GFAJ-1
Encyclopedia
GFAJ-1 is a strain
of rod-shaped
bacterium in the family Halomonadaceae
. The extremophile
was isolated from the hypersaline and alkaline Mono Lake
in eastern California
by a research team led by NASA astrobiologist Felisa Wolfe-Simon
. In a 2010 Science
journal publication, the authors claimed that the microbe, when starved of phosphorus
, is capable of substituting arsenic for a small percentage of its phosphorus and sustain its growth. Immediately after publication, other microbiologists and biochemists expressed doubt about this hypothesis, and the claim that this bacterium uses arsenic instead of phosphorus in its metabolism is robustly debated in the scientific community. More recently, on 27 May 2011, Felisa Wolfe-Simon
and her team responded to the criticism in a followup Science
journal publication. Nonetheless, the findings have not yet been independently confirmed.
Felisa Wolfe-Simon
, a NASA
astrobiology
fellow in residence at the US Geological Survey in Menlo Park, California
. GFAJ stands for "Give Felisa a Job". The organism was isolated and cultured beginning in 2009 from samples she and her colleagues collected from sediments at the bottom of Mono Lake
, California, U.S.A. Mono Lake is hypersaline (about 90 grams/liter) and highly alkaline (pH
9.8). It also has one of the highest natural concentrations of arsenic in the world (200 μM). The discovery was widely publicized on 2 December 2010.
sequences shows GFAJ-1 to be closely related to other moderate halophile
("salt-loving") bacteria of the family Halomonadaceae
. Although the authors produced a cladogram
in which the strain is nested among members of Halomonas
, including H. alkaliphila
and H. venusta
, they did not explicitly assign the strain to that genus. Many bacteria are known to be able to tolerate high levels of arsenic, and to have a proclivity to take it up into their cells. However, GFAJ-1 has now been proposed to go a step further; when starved of phosphorus, it may instead incorporate arsenic into its metabolites and macromolecules and continue growing.
of Halomonadaceae and not as a new species
. The International Code of Nomenclature of Bacteria
, the set of regulations which govern the taxonomy
of bacteria, and certain articles in the International Journal of Systematic and Evolutionary Microbiology
contain the guidelines and minimal standards to describe a new species, e.g. the minimal standards to describe a member of the Halomonadaceae. Organisms are described as new species if they meet certain physiological and genetic condition, such as generally less than 97% 16S rRNA
sequence identity to other known species) and metabolic differences allowing them to be discerned apart. In addition to indicators to tell the novel species from other species, other analyses are required, such as fatty acid composition
, respiratory quinone used and tolerance ranges and deposition of the strain in at least two microbiological repositories. New proposed names are given in italics followed by sp. nov. (and gen. nov. if it is a novel genus according to the descriptions of that clade
). In the instance of the GFAJ-1 strain these criteria are not met, and the strain is not claimed to be a new species. When a strain is not assigned to a species (e.g. due to insufficient data or author choice) it is often labeled as the genus name followed by "sp." (i.e., undetermined species of that genus) and the strain name. In the case of GFAJ-1 the authors chose to refer to the strain by strain designation only. Strains closely related to GFAJ-1 include Halomonas sp. GTW and Halomonas sp. G27, neither of which were described as valid species.
If the authors had formally assigned strain GFAJ-1 to the Halomonas genus, the name would be given as Halomonas sp. GFAJ-1.
(which actually contained 3.1 ± 0.3 μM of residual phosphate, from impurities in reagents) was used to culture the bacteria in a regime of increasing exposure to arsenate
; the initial level of 0.1 mM was eventually ramped up to 40 mM. Alternative media used for comparative experiments contained either high levels of phosphate
(1.5 mM) with no arsenate, or had neither added phosphate nor added arsenate. It was observed that GFAJ-1 could grow through many doublings in cell numbers when cultured in either phosphate or arsenate media, but could not grow when placed in a medium of a similar composition to which neither phosphate nor arsenate was added. The phosphorus content of the arsenic-fed, phosphorus-starved bacteria (as measured by ICP-MS) was only 0.019 (± 0.001) % by dry weight, one thirtieth of that when grown in phosphate-rich medium. This phosphorus content was also only about one tenth of the cells' average arsenic content (0.19 ± 0.25 % by dry weight). The arsenic content of cells as measured by ICP-MS varies widely and can be lower than the phosphorus contents in some experiments, and up to fourteen times higher in others. Other data from the same study obtained with nano-SIMS
suggest a ~75-fold excess of phosphate (P) over arsenic (As) when expressed as P:C and As:C ratios, even in cells grown with arsenate and no added phosphate. When cultured in the arsenate solution, GFAJ-1 only grew 60% as fast as it did in phosphate solution. The phosphate-starved bacteria had an intracellular volume 1.5 times normal; the greater volume appeared to be associated with the appearance of large "vacuole
-like regions".
When the researchers added isotope-labeled
arsenate to the solution to track its distribution
, they found that arsenic was present in the cellular fractions containing the bacteria's protein
s, lipid
s and metabolites such as ATP
, as well as its DNA
and RNA
. Nucleic acids from stationary phase
cells starved of phosphorus were concentrated via five extraction
s (one with phenol
, three with phenol-chloroform
and one with chloroform
extraction solvent), followed by ethanol precipitation. Although direct evidence of the incorporation of arsenic into biomolecules is still lacking, radioactivity measurements suggested that approximately one-tenth (11.0 ± 0.1 %) of the arsenic absorbed by these bacteria ended up in the fraction that contained the nucleic acids (DNA and RNA) and all other co-precipitated compounds not extracted by the previous treatments. A comparable control experiment with isotope-labeled phosphate was not performed.
-3-hydroxybutyrat.svg.png)
Arsenate ester
s, such as those that would be present in DNA, are generally expected to be orders of magnitude less stable to hydrolysis
than corresponding phosphate ester
s. dAMAs, the structural arsenic analog of the DNA building block dAMP
, has a half-life
of 40 minutes in water at neutral pH. Estimates of the half-life in water of arsenodiester bonds, which would link the nucleotides together, are as short as 0.06 seconds—compared to 30 million years for the phosphodiester bonds in DNA. The authors speculate that the bacteria may stabilize arsenate esters to a degree by using poly-β-hydroxybutyrate
(which has been found to be elevated in "vacuole-like regions" of related species of the genus Halomonas
) or other means to lower the effective concentration
of water. Polyhydroxybutyrates are used by many bacteria for energy and carbon storage under conditions when growth is limited by elements other than carbon, and typically appear as large waxy granules closely resembling the "vacuole-like regions" seen in GFAJ-1 cells. The authors present no mechanism by which insoluble polyhydroxybutyrate may lower the effective concentration of water in the cytoplasm sufficiently to stabilize arsenate esters. Although all halophiles must reduce the water activity
of their cytoplasm by some means to avoid desiccation, the cytoplasm always remains an aqueous environment.
, as this could suggest that life
may form in the absence of large amounts of available phosphorus, thus increasing the probability of finding life elsewhere
in the universe
. If the study is correct, this finding may support the long-standing hypothesis
that life on other planets may have a chemical makeup differing from that of known organisms in fundamental ways, and could help in the search for extraterrestrial life
. It has also been speculated that use of arsenic in place of phosphorus on Earth may date back to the origin of life
, which may have occurred in arsenic-rich hydrothermal vent
environments.
commented "although the discovery of alien life, if it ever happens, would be one of the biggest stories imaginable, this was light-years from that."
In addition, many experts who have evaluated the paper have concluded that the reported studies do not provide enough evidence to support the claims made by the authors. In an online article on Slate
, science writer Carl Zimmer
discussed the skepticism of several scientists: "I reached out to a dozen experts ... Almost unanimously, they think the NASA scientists have failed to make their case".
Chemist Steven A. Benner has expressed doubts that arsenate
has replaced phosphate in the DNA of this organism. He suggested that the trace contaminants
in the growth medium used by Wolfe-Simon in her laboratory cultures are sufficient to supply the phosphorus needed for the cells' DNA. He believes that it is more likely that arsenic is being sequestered elsewhere in the cells. University of British Columbia
microbiologist
Rosemary Redfield said that the paper "doesn't present any convincing evidence that arsenic has been incorporated into DNA or any other biological molecule," and suggests that the experiments lacked the washing steps and controls
necessary to properly validate their conclusions. Harvard microbiologist Alex Bradley said that arsenic-containing DNA would be so unstable in water it could not have survived the analysis procedure.
On 8 December 2010, Science
published a response by Wolfe-Simon, in which she stated that criticism of the research was expected. In response, a "Frequently Asked Questions" page to improve understanding of the work was posted on 16 December 2010. The team plans to deposit the GFAJ-1 strain in the ATCC
and DSMZ
culture collections to allow widespread distribution. In late May 2011, the strain has also been made available upon request directly from the laboratory of the authors. Science has made the article freely available. The article was published in print six months after acceptance in the June 3, 2011 issue of Science. The publication was accompanied by eight technical comments addressing various concerns regarding the article's experimental procedure and conclusion, as well as a response by the authors to these concerns. The editor in chief
has indicated that some issues remain and that their resolution is likely to be a long process. A review by Rosen et al., in the March 2011 issue of journal Bioessays
, discusses the technical issues with the Science paper, provides alternative explanations, and highlights known biochemistry of other arsenic resistant and arsenic utilizing microbes.
, following issues with the growth conditions, investigated the growth requirements of GFAJ-1, and found that the strain grows better on solid agar
medium than in liquid culture. Redfield attributed this to low potassium levels and hypothesized that the potassium levels in basal ML60 medium may be too low to support growth. As of November 2011, the incorporation of arsenic into the genomic DNA or other biomolecules had not yet been addressed and had been neither confirmed nor refuted.
Strain (biology)
In biology, a strain is a low-level taxonomic rank used in three related ways.-Microbiology and virology:A strain is a genetic variant or subtype of a micro-organism . For example, a "flu strain" is a certain biological form of the influenza or "flu" virus...
of rod-shaped
Bacillus (shape)
The word bacillus may be used to describe any rod-shaped bacterium, and such bacilli are found in many different taxonomic groups of bacteria. However, the name Bacillus, capitalized and italicized, refers to a specific genus of bacteria...
bacterium in the family Halomonadaceae
Halomonadaceae
The Halomonadaceae are a family of halophilic Proteobacteria.-History:The family was originally created in 1988 to contain the genera Halomonas and Deleya....
. The extremophile
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...
was isolated from the hypersaline and alkaline Mono Lake
Mono Lake
Mono Lake is a large, shallow saline lake in Mono County, California, formed at least 760,000 years ago as a terminal lake in a basin that has no outlet to the ocean...
in eastern California
California
California is a state located on the West Coast of the United States. It is by far the most populous U.S. state, and the third-largest by land area...
by a research team led by NASA astrobiologist Felisa Wolfe-Simon
Felisa Wolfe-Simon
Felisa Wolfe-Simon is an American microbial geobiologist and biogeochemist. As a NASA research fellow in residence at the US Geological Survey and a member of the NASA Astrobiology Institute, Wolfe-Simon led the team that discovered GFAJ-1, an extremophile bacterium that they claim is capable of...
. In a 2010 Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
journal publication, the authors claimed that the microbe, when starved of phosphorus
Phosphorus
Phosphorus is the chemical element that has the symbol P and atomic number 15. A multivalent nonmetal of the nitrogen group, phosphorus as a mineral is almost always present in its maximally oxidized state, as inorganic phosphate rocks...
, is capable of substituting arsenic for a small percentage of its phosphorus and sustain its growth. Immediately after publication, other microbiologists and biochemists expressed doubt about this hypothesis, and the claim that this bacterium uses arsenic instead of phosphorus in its metabolism is robustly debated in the scientific community. More recently, on 27 May 2011, Felisa Wolfe-Simon
Felisa Wolfe-Simon
Felisa Wolfe-Simon is an American microbial geobiologist and biogeochemist. As a NASA research fellow in residence at the US Geological Survey and a member of the NASA Astrobiology Institute, Wolfe-Simon led the team that discovered GFAJ-1, an extremophile bacterium that they claim is capable of...
and her team responded to the criticism in a followup Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
journal publication. Nonetheless, the findings have not yet been independently confirmed.
Discovery
The GFAJ-1 bacterium was discovered by geomicrobiologistGeomicrobiology
Geomicrobiology is the result of the combination of geology and microbiology. The field of geomicrobiology concerns the role of microbe and microbial processes in geological and geochemical processes and vice-versa...
Felisa Wolfe-Simon
Felisa Wolfe-Simon
Felisa Wolfe-Simon is an American microbial geobiologist and biogeochemist. As a NASA research fellow in residence at the US Geological Survey and a member of the NASA Astrobiology Institute, Wolfe-Simon led the team that discovered GFAJ-1, an extremophile bacterium that they claim is capable of...
, a NASA
NASA Astrobiology Institute
The NASA Astrobiology Institute was established in 1998 by the National Aeronautics and Space Administration "to develop the field of astrobiology and provide a scientific framework for flight missions". The NAI is a virtual, distributed organization that integrates astrobiology research and...
astrobiology
Astrobiology
Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. This interdisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System, the search for evidence of prebiotic chemistry,...
fellow in residence at the US Geological Survey in Menlo Park, California
Menlo Park, California
Menlo Park, California is a city at the eastern edge of San Mateo County, in the San Francisco Bay Area of California, in the United States. It is bordered by San Francisco Bay on the north and east; East Palo Alto, Palo Alto, and Stanford to the south; Atherton, North Fair Oaks, and Redwood City...
. GFAJ stands for "Give Felisa a Job". The organism was isolated and cultured beginning in 2009 from samples she and her colleagues collected from sediments at the bottom of Mono Lake
Mono Lake
Mono Lake is a large, shallow saline lake in Mono County, California, formed at least 760,000 years ago as a terminal lake in a basin that has no outlet to the ocean...
, California, U.S.A. Mono Lake is hypersaline (about 90 grams/liter) and highly alkaline (pH
PH
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...
9.8). It also has one of the highest natural concentrations of arsenic in the world (200 μM). The discovery was widely publicized on 2 December 2010.
Taxonomy and phylogeny
Molecular analysis based on 16S rRNA16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
sequences shows GFAJ-1 to be closely related to other moderate halophile
Halophile
Halophiles are extremophile organisms that thrive in environments with very high concentrations of salt. The name comes from the Greek for "salt-loving". While the term is perhaps most often applied to some halophiles classified into the Archaea domain, there are also bacterial halophiles and some...
("salt-loving") bacteria of the family Halomonadaceae
Halomonadaceae
The Halomonadaceae are a family of halophilic Proteobacteria.-History:The family was originally created in 1988 to contain the genera Halomonas and Deleya....
. Although the authors produced a cladogram
Cladogram
A cladogram is a diagram used in cladistics which shows ancestral relations between organisms, to represent the evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational...
in which the strain is nested among members of Halomonas
Halomonas
Halomonas is a genus of halophilic Proteobacteria. It grows over the range of 5 to 25% NaClThe type species of this genus is Halomonas elongata,.-Etymology:...
, including H. alkaliphila
Halomonas alkaliphila
Halomonas alkaliphila is a Gram-negative halophilic Proteobacteria. Its specific epithet stems from the Arabic word alkali , the ashes of saltwort and the Latin adjective philus -a -um, meaning "friend" or "loving": loving alkaline media....
and H. venusta
Halomonas venusta
Halomonas venusta is a Gram-negative halophilic Proteobacteria, first described as Alcaligenes venustus and later reclassified as Halomonas venusta, along with other species when the genera Deleya , Halomonas Halomonas venusta is a Gram-negative halophilic Proteobacteria, first described as...
, they did not explicitly assign the strain to that genus. Many bacteria are known to be able to tolerate high levels of arsenic, and to have a proclivity to take it up into their cells. However, GFAJ-1 has now been proposed to go a step further; when starved of phosphorus, it may instead incorporate arsenic into its metabolites and macromolecules and continue growing.
Species/strain
In the Science journal article, GFAJ-1 is referred to as a strainStrain (biology)
In biology, a strain is a low-level taxonomic rank used in three related ways.-Microbiology and virology:A strain is a genetic variant or subtype of a micro-organism . For example, a "flu strain" is a certain biological form of the influenza or "flu" virus...
of Halomonadaceae and not as a new species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
. The International Code of Nomenclature of Bacteria
International Code of Nomenclature of Bacteria
The International Code of Nomenclature of Bacteria or Bacteriological Code governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank...
, the set of regulations which govern the taxonomy
Taxonomy
Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
of bacteria, and certain articles in the International Journal of Systematic and Evolutionary Microbiology
International Journal of Systematic and Evolutionary Microbiology
The International Journal of Systematic and Evolutionary Microbiology is a peer-reviewed scientific journal in the field of microbial systematics, first published in 1951...
contain the guidelines and minimal standards to describe a new species, e.g. the minimal standards to describe a member of the Halomonadaceae. Organisms are described as new species if they meet certain physiological and genetic condition, such as generally less than 97% 16S rRNA
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
sequence identity to other known species) and metabolic differences allowing them to be discerned apart. In addition to indicators to tell the novel species from other species, other analyses are required, such as fatty acid composition
Fatty acid methyl ester
A fatty acid methyl ester can be created by an alkali catalyzed reaction between fats or fatty acids and methanol. The molecules in biodiesel are primarily FAMEs, usually obtained from vegetable oils by transesterification....
, respiratory quinone used and tolerance ranges and deposition of the strain in at least two microbiological repositories. New proposed names are given in italics followed by sp. nov. (and gen. nov. if it is a novel genus according to the descriptions of that clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
). In the instance of the GFAJ-1 strain these criteria are not met, and the strain is not claimed to be a new species. When a strain is not assigned to a species (e.g. due to insufficient data or author choice) it is often labeled as the genus name followed by "sp." (i.e., undetermined species of that genus) and the strain name. In the case of GFAJ-1 the authors chose to refer to the strain by strain designation only. Strains closely related to GFAJ-1 include Halomonas sp. GTW and Halomonas sp. G27, neither of which were described as valid species.
If the authors had formally assigned strain GFAJ-1 to the Halomonas genus, the name would be given as Halomonas sp. GFAJ-1.
Biochemistry
A phosphorus-free growth mediumGrowth medium
A growth medium or culture medium is a liquid or gel designed to support the growth of microorganisms or cells, or small plants like the moss Physcomitrella patens.There are different types of media for growing different types of cells....
(which actually contained 3.1 ± 0.3 μM of residual phosphate, from impurities in reagents) was used to culture the bacteria in a regime of increasing exposure to arsenate
Arsenate
The arsenate ion is AsO43−.An arsenate is any compound that contains this ion. Arsenates are salts or esters of arsenic acid.The arsenic atom in arsenate has a valency of 5 and is also known as pentavalent arsenic or As[V]....
; the initial level of 0.1 mM was eventually ramped up to 40 mM. Alternative media used for comparative experiments contained either high levels of phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
(1.5 mM) with no arsenate, or had neither added phosphate nor added arsenate. It was observed that GFAJ-1 could grow through many doublings in cell numbers when cultured in either phosphate or arsenate media, but could not grow when placed in a medium of a similar composition to which neither phosphate nor arsenate was added. The phosphorus content of the arsenic-fed, phosphorus-starved bacteria (as measured by ICP-MS) was only 0.019 (± 0.001) % by dry weight, one thirtieth of that when grown in phosphate-rich medium. This phosphorus content was also only about one tenth of the cells' average arsenic content (0.19 ± 0.25 % by dry weight). The arsenic content of cells as measured by ICP-MS varies widely and can be lower than the phosphorus contents in some experiments, and up to fourteen times higher in others. Other data from the same study obtained with nano-SIMS
Secondary ion mass spectrometry
Secondary ion mass spectrometry is a technique used in materials science and surface science to analyze the composition of solid surfaces and thin films by sputtering the surface of the specimen with a focused primary ion beam and collecting and analyzing ejected secondary ions...
suggest a ~75-fold excess of phosphate (P) over arsenic (As) when expressed as P:C and As:C ratios, even in cells grown with arsenate and no added phosphate. When cultured in the arsenate solution, GFAJ-1 only grew 60% as fast as it did in phosphate solution. The phosphate-starved bacteria had an intracellular volume 1.5 times normal; the greater volume appeared to be associated with the appearance of large "vacuole
Vacuole
A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain...
-like regions".
When the researchers added isotope-labeled
Isotopic labeling
Isotopic labeling is a technique for tracking the passage of a sample of substance through a system. The substance is 'labeled' by including unusual isotopes in its chemical composition...
arsenate to the solution to track its distribution
Pulse-chase analysis
In biochemistry and molecular biology, a pulse-chase analysis is a method for examining a cellular process occurring over time by successively exposing the cells to a labeled compound and then to the same compound in an unlabeled form...
, they found that arsenic was present in the cellular fractions containing the bacteria's protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, lipid
Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...
s and metabolites such as ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
, as well as its DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
. Nucleic acids from stationary phase
Bacterial growth
250px|right|thumb|Growth is shown as L = log where numbers is the number of colony forming units per ml, versus T Bacterial growth is the division of one bacterium into two daughter cells in a process called binary fission. Providing no mutational event occurs the resulting daughter cells are...
cells starved of phosphorus were concentrated via five extraction
Liquid-liquid extraction
Liquid–liquid extraction, also known as solvent extraction and partitioning, is a method to separate compounds based on their relative solubilities in two different immiscible liquids, usually water and an organic solvent. It is an extraction of a substance from one liquid phase into another liquid...
s (one with phenol
Phenol
Phenol, also known as carbolic acid, phenic acid, is an organic compound with the chemical formula C6H5OH. It is a white crystalline solid. The molecule consists of a phenyl , bonded to a hydroxyl group. It is produced on a large scale as a precursor to many materials and useful compounds...
, three with phenol-chloroform
Phenol-chloroform extraction
Phenol–chloroform extraction is a liquid–liquid extraction technique in biochemistry. It is widely used in molecular biology for isolating DNA, RNA and protein. Equal volumes of a phenol:chloroform mixture and an aqueous sample are mixed, forming a biphasic mixture...
and one with chloroform
Chloroform
Chloroform is an organic compound with formula CHCl3. It is one of the four chloromethanes. The colorless, sweet-smelling, dense liquid is a trihalomethane, and is considered somewhat hazardous...
extraction solvent), followed by ethanol precipitation. Although direct evidence of the incorporation of arsenic into biomolecules is still lacking, radioactivity measurements suggested that approximately one-tenth (11.0 ± 0.1 %) of the arsenic absorbed by these bacteria ended up in the fraction that contained the nucleic acids (DNA and RNA) and all other co-precipitated compounds not extracted by the previous treatments. A comparable control experiment with isotope-labeled phosphate was not performed.
Arsenate ester stability
Ester
Esters are chemical compounds derived by reacting an oxoacid with a hydroxyl compound such as an alcohol or phenol. Esters are usually derived from an inorganic acid or organic acid in which at least one -OH group is replaced by an -O-alkyl group, and most commonly from carboxylic acids and...
s, such as those that would be present in DNA, are generally expected to be orders of magnitude less stable to hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
than corresponding phosphate ester
Organophosphate
An organophosphate is the general name for esters of phosphoric acid. Phosphates are probably the most pervasive organophosphorus compounds. Many of the most important biochemicals are organophosphates, including DNA and RNA as well as many cofactors that are essential for life...
s. dAMAs, the structural arsenic analog of the DNA building block dAMP
Deoxyadenosine monophosphate
Deoxyadenosine monophosphate, also known as deoxyadenylate, or dAMP, is a derivative of the common nucleic acid AMP, or adenosine monophosphate, in which the -OH group on the 2' carbon on the nucleotide's pentose has been reduced to just a hydrogen atom . Deoxyadenosine monophosphate is...
, has a half-life
Half-life
Half-life, abbreviated t½, is the period of time it takes for the amount of a substance undergoing decay to decrease by half. The name was originally used to describe a characteristic of unstable atoms , but it may apply to any quantity which follows a set-rate decay.The original term, dating to...
of 40 minutes in water at neutral pH. Estimates of the half-life in water of arsenodiester bonds, which would link the nucleotides together, are as short as 0.06 seconds—compared to 30 million years for the phosphodiester bonds in DNA. The authors speculate that the bacteria may stabilize arsenate esters to a degree by using poly-β-hydroxybutyrate
Polyhydroxybutyrate
Polyhydroxybutyrate is a polyhydroxyalkanoate , a polymer belonging to the polyesters class that was first isolated and characterized in 1925 by French microbiologist Maurice Lemoigne. PHB is produced by microorganisms apparently in response to conditions of physiological stress...
(which has been found to be elevated in "vacuole-like regions" of related species of the genus Halomonas
Halomonas
Halomonas is a genus of halophilic Proteobacteria. It grows over the range of 5 to 25% NaClThe type species of this genus is Halomonas elongata,.-Etymology:...
) or other means to lower the effective concentration
Activity (chemistry)
In chemical thermodynamics, activity is a measure of the “effective concentration” of a species in a mixture, meaning that the species' chemical potential depends on the activity of a real solution in the same way that it would depend on concentration for an ideal solution.By convention, activity...
of water. Polyhydroxybutyrates are used by many bacteria for energy and carbon storage under conditions when growth is limited by elements other than carbon, and typically appear as large waxy granules closely resembling the "vacuole-like regions" seen in GFAJ-1 cells. The authors present no mechanism by which insoluble polyhydroxybutyrate may lower the effective concentration of water in the cytoplasm sufficiently to stabilize arsenate esters. Although all halophiles must reduce the water activity
Water activity
Water activity or aw was developed to account for the intensity with which water associates with various non-aqueous constituents and solids. Simply stated, it is a measure of the energy status of the water in a system...
of their cytoplasm by some means to avoid desiccation, the cytoplasm always remains an aqueous environment.
Possible implications
The discovery of a microorganism that uses arsenic to build some of its cellular components would have implications in the area of astrobiologyAstrobiology
Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. This interdisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System, the search for evidence of prebiotic chemistry,...
, as this could suggest that life
Life
Life is a characteristic that distinguishes objects that have signaling and self-sustaining processes from those that do not, either because such functions have ceased , or else because they lack such functions and are classified as inanimate...
may form in the absence of large amounts of available phosphorus, thus increasing the probability of finding life elsewhere
Drake equation
The Drake equation is an equation used to estimate the number of detectable extraterrestrial civilizations in the Milky Way galaxy. It is used in the fields of exobiology and the Search for ExtraTerrestrial Intelligence...
in the universe
Universe
The Universe is commonly defined as the totality of everything that exists, including all matter and energy, the planets, stars, galaxies, and the contents of intergalactic space. Definitions and usage vary and similar terms include the cosmos, the world and nature...
. If the study is correct, this finding may support the long-standing hypothesis
Hypothesis
A hypothesis is a proposed explanation for a phenomenon. The term derives from the Greek, ὑποτιθέναι – hypotithenai meaning "to put under" or "to suppose". For a hypothesis to be put forward as a scientific hypothesis, the scientific method requires that one can test it...
that life on other planets may have a chemical makeup differing from that of known organisms in fundamental ways, and could help in the search for extraterrestrial life
Extraterrestrial life
Extraterrestrial life is defined as life that does not originate from Earth...
. It has also been speculated that use of arsenic in place of phosphorus on Earth may date back to the origin of life
Abiogenesis
Abiogenesis or biopoesis is the study of how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose...
, which may have occurred in arsenic-rich hydrothermal vent
Hydrothermal vent
A hydrothermal vent is a fissure in a planet's surface from which geothermally heated water issues. Hydrothermal vents are commonly found near volcanically active places, areas where tectonic plates are moving apart, ocean basins, and hotspots. Hydrothermal vents exist because the earth is both...
environments.
Criticism
NASA's announcement of a news conference "that will impact the search for evidence of extraterrestrial life" was criticized as sensationalistic and misleading; an editorial in New ScientistNew Scientist
New Scientist is a weekly non-peer-reviewed English-language international science magazine, which since 1996 has also run a website, covering recent developments in science and technology for a general audience. Founded in 1956, it is published by Reed Business Information Ltd, a subsidiary of...
commented "although the discovery of alien life, if it ever happens, would be one of the biggest stories imaginable, this was light-years from that."
In addition, many experts who have evaluated the paper have concluded that the reported studies do not provide enough evidence to support the claims made by the authors. In an online article on Slate
Slate (magazine)
Slate is a US-based English language online current affairs and culture magazine created in 1996 by former New Republic editor Michael Kinsley, initially under the ownership of Microsoft as part of MSN. On 21 December 2004 it was purchased by the Washington Post Company...
, science writer Carl Zimmer
Carl Zimmer
Carl Zimmer is a popular science writer and blogger, especially regarding the study of evolution and parasites. He has written several books and contributes science essays to publications such as The New York Times and Discover...
discussed the skepticism of several scientists: "I reached out to a dozen experts ... Almost unanimously, they think the NASA scientists have failed to make their case".
Chemist Steven A. Benner has expressed doubts that arsenate
Arsenate
The arsenate ion is AsO43−.An arsenate is any compound that contains this ion. Arsenates are salts or esters of arsenic acid.The arsenic atom in arsenate has a valency of 5 and is also known as pentavalent arsenic or As[V]....
has replaced phosphate in the DNA of this organism. He suggested that the trace contaminants
Trace element
In analytical chemistry, a trace element is an element in a sample that has an average concentration of less than 100 parts per million measured in atomic count, or less than 100 micrograms per gram....
in the growth medium used by Wolfe-Simon in her laboratory cultures are sufficient to supply the phosphorus needed for the cells' DNA. He believes that it is more likely that arsenic is being sequestered elsewhere in the cells. University of British Columbia
University of British Columbia
The University of British Columbia is a public research university. UBC’s two main campuses are situated in Vancouver and in Kelowna in the Okanagan Valley...
microbiologist
Microbiologist
A microbiologist is a scientist who works in the field of microbiology. Microbiologists study organisms called microbes. Microbes can take the form of bacteria, viruses, fungi, and protists...
Rosemary Redfield said that the paper "doesn't present any convincing evidence that arsenic has been incorporated into DNA or any other biological molecule," and suggests that the experiments lacked the washing steps and controls
Scientific control
Scientific control allows for comparisons of concepts. It is a part of the scientific method. Scientific control is often used in discussion of natural experiments. For instance, during drug testing, scientists will try to control two groups to keep them as identical and normal as possible, then...
necessary to properly validate their conclusions. Harvard microbiologist Alex Bradley said that arsenic-containing DNA would be so unstable in water it could not have survived the analysis procedure.
On 8 December 2010, Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
published a response by Wolfe-Simon, in which she stated that criticism of the research was expected. In response, a "Frequently Asked Questions" page to improve understanding of the work was posted on 16 December 2010. The team plans to deposit the GFAJ-1 strain in the ATCC
American Type Culture Collection
The American Type Culture Collection is a private, not-for-profit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the...
and DSMZ
Deutsche Sammlung von Mikroorganismen und Zellkulturen
The Deutsche Sammlung von Mikroorganismen und Zellkulturen - DSMZ - GmbH was founded 1969 as the national culture collection in Germany...
culture collections to allow widespread distribution. In late May 2011, the strain has also been made available upon request directly from the laboratory of the authors. Science has made the article freely available. The article was published in print six months after acceptance in the June 3, 2011 issue of Science. The publication was accompanied by eight technical comments addressing various concerns regarding the article's experimental procedure and conclusion, as well as a response by the authors to these concerns. The editor in chief
Bruce Alberts
Bruce Michael Alberts is an American biochemist known for his work in science public policy and as an original author of the Molecular Biology of the Cell...
has indicated that some issues remain and that their resolution is likely to be a long process. A review by Rosen et al., in the March 2011 issue of journal Bioessays
Bioessays
BioEssays is a monthly scientific review journal that publishes reviews, hypotheses, insights and commentary in the field of biology. Areas covered include cell biology, molecular biology, biochemistry, genetics, genomics, evolution, neuroscience, physiology, molecular pathogenesis, Applied Biology...
, discusses the technical issues with the Science paper, provides alternative explanations, and highlights known biochemistry of other arsenic resistant and arsenic utilizing microbes.
Independent investigations
With the distribution of the strain in mid-2011, other labs began to independently test the validity of the discovery. Prof. Rosie Redfield from the University of British ColumbiaUniversity of British Columbia
The University of British Columbia is a public research university. UBC’s two main campuses are situated in Vancouver and in Kelowna in the Okanagan Valley...
, following issues with the growth conditions, investigated the growth requirements of GFAJ-1, and found that the strain grows better on solid agar
Agar
Agar or agar-agar is a gelatinous substance derived from a polysaccharide that accumulates in the cell walls of agarophyte red algae. Throughout history into modern times, agar has been chiefly used as an ingredient in desserts throughout Asia and also as a solid substrate to contain culture medium...
medium than in liquid culture. Redfield attributed this to low potassium levels and hypothesized that the potassium levels in basal ML60 medium may be too low to support growth. As of November 2011, the incorporation of arsenic into the genomic DNA or other biomolecules had not yet been addressed and had been neither confirmed nor refuted.
See also
- Arsenic biochemistryArsenic biochemistryArsenic biochemistry refers to biochemical processes that can use arsenic or its compounds, such as arsenate. Arsenic is a moderately abundant element on the earth's crust, and although many arsenic compounds are often considered highly toxic, a wide variety of organoarsenic compounds are produced...
- Arsenic poisoningArsenic poisoningArsenic poisoning is a medical condition caused by increased levels of the element arsenic in the body. Arsenic interferes with cellular longevity by allosteric inhibition of an essential metabolic enzyme...
- Arsenic toxicityArsenic toxicityArsenic and many of its compounds are especially potent poisons. Arsenic disrupts ATP production through several mechanisms. At the level of the citric acid cycle, arsenic inhibits pyruvate dehydrogenase and by competing with phosphate it uncouples oxidative phosphorylation, thus inhibiting...
- Hypothetical types of biochemistry
- Nucleic acid analoguesNucleic acid analoguesNucleic acid analogues are compounds structurally similar to naturally occurring RNA and DNA, used in medicine and in molecular biology research....
- Organoarsenic chemistry
- Prebiotic arsenic
External links
- NASA - Official Presentation on 2010-12-02 — Video (56:53) and related information. — (3 December 2010)
- NASA.gov: "NASA-Funded Research Discovers Life Built With Toxic Chemical" — (2 December 2010)
- NASA – Astrobiology Magazine: "Searching for Alien Life, on Earth". — (9 October 2009)
- Felisa Wolfe-Simon's web site