chiaravi@copper.ucs.indiana.edu (Lucius Chiaraviglio) (09/29/90)
_
Something that has intrigued me (and some microbiologists) for a while
is the process, so far as I know almost completely uncharacterized, of
phosphine production in marshes. Most of marsh gas is methane and carbon
dioxide, but it also contains hydrogen sulfide and can contain small amounts
of phosphine (PH[3]), and probably also traces of P[2]H[4], since marsh gas
can auto-ignite upon contact with air. The biogenesis of carbon dioxide,
methane, and hydrogen sulfide has been extensively studied (although by no
means to completion at least in the case of the latter two), and many
organisms have been found which produce these gases (-: just about everybody
makes carbon dioxide, although numerous organisms consume more than they
produce :-). However, no organisms have yet been found which produce
phosphine, or P[2]H[4] for that matter, and we remain completely ignorant of
the biochemistry of this process.
Phosphate seems to be the most likely source of the phosphorus in
phosphine, given that it is by far the most common phosphorus-containing
compound (for that matter, has anyone heard of any other naturally-occurring
phosphorus-containing compounds found in nature, except for the phosphine and
P[2]H[4]?). What I am wondering is whether the reduction of phosphate to
phosphine would be thermodynamically favorable for microorganisms. To make it
simpler, assume that they use hydrogen gas as the reductant -- many organisms
actually do use hydrogen gas at partial pressures of <0.01 atm, and common
internally-used reductants such as NADH are thermodynamically not too far from
equilibrium with the corresponding oxidized compound (such as NAD+) and
hydrogen gas at low partial pressure. I would go ahead and figure this out
myself and post it, except that the table of standard free energies of
formation of various compounds in the excellent review article I have on
energy conservation in anaerobic bacteria (unfortunately, no mention of
phosphine generation) lacks phosphorus-containing compounds, and a table of
bond energies just won't cut it (the one in my organic chemistry textbook
doesn't have phosphorus-containing bonds anyway, even though a later part of
the book discusses phosphorus chemistry). Could someone point me to a
suitable table of standard free energies of formation, and/or would someone
like to take a crack at this problem themselves?
| Lucius Chiaraviglio | Internet: chiaravi@copper.ucs.indiana.edu
BITNET: chiaravi@IUBACS.BITNET (IUBACS hoses From: fields; INCLUDE RET ADDR)
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Alt Internet-gatewayed BITNET: chiaravi%IUBACS.BITNET@cunyvm.cuny.edularry@kitty.UUCP (Larry Lippman) (09/30/90)
In article <60883@iuvax.cs.indiana.edu>, chiaravi@copper.ucs.indiana.edu (Lucius Chiaraviglio) writes: > Something that has intrigued me (and some microbiologists) for a while > is the process, so far as I know almost completely uncharacterized, of > phosphine production in marshes. Most of marsh gas is methane and carbon > dioxide, but it also contains hydrogen sulfide and can contain small amounts > of phosphine (PH[3]), and probably also traces of P[2]H[4], since marsh gas > can auto-ignite upon contact with air. > ... > However, no organisms have yet been found which produce > phosphine, or P[2]H[4] for that matter, and we remain completely ignorant of > the biochemistry of this process. Phosphine has long been known as an end product of putrefaction, especially putrefaction occuring under water or in damp locations. As an interesting coincidence, phosphine has an odor which resembles that of decaying fish smothered in garlic. [yummmy] :-) It is my belief that an explanation of the mechanism behind the biological production of phosphine requires consideration of the various processes involved in putrefaction. It is also my feeling that there exists more than one putrefactive mechanism for the production of phosphine. The following represents pure *speculation* on my part with respect to a *possible* mechanism for production of phosphine as a consequence of putrefaction: Consider that the majority of phosphoglycerides are phosphatidates. Further consider that E. coli and other bacteria produce phosphatidylserine from L-serine and (I believe) cytidine diphosphoacylglycerol. Putrefaction chiefly involves deamination and/or decarboxylation. The decarboxylation products of phosphatidylserine are carbon dioxide and phosphatidylethanolamine. While free serine apparently will not undergo decarboxylation (or deamination, for that matter), the phosphatidyl form will. It is therefore my speculation that as a putrefactive process, phosphine results from the successive decarboxylation of phosphatidylserine, through phosphatidylethanolamine, eventually into phosphine (and perhaps, diphosphine). I know of no reference to support this speculation, but I suspect a modest amount of literature research will readily prove or disprove its feasibility. > Phosphate seems to be the most likely source of the phosphorus in > phosphine, given that it is by far the most common phosphorus-containing > compound (for that matter, has anyone heard of any other naturally-occurring > phosphorus-containing compounds found in nature, except for the phosphine and > P[2]H[4]?). While most biological phosphorous is in the form of phosphate esters and diesters, there are some exceptions. Consider as an example, 2-aminoethylphosphonic acid, which is found in some protozoa. > To make it > simpler, assume that they use hydrogen gas as the reductant -- many organisms > actually do use hydrogen gas at partial pressures of <0.01 atm, and common > internally-used reductants such as NADH are thermodynamically not too far from > equilibrium with the corresponding oxidized compound (such as NAD+) and > hydrogen gas at low partial pressure. I don't believe that any free hydrogen under any biological conditions is going to result in, or otherwise aid, the formation of phosphine. > and/or would someone > like to take a crack at this problem themselves? Why don't you do a little investigation along the lines I suggested? If you publish a paper as a result, you can include a note of thanks. :-) Larry Lippman @ Recognition Research Corp. "Have you hugged your cat today?" VOICE: 716/688-1231 {boulder, rutgers, watmath}!ub!kitty!larry FAX: 716/741-9635 {utzoo, uunet}!/ \aerion!larry
chiaravi@copper.ucs.indiana.edu (Lucius Chiaraviglio) (09/30/90)
In article <4067@kitty.UUCP> larry@kitty.UUCP (Larry Lippman) writes: >In article <60883@iuvax.cs.indiana.edu>, chiaravi@copper.ucs.indiana.edu >(Lucius Chiaraviglio) writes: >> Something that has intrigued me (and some microbiologists) for a while >> is the process, so far as I know almost completely uncharacterized, of >> phosphine production in marshes. [. . .] > > It is my belief that an explanation of the mechanism behind the >biological production of phosphine requires consideration of the various >processes involved in putrefaction. It is also my feeling that there >exists more than one putrefactive mechanism for the production of phosphine. > > Consider that the majority of phosphoglycerides are phosphatidates. >Further consider that E. coli and other bacteria produce phosphatidylserine >from L-serine and (I believe) cytidine diphosphoacylglycerol. So far, all phosphates. . . > Putrefaction chiefly involves deamination and/or decarboxylation. >The decarboxylation products of phosphatidylserine are carbon dioxide and >phosphatidylethanolamine. While free serine apparently will not undergo >decarboxylation (or deamination, for that matter), the phosphatidyl form >will. That sounds bizarre -- I have read that some methylotrophic bacteria are able to transaminate serine just fine, to get hydroxypyruvate (meanwhile converting another alpha-keto-acid into an amino acid), which is then phosphorylated to 3-phosphoglycerate (which then goes into the glycolytic pathway -- more explanation in another message, if people are interested). On the other hand, phosphorylating the serine in the first place would certainly work; maybe the bacteria actually do it that way (or maybe both ways), and somebody determining the serine-involving methylotrophic pathway messed up. (Sorry, I won't be able to check the references until the University of Chicago (where I actually am now) online catalog comes back on line :-( ). Any particular reason why decarboxylation or deamination of serine shouldn't work? > It is therefore my speculation that as a putrefactive process, >phosphine results from the successive decarboxylation of phosphatidylserine, >through phosphatidylethanolamine, eventually into phosphine (and perhaps, >diphosphine). Out of curiosity, how would this work? Phosphatidylethanolamine could be oxidatively deaminated to O2-phosphatidylhydroxyacetaldehyde, which could then be oxidized to O2-phosphatidylglycolate (with the energy conserved as a high-energy phosphate by way of the O1-phospho-O2-phosphatidylglycolate intermediate which might be expected to be formed by bacterial oxidation of an aldehyde). After that, I suppose you could do something really wierd like decarboxylate this compound (I don't know if that would work) to a methyl phosphatide, but I don't know what the profit would be in doing that, and the phosphate still hasn't been reduced. What next (or where would you branch off from the pathway I described)? (Hey, isn't thinking up biochemical pathways and their reaction mechanisms fun?) > I know of no reference to support this speculation, but I suspect >a modest amount of literature research will readily prove or disprove its >feasibility. Well, last night I stumbled on some information (that is, I managed to find what actually appears to be a decent chemistry text) which shows that no reduction of phosphate to phosphine is going to be energetically profitable, and in fact it would be rather difficult for terrestrial biochemistry to do at all (and if it did it, it would have to be for something other than an energy- generation pathway). See below, and despair. :-) > While most biological phosphorous is in the form of phosphate >esters and diesters, there are some exceptions. Consider as an example, >2-aminoethylphosphonic acid, which is found in some protozoa. Anyone know what this does for those protozoa, or how they make it? > I don't believe that any free hydrogen under any biological >conditions is going to result in, or otherwise aid, the formation of >phosphine. For the reasons coming up, you're right. > Why don't you do a little investigation along the lines I suggested? >If you publish a paper as a result, you can include a note of thanks. :-) I stumbled on this information last night, but decided to wait on posting until others had had a chance to squirm in it. :-) Basically, no matter what the pH in aqueous solution, the reduction of phosphate to phosphine is strongly endergonic. Under standard conditions (pH = 0), the reaction H[3]PO[4] + 8H(+) + 8e(-) --> PH[3] + 4H[2]O consumes 45.1 kcal/mole; if you modify the conditions so that pH is now physiological (~7), the reaction will consume much more (because hydrogen ion concentration is reduced, and it is eighth-order in the equilibrium constant). Not having handy at the moment a calculator with a natural logarithm (or any logarithm) function on it, and having eight minutes to catch my last bus, I will leave it as an exercise for the reader to determine how much more energy the reaction would consume at pH = 7. :-) | Lucius Chiaraviglio | Internet: chiaravi@copper.ucs.indiana.edu BITNET: chiaravi@IUBACS.BITNET (IUBACS hoses From: fields; INCLUDE RET ADDR) Internet-gatewayed BITNET: chiaravi%IUBACS.BITNET@vm.cc.purdue.edu Alt Internet-gatewayed BITNET: chiaravi%IUBACS.BITNET@cunyvm.cuny.edu
larry@kitty.UUCP (Larry Lippman) (10/01/90)
In article <61152@iuvax.cs.indiana.edu>, chiaravi@copper.ucs.indiana.edu (Lucius Chiaraviglio) writes: > >> Something that has intrigued me (and some microbiologists) for a while > >> is the process, so far as I know almost completely uncharacterized, of > >> phosphine production in marshes. [. . .] > > > > It is my belief that an explanation of the mechanism behind the > >biological production of phosphine requires consideration of the various > >processes involved in putrefaction. It is also my feeling that there > >exists more than one putrefactive mechanism for the production of phosphine. Congratulations, Lucius. You have posed a problem which has been bugging the hell out of me for the past two days! As if I didn't have enough work and other things to occupy my time... :-) I should have some more to say on this issue in a day or so. In the meantime, here are some random thoughts going through my mind: 1. Some extensive studies which *might* offer suggestions as to the mechanism for biological production of phosphine deal with the biochemistry and microbiology of the rumen. Take a look at a copy of "Dukes' Physiology of Domestic Animals" and you might see one path of my reasoning. This book is well endowed with literature references. I have used literature on the rumen to find answers not available elsewhere to questions on industrial fermentation matters, and on the toxicology and metabolism of methane. 2. I may have been too hasty in dismissing the possible role of hydrogen as a reducing agent (as you originally suggested). Consider that in the rumen, virtually all of the hydrogen formed through bacterial action is used to reduce CO2 to methane. This surpised me, for various reasons. 3. There is some similarity beteen phosphine and ammonia. So, I got to thinking about NADPH and ferredoxin. Ferredoxin is quite a respectable reducing agent. Consider, as an example, that ferredoxin possessed by certain anaerobic bacteria can readily form pyruvate from reductive carboxylation of acetate (plus CO2). 4. If we can establish the biological formation of hypophosphorous acid, then I might have a mechanism which to explain phosphine production. 5. Something about mevalonic acid and the geranium plant is ringing a bell. This is really a *bizarre* thought: could the geranium plant somehow produce a small amount of phosphine as part of its characteristic odor? > (Hey, isn't thinking up biochemical pathways > and their reaction mechanisms fun?) Yup! :-) > > While most biological phosphorous is in the form of phosphate > >esters and diesters, there are some exceptions. Consider as an example, > >2-aminoethylphosphonic acid, which is found in some protozoa. > > Anyone know what this does for those protozoa, or how they make it? No, but I found two references: (1) M. Horiguchi and M. Kandatsu, "Nature", 184, 901 (1959); and (2) L. D. Quin, "Topics in Phosphorous Chemistry", 4, 23 (1967). Now, if I could only find a reference to explain the production of phosphine... :-) Larry Lippman @ Recognition Research Corp. "Have you hugged your cat today?" VOICE: 716/688-1231 {boulder, rutgers, watmath}!ub!kitty!larry FAX: 716/741-9635 {utzoo, uunet}!/ \aerion!larry
saj@chinet.chi.il.us (Stephen Jacobs) (10/02/90)
Given that some microorganisms seem to be able to make particles of iron, it
may be worth considering that the powerful reductant needed to reduce the
oxygens off phosphorus might be dissolving metal.
Steve J.larry@kitty.UUCP (Larry Lippman) (10/03/90)
In article <1990Oct02.143943.18824@chinet.chi.il.us>, saj@chinet.chi.il.us (Stephen Jacobs) writes: > Given that some microorganisms seem to be able to make particles of iron, it > may be worth considering that the powerful reductant needed to reduce the > oxygens off phosphorus might be dissolving metal. That's precisely why the thought of ferredoxin as a reducing agent came to mind in my previous article. Yet another possibility is an enzyme containing zinc, something like carbonic anhydrase, which does a nice job of catalyzing the hydration of CO2 to carbonic acid. If we could somehow form hypophosphorous acid, then I can see a possible mechanism for production of phosphine. A third possibility is that the production of phosphine is solely the result of an exobiological phenomenon, which is proof that there are indeed LGM (Little Green Men) living in swamps. :-) Larry Lippman @ Recognition Research Corp. "Have you hugged your cat today?" VOICE: 716/688-1231 {boulder, rutgers, watmath}!ub!kitty!larry FAX: 716/741-9635 {utzoo, uunet}!/ \aerion!larry