine, histidine, tryptophane and phenylalanine, is in the same subgroup as tyrosine, and in the same group as histidine and lysine.

It's almost spooky, don't you think?

A number of genetic code diagrams

2007-09-10T15:22:00.007+01:00

Bresch and Hausmann took Crick's matrix table of the genetic code, i.e. the decoding instructions of translation in which the information stored in the sequence of nucleic acids is transferred to the sequence of amino acids, and were the first to publish a circular diagram of the code.

However, the arrangements of codon bases is in some way arbitrary. The repetitive motif UCAG separates bases according to size (pyrimidine bases U and C, purine bases A and G fall together), groups the inosine-binding bases U, C and A together and allows for the amino acids methionine and isoleucine to be listed in separate groups. When adhering to a constant string of bases, the UCAG motif offers a higher degree of packing of the code as demonstrated by Serguei Lenski on his homepage, which contains a mathematical approach to packing of the genetic code. His results indicate that listing codons in the order of 2-1-3 and retaining the UCAG motif offers an optimal amount of packing, but that does not mean that there aren't any other ways to represent the code. The physicist Yurij Rumer (1901-1985) preferred the motif CGUA for various reasons, placing more emphasis on the strength of bonds formed between the cognate bases (C-G forming three hydrogen bonds, A-U forming only two, see D. A. Semenov's paper if you have no access Rumer's original publication in Russian: Rumer IuB. [Codon systematization in the genetic code] Dokl Akad Nauk SSSR. 1966 Apr 21;167(6):1393-4.).

I believe that the motif AGCU (or UCGA) when viewed from a circular perspective offers a happy compromise between the two. Furthermore, by placing the second codon base at the centre of the diagram it becomes possible to unite the codons of leucine, serine, arginine and stop and to see codons cluster into groups according to the chemical properties of the respective amino acid: M, I, V, L, F are all hydrophobic; K, N, D, E, Q, H, Y are all hydrophilic, T, S and hydoxy-proline carry hydroxyl groups whilst A is structurally related to S; the last group comprises amino acids at the extremes from the smallest G to the largest W, the most hydrophilic R to the hydrophobe C, however S is structurally related to C and C, U, S and G can be converted into one another biosynthetically. In addition, S is a substrate for W synthesis (for more information on the role of biosynthetic pathways in shaping the genetic code, I would recommend: Wong JT. A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A. 1975 May;72(5):1909-12.). Finally, the rare genetically encoded amino acid pyrrolysine (O) found in members of the Methanosarcinaceae family of archeaea is a lysine derivative contianing a pyrrol ring, which reminds me of the structures found in the amino acids W, Y and H and somehow fits neatly into the scheme with proximity to K, H, Y and W.

The 3D model of the genetic code along 2-1-3 rules allows a number of projections that represent distorted "maps" of the code. In this post are three projections of the standard code as well as four diagrams for variants of the standard code, found in mitochondria, mycoplasma, cilliates and green algae, although these graphs are oversimplified. For the recently evolved genetic code in Candida where an L codon has changed into an S codon it is not possible to combine the codons in a way that allows for all codons to be grouped together according to their respective amino acid. Even so, one can follow the small changes that make such a big difference, with the bases 1 and 2 both remaining pyrimidines in the genetic code of Candida. For details of these and more variants of the standard code I would like to draw your attention to the taxonomy browser at NCBI. For more of my thoughts on the genetic code you can follow this link to blog.rna-game.org. Thank you.

Standard code: 1

Standard code: 2

Standard code: 3

Vertebrate Mitochondria Code

Invertebrate Mitochondria Code

Yeast Mitochonria Code
(Codons CGA and CGC absent)

Mycoplasma

Cilliates and green algae

Cilliates

Another model

2007-08-23T23:54:00.009+01:00

When I set out to do realign the genetic code, it was almost like playing a game of sudoku. The intention was to see if there was a way to simplify the way the code was represented as an answer to some who claimed that the code was too complex to have evolved on its own. Now that it looks so shockingly simple, some might claim that it is so perfectly simple that only a designer could have made it. This I cannot agree with, it's not perfect whatever that may mean, but simple physical and chemical forces appear to sufficiently explain the evolution of the code based on the material that was available at the time. There are countless little and big influences that made me have a go at the code, but Tetris and Calder are sure to have played a role in this...

I would suggest that a three-dimensional representation would be an even better model. All you need if you want to build a model yourself at home is a couple of molecular building block kits. Make sure that you have blocks that allow for tetra- and penta-valent binding (e.g. carbon atoms in normal and transitional state).

Start with a tetravalent-binding block at the centre to get the tetrahedrical base, use the binding elements to represent A, G, C, and U and continue with the pentavalent-binding blocks until you reach the level of amino acids where you then can use different coloured blocks to symbolise the individual amino acids.

This approach lets you bring amino acid codons that seemed at opposite poles into close proximity (e.g. K and R or F and Y). I know, it may look confusing to begin with, but it adds another layer of information. The categories for grouping the amino acid codons on www.rna-game.org are after all somewhat subjective (non-polar, transitional, special, polar), maybe there are other categories that should be used to group the codons.

I guess what I mean to say is, have fun. Of course sincerety and truth remain the essence of science and empirical and rational thinking are the backbone of this line of work, but intuition and a sense of wonder are crucial elements as well.

The graphs on www.rna-game.org and blog.rna-game.org are distorted two-dimensional maps of the genetic code in three dimensions as shown above.

Leishmania, inbred strains of mice, SOCS and DNA hypermethylation

2007-08-18T10:21:00.013+01:00

While most strains of inbred mice are able to control and largely eliminate parasitic L. major, BALB/c and DBA/2 mice develop non-healing lesions [1]. It has been clearly established that Th1-type cytokines such as IFN‑γ offer protection to the intracellular parasite, while Th2-type cytokines such as IL‑4 are linked to susceptibility [2-5]. Macrophages play a dual role in Leishmania infection because they are part of the innate immune system but also are the primary host cells for the parasite. It has been demonstrated that IFN‑γ drives macrophages to acquire the classically activated phenotype characterised by iNOS expression in murine cells, whereas IL‑4 stimulation of macrophages is recognised to drive them to an alternative state of activation typically expressing the enzyme arginase1 [6-8]. The activity of arginase1 has been correlated to parasite proliferation [9;10]. Arginase breaks down arginine to produce urea and ornithine, which then can be metabolised further to proline (a possible source of energy and a building block for protein synthesis in parasites), polyamines (DNA packaging) and possibly nucleotide biosynthesis (ornithine to glutamine to purine and/or ornithine via ornithine transcarbamoylase to pyrimidine bases?), all of which could or do act as nutrients for the proliferating parasite. (see: "http://www.nature.com/nri/journal/v2/n7/full/nri843.html")

In mice, iNOS plays a very important role in controlling the disease (humans have evolved other mechanisms of Th1 mediation, e.g. Vitamin D receptor-mediated mechanisms [11], which seem to be easily available to sun-exposed humans compared to nocturnal mice). Normally resistant mice that have been made deficient in iNOS become susceptible to L. major, while phox-deficient mice are able to control the disease, implying different modes of action by reactive oxygen species (ROS) generated by phox and reactive nitrogen intermediates (RNI) such as NO [12]. iNOS competes with arginase for the same substrate, arginine. But unlike arginase, iNOS produces citrulline and the radical NO which is not further metabolised to produce a source of energy, building blocks or nucleotide synthesis. In fact, a complex inter-regulatory network of competition and inhibition exists between arginase and iNOS on an enzymatic level (iNOS produces NOHA in the first step to NO catalysis, which acts as an inhibitor to arginase1 [13]) as well as on the complex cross-regulation of cytokines that induce these enzymes (reviewed elsewhere and in [14-16]).

The balance between these two enzymes is therefore of crucial importance to the parasite, with the activity leading to proliferation and the other to parasite killing.

I propose that the observed differences between the healing and non-healing strains of mice is due to different levels of suppression of the arginase-inducing cytokine signalling. In particular, I hypothesise that differences in SOCS expression, possibly due to DNA hypermethylation, are central elements controlling the outcome of the disease. The role of S-adenosylmethionine in this model system may offer clues to possible drug candidates not necessarily limited to parasitic diseases.

SOCS

SOCS proteins are a relatively recently discovered group of at least eight intracellular proteins that act as negative regulators of cell signalling [17-19]. Their SH2 domain binds to phosphorylated Tyrosine (pY) residues and disrupts cell signalling involving Tyrosine kinases, while their SOCS box-domain has been shown to have ubiquitin E3 ligase activity [20-24]. One major route for poly-ubiquitinated cytosolic proteins is their degradation by the proteasome while mono- or multi-ubiquitination of membrane proteins leads to the internalisation or even lysosomal degradation of these proteins [25]. (see: "http://www.nature.com/nri/journal/v2/n6/full/nri818.html")

Many major cytokine receptors such as IFN‑γR, and IL‑4R do not have an inherent Tyrosine kinase activity themselves, but ligand-induced dimerisation leads to recruitment and activation of Tyrosine kinases of the JAK family which in turn lead to the phosphorylation and activation of STAT transcription factors [19]. Tyrosine phosphorylation is a widely used messaging system for short-lived, reversible and regulated signal transduction. In addition to cytokines such as IFN‑γ and IL‑4, many other receptors use phosphorylation of Tyrosine residues as a signal. They either act directly as Tyrosine kinases themselves, (the insulin receptor phosphorylating itself and its substrates IRS1 and IRS2 see review by Youngren accepted for publication in CMLS 2007), or recruit Tyrosine kinases to phosphorylate downstream signalling adapters for them. Phosphorylation of proteins can also be used to facilitate the recruitment of individual components into larger signalling complexes held together and assembled in the correct order by pY – SH2 domain binding (for instance, it may be possible that phosphorylation of the TLR leads to its recruitment into complexes involving other signalling molecules such as PI3 kinases, adenylate cyclases or G-proteins or other proteins with kinase or lipase activity, not to mention other substrates [26;27]).

Members of the SOCS family (CIS and SOCS1 to SOCS7) have distinct but possibly also overlapping functions due to differences in expression (quantity, time, location) and affinity to their respective different target proteins not all of which have been characterised as yet. Many cytokine signals induce SOCS expression resulting in negative feedback either limiting the intensity/duration of the initial signal (IFN‑γ inducing SOCS1, which disrupts IFN‑γ signalling via STAT1) or rendering cells unresponsive to following stimuli (IFN‑γ-induced SOCS1 blocking IL‑4 signalling via STAT6) [19;28]. These proteins can confer protective as well as destructive effects on cell and tissue function/physiology: over-expression of SOCS1 in pancreatic cells can protect β-islet cells from IFN‑α/β-induced cell death (possible protection from type-I diabetes) [29], but over-expression of SOCS1 in muscle tissue can render the cells insulin-resistant (possibly leading to type-II diabetes) [30].

Generating knockout animals with disrupted SOCS genes has proven difficult in some cases, due to embryonic lethality for SOCS1 and SOCS3 expression. In the case of SOCS1, it was possible to obtain mice with SOCS1-deficient animals if they also were IFN‑γ-deficient [31-33]. SOCS3-deficient mice died because of placental defects [34].

Because they are induced by cytokines such as IL‑4 and IFN‑γ, it should come as no surprise that SOCS proteins are differentially expressed in different types of T helper cells, as indeed they are, playing an important regulatory role in the development of different cell types [35].

Toll-like receptors have also been shown to up-regulate SOCS proteins either directly through cell signalling involving TIR domain-containing adapter protein or indirectly through auto- and paracrine actions of induced cytokine production (such as type I interferon, IL‑6 and TNF‑α) [36] while endotoxin tolerance was not observed in SOCS1-deficient mice [37].

Recently, it had been shown that certain forms of cancer had switched the expression of some or many SOCS genes off [38-47]. The absence of the negative feedback mechanism allowed them to receive continuous and uninhibited growth signals via cytokine receptors such as IL‑6 (e.g. prostate cancer). Some breast cancer cell lines expressed high levels of a number of SOCS, but these were later shown to have a mutation in a STAT, which meant that the cells continued to receive growth signals in the absence of any external stimulus and despite the presence of SOCS proteins [41]. In fact it might be speculated that shutting down other cytokine signalling pathways ensured that the cells remained in an incompletely differentiated state and contributed to the malignancy. Where cancer cells had down-regulated the transcription of SOCS genes, it was often found that this had been achieved by hypermethylation of the relevant promoter sequence.

Mice

To my knowledge, no one has looked specifically for differences in SOCS expression in mice with the aim of comparing differences between strains of inbred mice. However, the following observations seem to suggest an involvement of SOCS:

1) The order of resistance to L. major infections from most resistant to most susceptible strain of mouse is: 1) CBA, 2) C57BL/6, 3) DBA/2 and BALB/c [1]. This is exactly mirroring their respective risks to succumb to obesity/type II diabetes-associated pathology such as atherosclerosis: 1) CBA, 2) C57BL/6, 3) DBA/2 and BALB/c (according to the Jackson laboratory’s website: http://jaxmice.jax.org/info/ready.html, http://jaxmice.jax.org/strain/000654_2.html, http://jaxmice.jax.org/strain/000651.html, http://www.informatics.jax.org/external/festing/mouse/docs/DBA.shtml ). It is also worth noting that males seem to have an increased risk to develop atherosclerosis/type II diabetes/obesity whilst being slightly better at coping with Leishmania infections.

2) Leishmaniases are diseases affecting the young particularly harshly (in mice as well as in man, resistance seems to increase with age, or expressed another way the risk of disease drops with age) [48], whereas the risk of developing type II diabetes mellitus increases the older mice or humans get [49;50]. It was recently shown that SOCS expression increases in lymphocytes and granulocytes as well as the rat hypothalamus a consequence of ageing [51-54]. However, this phenomenon has not been shown directly for macrophages yet.

3) It was shown that BALB/c mice remained susceptible to certain infections with certain subtypes of L. major even when the major Th2 cytokine IL‑4 was knocked out [2]. This was probably due to other cytokines such as IL‑13 and IL‑6 being able to take over some of the functions performed by IL‑4 under normal conditions and to induce arginase in infected and bystander macrophages [55].

4) It was observed that there is an early immune response to L. major in susceptible mice producing an early wave of IL‑4 the intensity and kinetics of which suggested a recall/memory response of pre-existing T cells rather than freshly primed and differentiated T lymphocytes [56;57]. A T cell population with a specific TCRαβ usage was shown to react to Leishmania LACK antigen and to be the source of the early wave of IL‑4. The population probably arose primed by gut antigen and deletion of these T cells prevented early IL‑4 release and prevented the development of non-healing lesions [58-60]. However, it was shown that early IL‑4 could be detected equally in resistant mice such as C57BL/6 and therefore did not predict the susceptibility to Leishmania infections [61]. This argues for an active switch from Th2 response to Th1 response that is not being carried out in BALB/c mice.

5) Whilst it has often been said that BALB/c are generally more Th2-prone than C57BL/6 mice and Th2 responses have been shown to be crucial to resistance against the filarial nematode Litomosoides sigmodontis, BALB/c are susceptible to the infection while C57BL/6 are resistant [62;63]. Again gender seemed to have an effect on the outcome of the disease, with higher protection observed in males [62]. Mirroring results in L. major infection, BALB/c mice deficient in IL‑4 remained susceptible [63]. However, IL‑4 is required to prevent filarial nematode development in resistant mice, arguing that IL‑4 is necessary but not sufficient and that the nematode can develop in susceptible mice in-spite of IL‑4 present.

6) TLR have been implicated in the response to Leishmania either directly in vitro (TLR2 recognising Leishmania LPG und resulting in SOCS expression, TLR3 recognising unidentified PAMP in Leishmania which may be gRNA double-stranded RNA) [64;65] or indirectly in vivo (TLR4-deficient mice on a resistant background controlling the disease less efficiently: possible TLR4 activators: hyaluronan, heat-shock proteins, microbial PAMP due to unintentional co-infection, or as–yet unidentified Leishmania PAMP [66], involvement of MyD88 [64;67;68]).

7) Infection of mice on the BALB/c background with L. mexicana and promastigote-secreted gel (PSG) gave following results. Addition of PSG to infections of wild-type BALB/c exacerbated the course of the disease. Adding PSG to infections of IL‑4-deficient BALB/c was beneficial to the mice for a short while (smaller lesions) but lesions were nonhealing all the same. Adding PSG to infections of BALB/c mice deficient in T1/ST2 showed no significant difference to the courses of infection in the absence of PSG (Matthew Rogers, personal communication). I interpret these results in such a way that PSG multiplies the effects of the prevailing cytokine environment in an at least partially T1/ST2-dependent way.

8) T1/ST2 is the receptor for IL‑33 [69-71] and has been shown to be critical for LPS tolerance in vivo, acting as a negative regulator of TLR signalling [72;73], possibly functioning by inducing SOCS expression.

9) The current method to treat leishmaniases is heavily reliant on preparations of the heavy metal antimony (Sb, drugs: pentostam, stiboglucanate) a member of the same group of elements as arsenic (As). (see: "http://upload.wikimedia.org/wikipedia/commons/thumb/f/fe/Circular_form_of_periodic_table.svg/400px-Circular_form_of_periodic_table.svg.png")

The mechanism of action is not entirely clear although or (paradoxically perhaps) because antimony had been used as a medicine since antiquity and in its modern preparation since the first half of the 20^th century. Based on observations in responses to helminthic infections, it had been speculated that antimony could interfere with the sugar metabolism of the parasite [74], but promastigotes do seem to be able to survive culture in the presence of antimony. Apart from applications in anti-leishmanial chemotherapy very little is know about the pharmacological properties of antimony. However, arsenic, its smaller and more famous cousin, has been used in a number of pharmacological studies. It ranks highly in the lists of toxic agents and chronic low-dose arsenic exposure has been linked to a number of cancers. However, the mechanism of carcinogenesis is not fully understood yet. It is a known carcinogen yet it is not a potent mutagen in itself. The lack of any prominent signal transduction pathway and animal model for arsenic carcinogenesis has led to the belief that it acts as an epigenetic carcinogen. It was only recently shown that long-term low-dose exposure of arsenic leads to a reduction in intracellular S-adenosylmethionine (SAM) and a loss of DNA methylation [75]. This is most likely due to methylation of arsenic depleting intracellular levels of SAM and an observed repression of DNA methyltransferases DNMT1 and DNMT3A gene expression. (see: "www.ehponline.org/members/2005/8600/8600.html" and "www-ermm.cbcu.cam.ac.uk")

Model

The model I propose consists of the following elements:

Parasite survival is dependant on the macrophage actively providing Leishmania with nutrients. One, if not the main, pathway for the parasite to obtain nutrients is via arginase which acts in competition with iNOS in mouse macrophages. (Arginine depletion in the environment as a result of increased arginase activity further exacerbates the disease by preventing T cells from functioning properly.)

It is not so much the cytotoxic activity of NO radicals that prove fatal to the parasite, but the inhibition of arginase. Arginase and iNOS compete not only for the same substrate, but iNOS produces an inhibitor of arginase (NOHA) as an intermediate product of its catalysis of arginine to citrulline and NO. In addition, the two enzymes are induced by cytokines that have inhibitory/regulatory effects on the other cytokine (IFN‑γ induces iNOS, IL‑4 induces arginase, IFN‑γ inhibits effects of IL‑4 signalling and vice versa). NO leads to TNF‑α expression and therefore indirectly to increased SOCS expression, adding another layer of regulation to this network. IFN‑γ signalling leads to STAT1 phosphorylation and activation, which drives transcription of IFN‑γ-responsive genes, including SOCS1 and SOCS3, in macrophages. IL‑4 signalling most commonly involves phosphorylation and activation of STAT6, leading to increased expression of genes such as of SOCS1 and SOCS2 in macrophages. The different SOCS have different affinities for their target proteins, at limiting concentrations SOCS may therefore inhibit one type of cell signalling, but at higher concentrations inhibit additional signalling pathways that were only “second choice”. Cells may thus limit their ability to be affected by stimuli arriving after the first cell signalling event in a highly receptor-specific way and integrate various signals to produce a qualitatively nuanced response.

The main point for macrophages and the immune system seems to be overcoming the initial IL‑4 response of pre-primed T cells and shut down the signalling pathways leading to arginase expression. This can happen either by TLR activation or other mechanisms of innate immunity. Difference in SOCS expression in macrophages would be an obvious choice to look at. However, SOCS expression in macrophages might be downstream of differential SOCS expression in T cells. Once the adequate kind of SOCS expression has been established in the host cells (type of SOCS, quantity, timing, location, resulting from and affecting the immune response via various ways of regulation and feedback) the cells do not receive the orders to produce arginase and stop to provide the parasite with nutrients. The result is partly direct killing of parasites by cytotoxic mechanisms (radicals, etc), but perhaps even more importantly parasitic “death by neglect” (albeit an active, highly regulated and maintained form of neglect). This hypothesis is supported by the observation that SOCS1-deficient or impaired (heterozygous) mice show increased susceptibility to L. major infection [76] and L. donovani, L. amazonensis and L. major all induce various amounts of SOCS3 [77]. The expression of SOCS3 had been interpreted by the authors as a possible mechanism of suppression of activation, however the difference between classical and alternative activation had not been addressed. The authors seemed to suggest that SOCS3 expression may have beneficial effects on parasite survival, which might very well be the case in a Th1 environment, but under Th2 conditions SOCS activity might lead to the opposite outcome. De Veer and colleagues also showed TLR-induced SOCS3 expression, but I am unaware of any work following on from this demonstrating host-protective, parasite-killing effects of SOCS3 [64] which leaves the role of SOCS3 unresolved.

There are various ways that might explain why BALB/c might be less adapt at shutting off certain cytokine signals, but the most promising target to investigate seems to me to look at hypermethylation of SOCS (promoter) sequences.

SOCS proteins act as negative regulators to a great number of cell signalling processes including IL‑4R and insulin receptor signalling. The observed correlation between resistance to Leishmania infections (advantageous to the mouse) and insulin resistance (pathologic) in different strains of mice seems to suggest SOCS as the common link. Not only do they inhibit physical association of receptor and adapter proteins by occupying crucial pY residues, their SOCS box domains can act as ubiquitin-E3-ligases promoting the mono-, multi- or poly-ubiquitination of target proteins, resulting in down-regulation of trans-membrane receptors through internalisation, redistribution of membrane bound proteins to endosomal/lysosomal compartments (TLR [78]) or proteasomal degradation of cytosolic proteins (possibly STAT, other SOCS proteins [79]). The SOCS-induced shuttling of TLR to the endosomal/lysosomal pathway could be used in antigen-presenting cells as an efficient way to redirect microbial material to cellular compartments that then ensure preferential/efficient antigen presentation (as demonstrated in the case of Toxoplasma gondii and TLR11 [78]).

DNA methylation patterns develop over time and often are tissue- or cell-specific. In mammalian cells, DNA methyltransferases use SAM to preferentially methylate CG islands of genomic DNA. Maintenance methyltransferases ensure that methylation patterns are preserved and passed on to following generations of cells or organisms. Various cancers show hypermethylation of SOCS genes which leads to reduced SOCS-mediated signal inhibition and increased activational stimuli that the aberrant cancer cell line can use to proliferate and spread. Two compounds acting as DNA methylation inhibitors have recently been approved for treatment of certain cancers (e.g. 5-aza-2'-deoxycytidine) that may be especially effective in cancers reliant on activational/differentiation stimuli that have become reassigned growth and proliferative roles in cancer cells.

The fact that antimony’s homolog arsenic seems to function as an inhibitor of DNA methyltransferases can be exploited in the search for new treatments of leishmaniases. In theory, if SOCS proteins are indeed involved in the control of leishmaniases and are down-regulated because of DNA hypermethylation, then treatment with DNA hypomethylating agents such as 5-aza-2'-deoxycytidine might de-repress SOCS expression. SOCS proteins could then be efficiently expressed and could thus shut down the parasite’s life support system, by inhibiting IL‑4/IL‑13/IL‑10/IL‑6-driven arginase expression. I suggest that 5-aza-2'-deoxycytidine could be a prime drug candidate used in treating leishmaniases if it were possible to target the delivery of the molecule to the host cells. It is more efficient in demethylating DNA and functions in a different way to heavy metals such as antimony and arsenic which can be deactivated by leishmanial arsenate/antimonate reductases. In fact antimony-resistance of Leishmania is a serious and increasing problem that could be solved by switching to non-heavy metal-based drugs such as 5-aza-2'-deoxycytidine. Vice versa, antimony-based drugs might prove beneficial to treating certain forms of cancer. However, uptake into target cells, side effects and other issues such as costs have not been taken into account at this point. While the model offers a rational explanation for the treatment of leishmaniases, and brings together a number of areas of basic cell biology, immunology and parasitology, it remains highly speculative.

However, the rewards might outweigh the risks. The new drug candidate for treating leishmaniasis edelfosine looks to me like a potential inhibitor of DNA methylation (possibly inhibiting DNMT via its E18-O-CH3 group) and the observed effects of the drug on cell biology (vacuoles, uncoordinated cellular transportation and architecture) seem to imply consistency with the proposed upregulation of SOCS molecules resulting in ubiquitination and relocalisation of proteins and membranes to endosomal/lysosomal compartments.

In addition, the model does allow for a number of predictions that can be tested.

A) Are SOCS mRNA/proteins differentially expressed in mice / different cell types in mice? (SOCS3 in macrophages? (involved in downregulating cytokine signalling of IL‑4, IL‑13 and IL‑6), whereas SOCS2 has been shown to downregulate SOCS3 levels via ubiquitination [79] and would therefore be considered rather a negative influence on the control of Leishmania infections (in line with its association and induction by Th2 cytokine responses), SOCS5 is another potential candidate mediating protective effects, but there is more evidence suggesting that SOCS3 might be crucial).

B) Are there differences in methylation status of SOCS genes in different strains of mice / different cell types in mice? (Methylation specific real-time PCR analysis could be used to detect differences in gene-specific DNA methylation [80])

C) Are gender differences in susceptibility to certain diseases attributable to SOCS expression/ SAM content/ DNA methylation status?

D) Does antimony treatment result in a changed methylation profile of SOCS genes?

E) Is SAM content/ DNA methylation linked to pathogenesis of Leishmania in visceral leishmaniases?

F) Does 5-aza-2'-deoxycytidine act as an anti-leishmanial drug? Is edelfosine a demethylating agent and does it induce SOCS expression? (Complications due to TLR9-mediated recognition of unmethylated CpG need to be considered even if at one time it was very much debated whether TLR9 indeed recognises unmethylated CpG sequences or naked, single-stranded DNA instead. In the case of antimony treatment in patients and mice TLR9 activation may even be beneficial to resolving the disease (uptake of antimony via Glut1 transporter into infected macrophages [81], CpG is generated and activates TLR9, which then sets off a response characterised by IFN‑γ helping to shut down the arginase activity)).

G) Does the model explain complications in leishmaniasis such as post-kala azar dermal leishmaniasis? (Withdrawal of antimony may result in increased DNA methylation over time, affecting SOCS expression, host cells with latent infection receive instructions to increase arginase activity, resurgence of the Leishmania in areas that have been reached by latently infected cells….)

H) What would be the phenotype of mice derived from resistant (CBA, C57BL/6) mice with an IL‑4R that did not allow for inhibition by SOCS be regarding susceptibility to L. major?

I) Similarly, can this model be applied to L. sigmodontis infections in mice?

J) Does PSG lead to a reduction in SOCS expression?

K) Is T1/ST2 involved in the regulation of SOCS expression? (Implications for transplantation immunology, because of the link between mast cells expressing T1/ST2 and Treg. Possible links to LPS tolerance – treatments for sepsis (antimony-based, etc – compare to the effects of lead on LPS tolerance)).

L) Are SOCS responsible for/involved in targeting membrane TLR to the endosomal/lysosomal compartment upon TLR activation via receptor ubiquitination? (demethylating agents could lead to SOCS expression and deregulation of ubiquitin/sumo/etc-mediated intracellular trafficking.)

If all or at least some of this is found to be true, it might offer an advancement in our understanding of the way the parasite and the host cell interact and might help in the development of potential drug candidates. The possibility that DNA methylation might determine the biological age of organisms and therefore 6-8-week-old mice of different strains might have aged in different ways is quite an exciting concept. The potential of this idea seemed so big to me at the time that I could not help myself and tried to talk to people about it who were not interested. The hard part is getting experimental proof for all this theorising. Anyone who finds these ideas useful is welcome to "steal" them and to see if they are of any use in the real world. The role of SAM in epigenetics such as DNA methylation and histone modification is intriguing, but may not be the main or only role to consider. SAM also plays a very important role in polyamine synthesis, which might be a different line of research worth pursuing, especially given the role of spermidine and trypanothione.

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Epigenetics and evolution

2007-07-14T13:45:00.004+01:00

What if the methylation status of DNA can be seen as a means of switching from competitive to cooperative survival mechanisms?

Competitive mechanisms appear adequate survival tools in conditions characterised by limited resources.

Cooperative mechanisms appear adequate for life in an environment of abundance.

Fitness in evolutionary terms is a measure of the adequacy of the balance between competitive and cooperative mechanisms. Excessive competition and excessive cooperation will either adjust or fail to maintain the dynamic equilibrium.

Dropping science

2006-01-28T10:45:00.003Z

Good morning all you out there,

Another Saturday morning spent in the lab and the feeling that science is too cool to be misunderstood make me start this blog. I started pretty much without any sort of deliberation, this is all very much work in progress and a hopefully steep learning curve will make this blog enjoyable to read. Please be patient with me for a while as I get things sorted. I intend to use this blog as a forum to discuss the impact of life sciences on our daily existence and a means of sharing some of the enthusiasm for looking at life from a rationalist's perspective. Let's see where this takes me...