When I read that Science and
the NASA were organizing a press conference about the role of
arsenic as a central element in life elsewhere in the cosmos,
and that it could have played a central role in the origin
of life, I did not believe my eyes. But there it was. I immediately
wrote to Science a
short version of the text below, but got no answer (except
that my comment had been received). I therefore decided to publish
it in The
Journal of Cosmology.
My text was rapidly accepted there, but, curiously, amended in
order to place the blame only on peer-reviewers and editors and
in defence of the scientists involved in this nightmare.
scientific publications are now akin to advertisements (and scientists
have, indeed, to pay to be published, in many journals). It becomes
the more essential that scientists react and try to comply with
the scientific method. Science should go back to its original
process of construction, the
critical generative method.
We should all have remembered the paper published
by Frank Westheimer in 1987, aptly entitled: "Why
nature chose phosphates",
in the very same journal, Science: 235: 1173–1178, where he explained
the particular situation met by the metastability of phosphate
bonds, and the reason why phosphate is so important for life
as we know it. That we forgot this important article shows how
much science drifted from creation of knowledge to some kind
of signalling and "display" between humans, in a world of mass
media communication. Arsenic is a toxic contaminant of water
world-wide, and it is therefore essential to refrain spreading
wrong ideas about this metalloid.
Here was my first reaction in a letter to Science (unpublished,
december 3, 2010):
Wolfe-Simons and co-workers claim that they have identified a bacterial
species where arsenic plays most of the role played by phosphorous in
all known extant living species (1). I welcome the idea of discovering
novel examples of the extraordinary propensity of life to capture all
kinds of processes that may help it to transmit information over generations.
Yet, arsenic is very unlikely as a major component of the backbone of
nucleic acids, despite its similarity with phosphorus, essentially because
it would form extremely unstable macromolecules.
Life provides us already with a caveat in this domain. Quite a few modifications
of the (deoxy)ribose-phosphodiester backbone exist in nature, but they
seldom affect the phosphate group. In a case in point one atom of sulfur
replaces an oxygen of phosphate at places of the backbone of DNA in Streptomyces
lividans (2). This modification results in the degradation of DNA in vitro
by oxidative, double-stranded, site-specific cleavage during normal and
pulsed-field gel electrophoresis, making completion of genome sequencing
a difficult task. Several genomes from Cyanobacteria possess the same
modification, with similar instability of their DNA at the modified positions
(accounting for lack of completion of several genome projects). This modification,
which was long unidentified, is comparable to the phosphorous - arsenic
change, as sulfur belongs to the same family as oxygen in Mendeleiev's
table, but it is located at a much less crucial position in the backbone.
Performing experiments with "pure" compounds is notoriously
difficult. Many investigators have observed that Escherichia
coli in media
containing "pure" sodium salts will grow, albeit slowly. This
is not due to sodium replacing potassium but to a remarkable
enrichment of potassium present in elusive traces. Another -
unfortunately common - practice is to grow bacteria in synthetic media
where common salts (potassium, magnesium and iron) are included, without
any addition of essential metals such as zinc or manganese (3). Yet bacteria
grow, and grow well. I do not suspect them to be able to transmute matter,
or to universally substitute zinc or manganese by iron of magnesium. In
the same way the well known "fluoride
effect" results from extraction of aluminum from glassware, making
AlF4, which, in fact, mimicks phosphate (4).
But there is a stronger argument that should be taken into consideration.
I have belonged to a team that sequenced the genome of an arsenic-loving
organism, Herminiimonas arsenicoxydans (5). This organisms uses,
indeed, arsenic to perform electron transfers that permit it
to manage energy. It has also a way to detoxify this element.
A remarkable conjecture can be proposed to explain how it does
so. While this organism does not use selenium (as other bacteria
such as E.
to make selenocysteine, the 21st amino acid), it has the counterpart
of the selD gene.
I note that Halomonas elongata possesses the counterpart of this
gene (HELO_4105 ). SelD in "standard" bacteria is the enzyme
that makes selenophosphate, used to modify serine on a tRNA that
translates UGA codons into selenocysteine. Selenium is the counterpart
of sulfur in Medeleiev's table, it occupies a volume that is
slightly larger than the latter. A similar situation is met with
arsenic and phosphorous. Hence, a small distortion of the standard
SelD catalytic site would easily accomodate sulfur instead of
selenium and arsenate instead of phosphate. The role of SelD
would then be to make thioarsenate. This compound is insoluble
(it is found in stones), and this would be an excellent way to
detoxify arsenic, while removing it from the medium, leaving room for
minuscule traces of phosphate to be accumulated and play their normal
This hypothesis and others should be further explored before we propose
that life as we know it can develop using arsenic in the place of phosphorus.
1. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J,
Stolz JF, Webb SM, Weber PK, Davies PCW, Anbar AD, Oremland RS. A Bacterium
That Can Grow by Using Arsenic Instead of Phosphorus. Science 2010 dec
2. Zhou X, He X, Liang J, Li A, Xu T, Kieser T, Helmann JD, Deng
Z. A novel DNA modification by sulphur. Mol Microbiol. 2005 Sep;57(5):1428-38.
3. Miller, JH A short course in bacterial genetics. A laboratory
manual and handbook for Escherichia coli and related bacteria. 1992. Cold
Spring Harbor Laboratory Press
4. Bigay J, Deterre P, Pfister C, Chabre M. Fluoroaluminates
activate transducin-GDP by mimicking the gamma-phosphate of GTP in its
binding site. FEBS Lett. 1985 Oct 28;191(2):181-5.
5. Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla
E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C, Chandler M, Cournoyer
B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lièvremont
D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier
P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Van Dorsselaer
A, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN. A tale of two
oxidation states: bacterial colonization of arsenic-rich environments.
PLoS Genet. 2007 Apr 13;3(4):e53.
Naturally, we do not know yet how cells cope with
a considerable level of arsenic, but we begin to have some ideas
of the many biochemical solutions to the riddle. For example
we have found, in the sequencing of the genome
that oxido-reduction played a major role. Yet, the best way to
cope with a toxic compound is to fix it under an insoluble form.
Many biological polymers may allow this. Similar situations are
met with many metals, magnesium, calcium, iron and manganese
in particular. As a matter of fact metallurgic industry copes
with arsenic by forming insoluble compounds. Research on arsenophilic
bacteria should focus on biochemical processes resulting in the
formation of insoluble or low toxicity arsenic compounds. The
hypothesis proposed here (formation of monothioarsenate) is just
a conjecture. Many others should have been proposed.
April 2012: After discussion
with the geochemist Raoul-Marie Couture we wrote an article proposing
a detailed scenario whereby some bacteria could synthesise
monothioarsenate, a fairly innocuous derivative of arsenic. The
scenario is hypothetical and quite wild, of course,
but it shows that we should explore many biochemical hypotheses
before trying to challenge our standard knowledge of the constraints
of the laws of physics. This paper is published in Environmental
RM Couture , A Sekowska, G
Fang, A Danchin
Linking selenium biogeochemistry to the sulfur-dependent biological detoxification
Environ Microbiol (2012) Apr 20. doi: 10.1111/j.1462-2920.2012.02758.x.
Making stable informational polymers in water
at 300K limits chemical variations within extremely narrow borders.
This is why the basic atoms of life — those that are found in meteoritic
molecules — are hydrogen, carbon, nitrogen and oxygen. In these same
conditions, management of energy to support life used the unique property
of phosphorus to make energy-rich metastable phosphoester or polyphosphate
bonds. Analysis of the genome of arsenic-loving bacteria suggests that
arsenic can nevertheless be accumulated in bacteria via formation of
innocuous derivatives that may decorate inert (mostly non informational)
biopolymers. However, arsenic cannot replace phosphorus in this core
function of life. This has been previously firmly established by numerous
biochemical experiments. Likewise, recent claims by Wolfe-Simon et al.
(2010) that this replacement could happen, have not been experimentally
verified, and are based on experiments lacking proper controls; the
purpose of which was to substantiate these beliefs. However, the authors
are not sole to be blamed, but the journals that try to maintain their
high impact factors at all cost, publishing articles that should never
have reached the public.
As a present for the new year, back in 2008, a prophecy appeared
as a peer-reviewed pre-publication. It anticipated that arsenic
would be found in the backbone of nucleic acids of living organisms,
replacing the ubiquitous phosphorus. The prophecy, as is often
the case with this type of beliefs, also suggested a place
on Earth where this would happen: Lake Mono in California (Wolfe-Simon
et al., 2008). On April 6th, 2008, this prophecy was communicated
to the world by a popularization journal (Reilly, 2008). Now,
at the end of 2010, as a Christmas present (in Continental
Europe, december 2nd, the chosen date might have recalled
the sun of the napoleonian Victory of Austerlitz), the NASA
sent a sensational press release calling on journalists to
tell them that, yes, the prophecy had come true, and not on an exotic
planet, but on our old mother Earth and exactly at the place
where this was predicted to happen (Wolfe-Simon et al., 2010).
In pre-scientific times, the sayings of prophets were the norm, and
nobody would be bothered. Some would follow, some would be miscreants.
One may dispute the demarcation between science and non-science,
but, in any event, a core criterium to accept facts as belonging
to science is to understand that we
cannot get direct access to truth (if it ever exists) but only
make models of Nature. In this process we must avoid
trying to prove that the model is right, but, rather, try to
find where models are an inadequate representation of Nature
(Popper, 1972). If this fairly standard way or proceeding (explicitly
stated in the NIH guidelines, for example) had been followed,
rather than running after fame and recognition by mass media
(a kind of democratic voting to demarcate what should be true
and what should not via people’s acclamations), the Wolfe-Simon
et al., (2010) paper should never have reached the pages of scientific
journals, but would have remained among the many opinion pamphlets that
thrive everywhere, especially on the Internet.
To substantiate this contention I review here basic arguments
that should have come to mind before publication: chemical consequences
of placement of atoms in the periodic table of element; biochemical
experiments that demonstrate fragility of modifications of the phosphodiester
bond, and biochemical data documenting instability of arsenate derivatives
of nucleotides; ability of living organisms to concentrate elements present
in traces in the environment, and analysis of genomic data that
suggest a biochemical process permitting cells to alleviate arsenic toxicity.
Many ideas of what life could be have been
discussed for centuries and even millenia. The most imaginative
authors made it far from the life we know (see for example Fred
Hoyle's Dark Cloud (Hoyle, 1957)), but the present contentious
article assumes that life is based on principles that are identical
to those governing our life, but with one big difference: arsenic
would replace phosphorus in its construction (Wolfe-Simon et
al., 2010). This places us right in front of a textbook approach
of life: why are the elements we find in living organisms in
limited number, and why are they those we know?
The short answer is straightforward. Life develops around 300K,
with water as its bathing medium. A core property of its components
is that beside a limited number of small molecules (a few tens
of atoms), it is made of macromolecules: giant polymers obtained
by elimination of a water molecule between a small alphabet of
basic building blocks, amino acids and nucleotides. This seemingly
simple arrangement has a remarkable property in
terms of information:
while the backbone of these polymers is invariable, the side
chains can be arranged in an infinite variety of combinations.
This informational view must be associated with physico-chemical
constraints at the required temperature. Making molecules, and
a fortiori polymers, implies forming stable covalent bonds. A
covalent bond appears when electrons share their presence between
two or more atoms’ nuclei. Now, the electrons associated to a
nucleus are arranged along specific constraints ruled by quantum
physics laws. And the consequence of these laws is that the various atoms
of the universe can be arranged along rows and columns, according to the
way they match their electrons with the charge of their nuclei. This
constitutes the periodic table of elements (Figure 1).
As the rank of the row increases, the (negative) electrons of
the outer shell of the atom become more and more loosely attached
to the (positive) nucleus. In a nutshell, this makes that the
best candidates for making stable covalent links are, beside
hydrogen, some of the atoms present in the second row of the
periodic table. Further down, the atoms involved are mainly involved
in electrostatic bonds (much weaker than covalent bonds) and in electron
exchanges (oxido-reduction reactions). Another constraint, more anecdotal
but often ignored, concerns three atoms: lithium, beryllium and boron.
All three are rare in the universe for cosmological reasons (nucleosynthesis
during the first stages of formation of our universe (Bernas et al.
1967)). As a consequence, this limits the basic atoms of life to hydrogen,
carbon, nitrogen and oxygen (typically the atoms combined in extraterrestrial
molecules, when they are found).
As shown in the figure, other atoms are also involved in life.
Most, in fact, are playing important roles in specific features
of catalytic reactions needed to construct, modify and destroy
covalent bonds, electrostatic interactions (metals) and more or less complicated
electron exchanges (transition metals and complex anions such
as molybdate or tungstate).
Two exceptions remain, that have to be accounted for. Sulfur
(the higher homolog of oxygen) and phosphorus (the higher analog
of nitrogen). The former, being in a deeper row than oxygen,
is mainly involved in exchanges of electrons (its oxido-reduction
potential varies from -2 to +6), in formation of energy-rich thioesters
and via a remarkable affinity for iron, in making iron-sulfur
clusters that have probably had a seminal role on the origin of life on
where it is quite abundant (Wickramasinghe, 1973). The latter, phosphorus,
is the candidate that Wolfe-Simon and colleagues proposed to see replaced
by arsenic. This is not chemically possible, as we shall discuss now.
Phosphorus, in living cells, is essentially used as phosphate,
involved in three major processes: carrying and transporting
energy, forming the backbone of nucleic acids, and acting as
an energy-dependent tag for regulation. In fact the association
of phosphorus with oxygen atoms, making the phosphate anion,
has the property to make long chains (polyphosphates) when desiccated.
These chains are, of course, prone to hydrolysis, but remarkably,
in a highly metastable way. This means that while the
stable forms are those which results from hydrolysis (the phosphate
anions), to reach this stage, the compound needs to go through
a very high activation energy barrier. This is the reason why
the phosphate bond has been named energy-rich, since the discovery
of the role of ATP by Fritz Lipmann (Lipmann, 1975). And this
is why phosphate is the basic currency of energy in life. This
metastability extends to the formation of phosphoesters, and
in particular phosphodiester bonds. And this permitted the formation
of nucleic acids, which use a negatively charged backbone to
carry and protect from the environment fragile base pairs in
a double helical structure. We note here that the two ubiquitous
elements of the third row of Mendeleiev's table that are present
in all living cells, sulfur and phosphorus, are involved in the
storage of energy (thioesters and phosphates/phosphoesters).
Life warns us already of the intrinsic fragility of these metastable
bonds. Modifications of the (deoxy)ribose-phosphodiester backbone
exist in nature, but they seldom affect the phosphate group.
There is a modification, however, that is relevant in the present
context. In Streptomyces lividans a
DNA modification system replaces a side oxygen of phosphate by
an atom of sulfur at some specific places of the DNA backbone
(phosphorothioation (Zhou et al. 2005)). This modification makes
DNA unstable in vitro by
oxidative, double-stranded, site-specific cleavage during normal
and pulsed-field gel electrophoresis, making completion of genome
sequencing a difficult task. A database of genomes possessing
the same modification, which makes the completion of the corresponding
genome sequencing difficult, has been published (Ou et al. 2009).
This modification, which was long unidentified, has some conceptual
similarity to the phosphorous - arsenic swap, as sulfur belongs
to the same family as oxygen in Mendeleiev’s table, but it is
located at a much less crucial position in the backbone. It also
tells us that beside hydrolysis, oxidation may be central in
the instability of arsenic, if it were to replace phosphorus.
But there is even more direct biochemical
evidence that makes impossible for arsenic to play the role of a stable
component of a nucleic acid backbone in an aqueous environment. Arsenic
has been known as a poison for millenia. In recent times biochemists
looked into the many reasons accounting for that role. Beside
involvement in oxido-reduction reactions (which can be used both
to evolve arsenite into its more innocuous form arsenate, and
to recover energy), arsenic can indeed replace phosphorus in
many phosphorolytic reactions and even form carbohydrate arsenates
that are similar to their phosphate analogs (Lagunas & Sols, 1968).
However this is limited to exchange reactions that cannot lead
to stable and useful compounds. It is also possible to begin
to construct compounds along the line predicted to exist if phosphorus
could replace arsenic, for example by constructing an arsenical
analog of adenosine diphosphate (an essential pre-requisite if
the prophecy were true). While difficult, a synthesis in which
the phosphono-oxy group of ADP was replaced by the arsenomethyl
group (arsenate itself was far too unstable at this position, requiring
replacement of the bridging oxygen by a methylene group) was achieved
by Dixon and colleagues. The product was unable to compete for ADP in
any of its standard substrates (Webster et al. 1978). A further demonstration
puts the final nail in the coffin: the arsonomethyl analogue of AMP can
be used as a substrate for adenylate kinase. It permits transfer of a
phospho group from ATP, but like all anhydrides of arsonic acids breaks
down immediately, transforming the enzyme into an ATPase (Adams et al.
1984). The situation would be even worse if the hypothetical arsenical
analog of ATP could have existed.
Performing experiments with « pure »
compounds is notoriously difficult. Many investigators have observed
media containing « pure » sodium salts will grow, albeit slowly
and to a limited extent. This is not due to sodium replacing
potassium but to a remarkable enrichment of potassium present
in elusive traces. Another - unfortunately common
- practice is to grow bacteria in synthetic media where common
salts (potassium, magnesium and iron) are included, without any
addition of essential metals such as zinc or manganese (Miller,
1992). Yet bacteria grow, and grow well. I do not suspect them
to be able to transmute matter, or to universally substitute
zinc or manganese by iron or magnesium. In the same way the well
known « fluoride
effect » results from extraction of aluminum from glassware, making
AlF4, which, in fact, mimicks phosphate (Bigay et al. 1985). Specific
transporters are meant to import and export essential metals,
as well as to regulate their homeostasy in a variety of environments
where they usually exist as trace elements (Haas et al. 2009).
In Wolfe-Simon and colleagues experiments the traces of phosphate
present as contaminant at most steps in the building up of their
growth medium is certainly sufficient to permit growth of the
cells, with phosphorus playing its normal role. The main question
to answer, then, is not whether phosphate remains present with
its standard role, but how the cells cope with an environment
which is arsenic-replete.
The genome of several arsenic-loving
bacteria has been sequenced, in particular that of Herminiimonas
et al. 2007). This organisms uses arsenic to perform electron
transfers that permit it to manage energy while alleviating some
of its toxicity. But this cannot be enough, most probably, to
detoxify this element. Analysis of the genome sequence, as well
as that of other arsenophilic bacteria (including immediate kins
of the Halomonas species used in Wolfe-Simon and colleagues’
study) suggests a remarkable conjecture to explain how it does
so. While H. arsenicoxydans does not use selenium (as
other bacteria such as E. coli do, to make selenocysteine,
the 21st amino acid), it has the counterpart of the selD gene.
I note that Halomonas
elongata possesses the counterpart of this gene (HELO_4105). SelD
in « standard »
bacteria is the enzyme that makes selenophosphate, used to modify
serine on a tRNA that translates UGA codons into selenocysteine.
Selenium is the counterpart of sulfur in Medeleiev’s
table, it occupies a volume that is slightly larger than the
latter. A similar situation is met with arsenic and phosphorous.
Hence, a small distortion of the standard SelD catalytic site
would easily accomodate sulfur instead of selenium and arsenate
instead of phosphate. The role of SelD would then be to make
monothioarsenate (Figure 2). This compound can react with a variety
of compounds, biopolymers or minerals that it would decorate
with arsenic in an innocuous form. This would explain why arsenophilic
bacteria contain arsenic.
This hypothesis and others should be further explored before
we propose that life as we know it can develop using arsenic
in the place of phosphorus.
The idea that arsenic could have replaced phosphorus as a central
component of nucleic acids should never have been published in
a scientific journal.
This work benefited from discussions with Philippe
Marlière. It was supported by MICROME,
a Collaborative Project funded by the European Commission within its FP7
Programme, contract number 222886-2.
Adams, S. R., Sparkes, M. J., Dixon, H. B. (1984). The arsonomethyl
analogue of adenosine 5'-phosphate. An uncoupler of adenylate
kinase. Biochemical Journal. 221:829-836.
Bernas, R., Gradsztajn, E., Reeves, H. & Schatzman, E. (1967).
On the nucleosynthesis of lithium, beryllium, and boron. Annals
of Physics. 44:426-478.
Bigay, J., Deterre, P., Pfister, C., Chabre, M. (1985). Fluoroaluminates
activate transducin-GDP by mimicking the gamma-phosphate of GTP
in its binding site. FEBS Letters. 191:181-185.
Haas, C. E., Rodionov, D. A., Kropat, J., Malasarn, D., Merchant, S. S.,
de Crécy-Lagard, V. (2009). A subset of the diverse COG0523 family of
putative metal chaperones is linked to zinc homeostasis in all
kingdoms of life. BMC Genomics. 10: 470.
Hoyle, F. (1957). The Black Cloud. Harper. New York.
Lagunas, R., Sols, A. (1968). Arsenate induced activity of certain
enzymes on their dephosphorylated substrates. FEBS Letters. 1:32-34.
Lipmann, F. (1975). The roots of bioenergetics. Ciba Foundation
Symposium. 31: 3-22.
Miller, J. H. (1992). A short course in bacterial genetics. A
laboratory manual and handbook for Escherichia coli and related
bacteria. Cold Spring Harbor Laboratory Press.
Muller, D. and 36 colleagues. (2007). A tale of two oxidation
states: bacterial colonization of arsenic-rich environments.
PLoS Genetics. 3:e53.
Ou, H. Y., He, X., Shao, Y., Tai, C., Rajakumar, K., Deng, Z.
(2009). dndDB: a database focused on phosphorothioation of the
DNA backbone. PLoS One. 4:e5132
Popper, K. R. (1972). Conjectures and Refutations. The Growth
of Scientific Knowledge. Fourth Edition. Routledge and Kegan
Reilly, M. (2008). Early life could have relied on arsenic DNA.
New Scientist. 2653:10.
Webster, D., Sparkes, M. J., Dixon, H. B. (1978). An arsenical
analogue of adenosine diphosphate. Biochemical Journal. 169:239-244.
Wickramasinghe, R. H. (1973). Iron-sulphur proteins: their possible
place in the origin of life and the development of early metabolic
systems. Space Life Sciences. 4:341-352
Wolfe-Simon, F., Davies, P. C. W. & Anbar, A. D. (2008). Did nature also
choose arsenic? Nature Precedings; 2 Jan 2008. hdl:10101/npre.2008.1482.1 & International
Journal of Astrobiology, Published online by Cambridge University
Press 30 Jan 2009, doi:10.1017/S1473550408004394.
Wolfe-Simon, F. and 11 colleagues. (2010). A bacterium that can
grow by using arsenic instead of phosphorus. Science. Dec 2.
[Epub ahead of print]
Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann,
J. D., Deng, Z. (2005). A novel DNA modification by sulphur.
Molecular Microbiology. 57:1428-1438.