GFAJ-1

Last updated

Magnified cells of bacterium GFAJ-1 grown in medium containing arsenate GFAJ-1 (grown on arsenic).jpg
Magnified cells of bacterium GFAJ-1 grown in medium containing arsenate

GFAJ-1 is a strain of rod-shaped bacteria in the family Halomonadaceae. It is an extremophile that was isolated from the hypersaline and alkaline Mono Lake in eastern California by geobiologist Felisa Wolfe-Simon, a NASA research fellow in residence at the US Geological Survey. In a 2010 Science journal publication, [1] the authors claimed that the microbe, when starved of phosphorus, is capable of substituting arsenic for a small percentage of its phosphorus to sustain its growth. [2] [3] Immediately after publication, other microbiologists and biochemists expressed doubt about this claim, which was robustly criticized in the scientific community. Subsequent independent studies published in 2012 found no detectable arsenate in the DNA of GFAJ-1, refuted the claim, and demonstrated that GFAJ-1 is simply an arsenate-resistant, phosphate-dependent organism. [4] [5] [6] [7]

Contents

Discovery

Wolfe-Simon at Mono Lake, 2010 503354main Wolfe Simon.jpg
Wolfe-Simon at Mono Lake, 2010

The GFAJ-1 bacterium was discovered by geomicrobiologist Felisa Wolfe-Simon, a NASA astrobiology fellow in residence at the US Geological Survey in Menlo Park, California. [8] GFAJ stands for "Give Felisa a Job". [9] 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. [10] Mono Lake is hypersaline (about 90 grams/liter) and highly alkaline (pH 9.8). [11] It also has one of the highest natural concentrations of arsenic in the world (200 μM). [1] The discovery was widely publicized on 2 December 2010. [2]

Taxonomy and phylogeny

Escherichia coli strain O157:H7

Halomonas alkaliphila

Halomonas venusta strain NBSL13

GFAJ-1

Halomonas sp. GTW

Halomonas sp. G27

Halomonas sp. DH77

Halomonas sp. mp3

Halomonas sp. IB-O18

Halomonas sp. ML-185

Phylogeny of GFAJ-1 based on ribosomal DNA sequences. [12]

Molecular analysis based on 16S rRNA 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 , [12] they did not explicitly assign the strain to that genus. [1] [10] 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. [1] [13] However, GFAJ-1 was controversially proposed to go a step further; when starved of phosphorus, it was proposed to instead incorporate arsenic into its metabolites and macromolecules and continue growing. [10]

The sequence of the genome of the bacterium GFAJ-1 is now posted in GenBank. [14]

Species or strain

Tufa formations along the shore of Mono Lake Mono Lake 1.JPG
Tufa formations along the shore of Mono Lake

In the Science journal article, GFAJ-1 is referred to as a strain of Halomonadaceae and not as a new species. [1] 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. [15] Organisms are described as new species if they meet certain physiological and genetic conditions, such as generally less than 97% 16S rRNA sequence identity to other known species [16] 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). [17] [18]

In the instance of the GFAJ-1 strain these criteria are not met, and the strain is not claimed to be a new species. [1] When a strain is not assigned to a species (e.g. due to insufficient data or 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. [19] [20] If the authors had formally assigned strain GFAJ-1 to the genus Halomonas, [10] the name would be given as Halomonas sp. GFAJ-1.

The Genome Taxonomy Database assigns GFAJ-1 its own tentative species, Halomonas sp002966495. This means that the strain falls into Halomonas phylogenetically, and its whole-genome similarity compared to other defined species of the genus is low enough. Neither strain GTW nor strain G27 has a genome available for the database to run its classification. [21]

Biochemistry

A phosphorus-free growth medium (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. [1] 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). [1] 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. [22] 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. [12] When cultured in the arsenate solution, GFAJ-1 only grew 60% as fast as it did in phosphate solution. [2] 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". [1]

Scanning electron micrograph of GFAJ-1 cells grown in defined minimal medium supplemented with 1.5 mM phosphate GFAJ-1 (grown on phosphorus).jpg
Scanning electron micrograph of GFAJ-1 cells grown in defined minimal medium supplemented with 1.5 mM phosphate

When the researcher, Joseph Tolle 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 proteins, lipids and metabolites such as ATP, as well as its DNA and RNA. [2] Nucleic acids from stationary phase cells starved of phosphorus were concentrated via five extractions (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. [1] A comparable control experiment with isotope-labeled phosphate was not performed. With the distribution of the strain in mid-2011, other labs began to independently test the validity of the discovery. Rosemary Redfield from the University of British Columbia, 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. [23] Redfield after finding and addressing further issues (ionic strength, pH and the use of glass tubes instead of polypropylene) found that arsenate marginally stimulated growth, but didn't affect the final densities of the cultures, unlike what was claimed. [24] Subsequent studies using mass spectrometry by the same group found no evidence of arsenate being incorporated into the DNA of GFAJ-1. [25]

Arsenate ester stability

Structure of poly-b-hydroxybutyrate Poly-(R)-3-hydroxybutyrat.svg
Structure of poly-β-hydroxybutyrate

Arsenate esters, such as those that would be present in DNA, are generally expected to be orders of magnitude less stable to hydrolysis than corresponding phosphate esters. [26] dAMAs, the structural arsenic analog of the DNA building block dAMP, has a half-life of 40 minutes in water at neutral pH. [27] 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. [28] 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 [29] ) or other means to lower the effective concentration of water. [1] [10] 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. [30] 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, [31] the cytoplasm always remains an aqueous environment.

Criticism of Science study

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 Scientist 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". [32] [33]

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. [34] 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". [35] [36] 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. [2] [10] 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. [37] [38] Harvard microbiologist Alex Bradley said that arsenic-containing DNA would be so unstable in water it could not have survived the analysis procedure. [35] [39]

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. [40] The team plans to deposit the GFAJ-1 strain in the ATCC and DSMZ culture collections to allow widespread distribution. [41] In late May 2011 the strain was made available upon request directly from the laboratory of the authors. [42] Science has made the article freely available. [43] The article was published in print six months after acceptance in the 3 June 2011 issue of Science. The publication was accompanied by eight technical comments addressing various concerns regarding the article's experimental procedure and conclusion, [44] [45] [46] [47] [48] [49] [50] [51] [52] as well as a response by the authors to these concerns. [42] [53] The editor in chief Bruce Alberts has indicated that some issues remain and that their resolution is likely to be a long process. [54] A review by Rosen et al., [55] in the March 2011 issue of the 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.

On 27 May 2011, Wolfe-Simon and her team responded to the criticism in a follow-up Science journal publication. [42] Then in January 2012 a group of researchers led by Rosie Redfield at the University of British Columbia analyzed the DNA of GFAJ-1 using liquid chromatography–mass spectrometry and could not detect any arsenic, which Redfield calls a "clear refutation" of the original paper's findings. [56] Following the publication of the analysis, Wolfe-Simon stated that she and her colleagues "expect to publish new information in the next few months", [57] but as of 2024 has not submitted any new publications since 2011.

A simple explanation for the GFAJ-1 growth in medium supplied with arsenate instead of phosphate was provided by a team of researchers at the University of Miami in Florida. After labeling the ribosomes of a laboratory strain of Escherichia coli with radioactive isotopes (forming a radioactive tracer), they followed bacterial growth in medium containing arsenate but no phosphate. They found that arsenate induces massive degradation of ribosomes, thus providing sufficient phosphate for the slow growth of arsenate tolerant bacteria. Similarly, they suggest, GFAJ-1 cells grow by recycling phosphate from degraded ribosomes, rather than by replacing it with arsenate. [58]

Following the publication of the articles challenging the conclusions of the original Science article first describing GFAJ-1, the website Retraction Watch argued that the original article should be retracted because of misrepresentation of critical data. [59] [60] As of January 2024, the paper had not been retracted. [1]

See also

Related Research Articles

<span class="mw-page-title-main">Arsenic</span> Chemical element, symbol As and atomic number 33

Arsenic is a chemical element; it has symbol As and atomic number 33. It is a metalloid and one of the pnictogens, and therefore shares many properties with its group 15 neighbors phosphorus and antimony. Arsenic is a notoriously toxic heavy metal. It occurs naturally in many minerals, usually in combination with sulfur and metals, but also as a pure elemental crystal. It has various allotropes, but only the grey form, which has a metallic appearance, is important to industry.

<span class="mw-page-title-main">Hypothetical types of biochemistry</span> Possible alternative biochemicals used by life forms

Hypothetical types of biochemistry are forms of biochemistry agreed to be scientifically viable but not proven to exist at this time. The kinds of living organisms currently known on Earth all use carbon compounds for basic structural and metabolic functions, water as a solvent, and DNA or RNA to define and control their form. If life exists on other planets or moons it may be chemically similar, though it is also possible that there are organisms with quite different chemistries – for instance, involving other classes of carbon compounds, compounds of another element, or another solvent in place of water.

<span class="mw-page-title-main">Extremophile</span> Organisms capable of living in extreme environments

An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.

<i>Thiomargarita namibiensis</i> Species of bacterium

Thiomargarita namibiensis is a harmless, gram-negative, facultative anaerobic, coccoid bacterium found in the ocean sediments of the continental shelf of Namibia. The genus name Thiomargarita means "sulfur pearl." This refers to the appearance of the cells as they contain microscopic sulfur granules that scatter incident light, lending the cell a pearly luster. This causes the cells to form chains, resembling strings of pearls. The species name namibiensis means "of Namibia", which is an ode to their country of discovery and existence. Together, Thiomargarita namibiensis means “Sulfur pearl of Namibia".

<span class="mw-page-title-main">Paul Davies</span> British physicist

Paul Charles William Davies is an English physicist, writer and broadcaster, a professor in Arizona State University and director of BEYOND: Center for Fundamental Concepts in Science. He is affiliated with the Institute for Quantum Studies in Chapman University in California. He previously held academic appointments in the University of Cambridge, University College London, University of Newcastle upon Tyne, University of Adelaide and Macquarie University. His research interests are in the fields of cosmology, quantum field theory, and astrobiology.

<i>Prochlorococcus</i> Genus of bacteria

Prochlorococcus is a genus of very small (0.6 μm) marine cyanobacteria with an unusual pigmentation. These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynthetic organism on Earth. Prochlorococcus microbes are among the major primary producers in the ocean, responsible for a large percentage of the photosynthetic production of oxygen. Prochlorococcus strains, called ecotypes, have physiological differences enabling them to exploit different ecological niches. Analysis of the genome sequences of Prochlorococcus strains show that 1,273 genes are common to all strains, and the average genome size is about 2,000 genes. In contrast, eukaryotic algae have over 10,000 genes.

<span class="mw-page-title-main">Halomonadaceae</span> Family of bacteria

Halomonadaceae is a family of halophilic Pseudomonadota.

The arsenate is an ion with the chemical formula AsO3−4. Bonding in arsenate consists of a central arsenic atom, with oxidation state +5, double bonded to one oxygen atom and single bonded to a further three oxygen atoms. The four oxygen atoms orient around the arsenic atom in a tetrahedral geometry. Resonance disperses the ion's −3 charge across all four oxygen atoms.

<span class="mw-page-title-main">Redfield ratio</span>

The Redfield ratio or Redfield stoichiometry is the consistent atomic ratio of carbon, nitrogen and phosphorus found in marine phytoplankton and throughout the deep oceans.

<span class="mw-page-title-main">Phosphate solubilizing bacteria</span> Bacteria

Phosphate solubilizing bacteria (PSB) are beneficial bacteria capable of solubilizing inorganic phosphorus from insoluble compounds. P-solubilization ability of rhizosphere microorganisms is considered to be one of the most important traits associated with plant phosphate nutrition. It is generally accepted that the mechanism of mineral phosphate solubilization by PSB strains is associated with the release of low molecular weight organic acids, through which their hydroxyl and carboxyl groups chelate the cations [an ion that have positive charge on it.] bound to phosphate, thereby converting it into soluble forms. PSB have been introduced to the Agricultural community as phosphate Biofertilizer. Phosphorus (P) is one of the major essential macronutrients for plants and is applied to soil in the form of phosphate fertilizers. However, a large portion of soluble inorganic phosphate which is applied to the soil as chemical fertilizer is immobilized rapidly and becomes unavailable to plants. Currently, the main purpose in managing soil phosphorus is to optimize crop production and minimize P loss from soils. PSB have attracted the attention of agriculturists as soil inoculums to improve the plant growth and yield. When PSB is used with rock phosphate, it can save about 50% of the crop requirement of phosphatic fertilizer. The use of PSB as inoculants increases P uptake by plants. Simple inoculation of seeds with PSB gives crop yield responses equivalent to 30 kg P2O5 /ha or 50 percent of the need for phosphatic fertilizers. Alternatively, PSB can be applied through fertigation or in hydroponic operations. Many different strains of these bacteria have been identified as PSB, including Pantoea agglomerans (P5), Microbacterium laevaniformans (P7) and Pseudomonas putida (P13) strains are highly efficient insoluble phosphate solubilizers. Recently, researchers at Colorado State University demonstrated that a consortium of four bacteria, synergistically solubilize phosphorus at a much faster rate than any single strain alone. Mahamuni and Patil (2012) isolated four strains of phosphate solubilizing bacteria from sugarcane (VIMP01 and VIMP02) and sugar beet rhizosphere (VIMP03 and VIMP 04). Isolates were strains of Burkholderia named as VIMP01, VIMP02, VIMP03 and VIMP04. VIMP (Vasantdada Sugar Institute Isolate by Mahamuni and Patil) cultures were identified as Burkholderia cenocepacia strain VIMP01 (JQ867371), Burkholderia gladioli strain VIMP02 (JQ811557), Burkholderia gladioli strain VIMP03 (JQ867372) and Burkholderia species strain VIMP04 (JQ867373).

<span class="mw-page-title-main">Felisa Wolfe-Simon</span> American geomicrobiologist

Felisa Wolfe-Simon is an American microbial geobiologist and biogeochemist. In 2010, Wolfe-Simon led a team that discovered GFAJ-1, an extremophile bacterium that they claimed was capable of substituting arsenic for a small percentage of its phosphorus to sustain its growth, thus advancing the remarkable possibility of non-RNA/DNA-based genetics. However, these conclusions were immediately debated and criticized in correspondence to the original journal of publication, and have since come to be widely disbelieved, though they have never been disputed by any legitimate scientific studies. In 2012, two reports refuting the most significant aspects of the original results were published in the same journal in which the original findings had been previously published.

Arsenic biochemistry refers to biochemical processes that can use arsenic or its compounds, such as arsenate. Arsenic is a moderately abundant element in Earth's crust, and although many arsenic compounds are often considered highly toxic to most life, a wide variety of organoarsenic compounds are produced biologically and various organic and inorganic arsenic compounds are metabolized by numerous organisms. This pattern is general for other related elements, including selenium, which can exhibit both beneficial and deleterious effects. Arsenic biochemistry has become topical since many toxic arsenic compounds are found in some aquifers, potentially affecting many millions of people via biochemical processes.

<i>Halomonas titanicae</i> Species of bacterium

Halomonas titanicae is a gram-negative, halophilic species of bacteria which was isolated in 2010 from rusticles recovered from the wreck of the RMS Titanic. It has been estimated by Henrietta Mann, one of the researchers that first isolated it, that the action of microbes like Halomonas titanicae may bring about the total deterioration of the Titanic by 2030. While the bacteria have been identified as a potential danger to oil rigs and other man-made objects in the deep sea, they also have the potential to be used in bioremediation to accelerate the decomposition of shipwrecks littering the ocean floor.

<span class="mw-page-title-main">Mary Voytek</span> Director of NASA Astrobiology Program and USGS microbiologist

Dr. Mary A. Voytek is the director of the National Aeronautics and Space Administration (NASA) Astrobiology Program at NASA Headquarters in Washington, D.C. In 2015, Voytek formed Nexus for Exoplanet System Science (NExSS), a systems science initiative by NASA, to search for life on exoplanets. Voytek came to NASA from the U.S. Geological Survey in Reston, VA, where she headed the USGS Microbiology and Molecular Ecology Laboratory from 1998 to 2009.

Arsenate-reducing bacteria are bacteria which reduce arsenates. Arsenate-reducing bacteria are ubiquitous in arsenic-contaminated groundwater (aqueous environment). Arsenates are salts or esters of arsenic acid (H3AsO4), consisting of the ion AsO43−. They are moderate oxidizers that can be reduced to arsenites and to arsine. Arsenate can serve as a respiratory electron acceptor for oxidation of organic substrates and H2S or H2. Arsenates occur naturally in minerals such as adamite, alarsite, legrandite, and erythrite, and as hydrated or anhydrous arsenates. Arsenates are similar to phosphates since arsenic (As) and phosphorus (P) occur in group 15 (or VA) of the periodic table. Unlike phosphates, arsenates are not readily lost from minerals due to weathering. They are the predominant form of inorganic arsenic in aqueous aerobic environments. On the other hand, arsenite is more common in anaerobic environments, more mobile, and more toxic than arsenate. Arsenite is 25–60 times more toxic and more mobile than arsenate under most environmental conditions. Arsenate can lead to poisoning, since it can replace inorganic phosphate in the glyceraldehyde-3-phosphate --> 1,3-biphosphoglycerate step of glycolysis, producing 1-arseno-3-phosphoglycerate instead. Although glycolysis continues, 1 ATP molecule is lost. Thus, arsenate is toxic due to its ability to uncouple glycolysis. Arsenate can also inhibit pyruvate conversion into acetyl-CoA, thereby blocking the TCA cycle, resulting in additional loss of ATP.

<span class="mw-page-title-main">Julia Vorholt</span> Swiss microbiologist

Julia A. Vorholt is a full professor of microbiology at ETH Zurich and an elected member of the German Academy of Sciences Leopoldina.

<span class="mw-page-title-main">Rosemary Redfield</span> Microbiologist

Rosemary Jeanne Redfield is a microbiologist associated with the University of British Columbia where she worked as a faculty member in the Department of Zoology from 1993 until retiring in 2021.

<i>Crocosphaera watsonii</i> Species of bacterium

Crocosphaera watsonii is an isolate of a species of unicellular diazotrophic marine cyanobacteria which represent less than 0.1% of the marine microbial population. They thrive in offshore, open-ocean oligotrophic regions where the waters are warmer than 24 degrees Celsius. Crocosphaera watsonii cell density can exceed 1,000 cells per milliliter within the euphotic zone; however, their growth may be limited by the concentration of phosphorus. Crocosphaera watsonii are able to contribute to the oceanic carbon and nitrogen budgets in tropical oceans due to their size, abundance, and rapid growth rate. Crocosphaera watsonii are unicellular nitrogen fixers that fix atmospheric nitrogen to ammonia during the night and contribute to new nitrogen in the oceans. They are a major source of nitrogen to open-ocean systems. Nitrogen fixation is important in the oceans as it not only allows phytoplankton to continue growing when nitrogen and ammonium are in very low supply but it also replenishes other forms of nitrogen, thus fertilizing the ocean and allowing more phytoplankton growth.

<span class="mw-page-title-main">Ronald Oremland</span> American microbiologist

Ronald Oremland was an American microbiologist, astrobiologist, and emeritus senior scientist at the United States Geological Survey. He authored over 200 papers on the microbiology of extreme habitats.

Lulu Qian is a Chinese-American biochemist who is a professor at the California Institute of Technology. Her research uses DNA-like molecules to build artificial machines.

References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 Wolfe-Simon, Felisa; Blum, Jodi Switzer; Kulp, Thomas R.; Gordon, Gwyneth W.; Hoeft, Shelley E.; Pett-Ridge, Jennifer; Stolz, John F.; Webb, Samuel M.; et al. (2 December 2010). "A bacterium that can grow by using arsenic instead of phosphorus" (PDF). Science . 332 (6034): 1163–1166. Bibcode:2011Sci...332.1163W. doi: 10.1126/science.1197258 . PMID   21127214. S2CID   51834091.
  2. 1 2 3 4 5 Katsnelson, Alla (2 December 2010). "Arsenic-eating microbe may redefine chemistry of life". Nature News . doi:10.1038/news.2010.645 . Retrieved 2 December 2010.
  3. ↑ "Arsenic-loving bacteria may help in hunt for alien life". BBC News . 2 December 2010. Retrieved 2 December 2010.
  4. ↑ "Studies refute arsenic bug claim". BBC News. 9 July 2012. Retrieved 10 July 2012.
  5. ↑ Tobias J. Erb; Patrick Kiefer; Bodo Hattendorf; Detlef Gunter; Julia Vorholt (8 July 2012). "GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism". Science. 337 (6093): 467–70. Bibcode:2012Sci...337..467E. doi: 10.1126/science.1218455 . PMID   22773139. S2CID   20229329.
  6. ↑ RRResearch By Rosie Redfield. 16 January 2012
  7. ↑ Marshall Louis Reaves; Sunita Sinha; Joshua Rabinowitz; Leonid Kruglyak; Rosemary Redfield (8 July 2012). "Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells". Science. 337 (6093): 470–3. arXiv: 1201.6643 . Bibcode:2012Sci...337..470R. doi:10.1126/science.1219861. PMC   3845625 . PMID   22773140.
  8. ↑ Bortman, Henry (5 October 2009). "Searching for Alien Life, on Earth". Astrobiology Magazine (NASA). Retrieved 2 December 2010.
  9. ↑ Davies, Paul (4 December 2010). "The 'Give Me a Job' Microbe". Wall Street Journal . Retrieved 5 December 2010.
  10. 1 2 3 4 5 6 Bortman, Henry (2 December 2010). "Thriving on arsenic". Astrobiology Magazine (NASA). Retrieved 11 December 2010.
  11. ↑ Oremland, Ronald S.; Stolz, John F. (9 May 2003). "The ecology of arsenic" (PDF). Science . 300 (5621): 939–944. Bibcode:2003Sci...300..939O. doi:10.1126/science.1081903. PMID   12738852. S2CID   16828951. Archived from the original (PDF) on 20 December 2010.
  12. 1 2 3 Wolfe-Simon, Felisa; Blum, J. S.; et al. (2 December 2010). "A bacterium that can grow by using arsenic instead of phosphorus: Supporting online material". Science . 332 (6034): 1163–1166. Bibcode:2011Sci...332.1163W. doi: 10.1126/science.1197258 . PMID   21127214. S2CID   51834091.
  13. ↑ Stolz, John F.; Basu, Partha; Santini, Joanne M.; Oremland, Ronald S. (2006). "Arsenic and selenium in microbial metabolism". Annual Review of Microbiology. 60: 107–130. doi:10.1146/annurev.micro.60.080805.142053. PMID   16704340. S2CID   2575554.
  14. ↑ "Halomonas sp. GFAJ-1". U.S. National Library of Medicine. Retrieved 11 December 2011.
  15. ↑ Arahal, D. R.; Vreeland, R. H.; Litchfield, C. D.; Mormile, M. R.; Tindall, B. J.; Oren, A.; Bejar, V.; Quesada, E.; Ventosa, A. (2007). "Recommended minimal standards for describing new taxa of the family Halomonadaceae". International Journal of Systematic and Evolutionary Microbiology. 57 (Pt 10): 2436–2446. doi: 10.1099/ijs.0.65430-0 . PMID   17911321.
  16. ↑ Stackebrandt, Erko; Ebers, Jonas (2006). "Taxonomic parameters revisited: tarnished gold standards" (PDF). Microbiology Today. 33 (4): 152–155. Archived from the original (PDF) on 22 July 2011.
  17. ↑ Sneath, P.H.A (1992). Lapage S.P.; Sneath, P.H.A.; Lessel, E.F.; Skerman, V.B.D.; Seeliger, H.P.R.; Clark, W.A. (eds.). International Code of Nomenclature of Bacteria. Washington, D.C.: American Society for Microbiology. ISBN   978-1-55581-039-9. PMID   21089234.
  18. ↑ Euzéby J.P. (2010). "Introduction". List of Prokaryotic names with Standing in Nomenclature. Archived from the original on 13 June 2011. Retrieved 11 December 2010.
  19. ↑ Guo, Jianbo; Zhou, Jiti; Wang, Dong; Tian, Cunping; Wang, Ping; Uddin, M. Salah (2008). "A novel moderately halophilic bacterium for decolorizing azo dye under high salt condition". Biodegradation. 19 (1): 15–19. doi:10.1007/s10532-007-9110-1. PMID   17347922. S2CID   30010282.
  20. ↑ Kiesel, B.; Müller, R.H.; Kleinsteuber, R. (2007). "Adaptative potential of alkaliphilic bacteria towards chloroaromatic substrates assessed by a gfp-tagged 2,4-D degradation plasmid". Engineering in Life Sciences. 7 (4): 361–372. Bibcode:2007EngLS...7..361K. doi:10.1002/elsc.200720200. S2CID   84276654.
  21. ↑ "GTDB - GCF_002966495.1". gtdb.ecogenomic.org.
  22. ↑ Felisa Wolfe-Simon. "Geobiochemistry: Microbes and the four basic strategies for Life on Earth" (PDF). Archived from the original (PDF) on 4 June 2016. Retrieved 26 January 2011.
  23. ↑ Rosie Redfield. "RRResearch: Two mistakes discovered".
  24. ↑ Rosie Redfield. "RRResearch: Growth of GFAJ-1 in arsenate".
  25. ↑ Rosie Redfield (16 January 2012). "The CsCl/mass spectrometry data". rrresearch.fieldofscience.com.
  26. ↑ Westheimer, F.H. (6 June 1987). "Why nature chose phosphates" (PDF). Science . 235 (4793): 1173–1178. Bibcode:1987Sci...235.1173W. CiteSeerX   10.1.1.462.3441 . doi:10.1126/science.2434996. PMID   2434996. Archived from the original (PDF) on 16 June 2011.
  27. ↑ Lagunas, Rosario; Pestana, David; Diez-Masa, Jose C. (1984). "Arsenic mononucleotides. Separation by high-performance liquid chromatography and identification with myokinase and adenylate deaminase". Biochemistry . 23 (5): 955–960. doi:10.1021/bi00300a024. PMID   6324859.
  28. ↑ Fekry, M. I.; Tipton, P. A.; Gates, K. S. (2011). "Kinetic Consequences of Replacing the Internucleotide Phosphorus Atoms in DNA with Arsenic". ACS Chemical Biology. 6 (2): 127–30. doi:10.1021/cb2000023. PMID   21268588.
  29. ↑ Mulyana, Ilham; Satoko, Nakanomori; Takahiro, Kihara; Ayaka, Hokamura; Matsusaki, Hiromi; Takeharu, Tsuge; Kouhei, Mizuno (2014). "Characterization of Polyhydroxyalkanoate Synthases from Halomonas sp. O-1 and Halomonas elongata DSM2581: Site-Directed Mutagenesis and Recombinant Expression". Polymer Degradation and Stability. 109: 416–429. doi:10.1016/j.polymdegradstab.2014.04.024.
  30. ↑ Quillaguamána, Jorge; Delgado, Osvaldo; Mattiasson, Bo; Hatti-Kaul, Rajni (January 2006). "Poly(β-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1". Enzyme and Microbial Technology. 38 (1–2): 148–154. doi:10.1016/j.enzmictec.2005.05.013. hdl: 11336/45869 .
  31. ↑ Oren, Aharon (June 1999). "Bioenergetic aspects of halophilism". Microbiology and Molecular Biology Reviews . 63 (2): 334–48. doi:10.1128/MMBR.63.2.334-348.1999. ISSN   1092-2172. PMC   98969 . PMID   10357854.
  32. ↑ Opinion (8 December 2010). "Curb your enthusiasm for aliens, NASA". New Scientist . No. 2790. p. 5. Retrieved 9 December 2010.
  33. ↑ "MEDIA ADVISORY : M10-167, NASA Sets News Conference on Astrobiology Discovery; Science Journal Has Embargoed Details". 29 November 2010. Archived from the original on 28 January 2012. Retrieved 20 December 2010.
  34. ↑ Carmen Drahl (2010). "Arsenic Bacteria Breed Backlash". Chemical & Engineering News . 88 (50): 7. doi:10.1021/cen112210140356.
  35. 1 2 Zimmer, Carl (7 December 2010). "Scientists see fatal flaws in the NASA study of arsenic-based life". Slate . Retrieved 7 December 2010.
  36. ↑ Zimmer, Carl (27 May 2011). "The Discovery of Arsenic-Based Twitter". Slate . Retrieved 29 May 2011.
  37. ↑ Redfield, Rosemary (4 December 2010). "Arsenic-associated bacteria (NASA's claims)". RR Research blog]. Retrieved 4 December 2010.
  38. ↑ Redfield, Rosemary (8 December 2010). "My Letter to Science". RR Research blog. Retrieved 9 December 2010.
  39. ↑ Bradley, Alex (5 December 2010). "Arsenate-based DNA: a big idea with big holes". Science Blogs – We, Beasties blog]. Archived from the original on 8 December 2010. Retrieved 9 December 2010.
  40. ↑ Wolfe-Simon, Felisa (16 December 2010). "Response to Questions Concerning the Science Article" (PDF). Archived from the original (PDF) on 30 December 2010. Retrieved 17 December 2010.
  41. ↑ "NASA Science Seminar: Arsenic and the Meaning of Life". 21 December 2010. Retrieved 30 January 2010.
  42. 1 2 3 Wolfe-Simon, Felisa; Blum, Jodi Switzer; Kulp, Thomas R.; Gordon, Gwyneth W.; Hoeft, Shelley E.; Pett-Ridge, Jennifer; Stolz, John F.; Webb, Samuel M.; et al. (27 May 2011). "Response to Comments on 'A Bacterium That Can Grow Using Arsenic Instead of Phosphorus'". Science . 332 (6034): 1149. Bibcode:2011Sci...332.1149W. doi: 10.1126/science.1202098 . S2CID   95731255.
  43. ↑ Pennisi, Elizabeth (8 December 2010). "Author of controversial arsenic paper speaks". Science Insider. Science. Archived from the original on 12 December 2010. Retrieved 11 December 2010.
  44. ↑ Cotner, J. B.; Hall, E. K. (27 May 2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332R1149C. doi: 10.1126/science.1201943 . PMID   21622705.
  45. ↑ Redfield, R. J. (27 May 2011). "Comment on "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus"". Science. 332 (6034): 1149. Bibcode:2011Sci...332.1149R. doi: 10.1126/science.1201482 . PMID   21622706.
  46. ↑ Schoepp-Cothenet, B.; Nitschke, W.; Barge, L. M.; Ponce, A.; Russell, M. J.; Tsapin, A. I. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332.1149S. doi: 10.1126/science.1201438 . PMID   21622707.
  47. ↑ Csabai, I.; Szathmary, E. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332Q1149C. doi: 10.1126/science.1201399 . PMID   21622708.
  48. ↑ Borhani, D. W. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332R1149B. doi: 10.1126/science.1201255 . PMID   21622711.
  49. ↑ Benner, S. A. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332Q1149B. doi: 10.1126/science.1201304 . PMID   21622712.
  50. ↑ Foster, P. L. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): i–1149. Bibcode:2011Sci...332.1149F. doi: 10.1126/science.1201551 . PMID   21622713.
  51. ↑ Oehler, S. (2011). "Comment on 'A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus'". Science. 332 (6034): 1149. Bibcode:2011Sci...332.1149O. doi: 10.1126/science.1201381 . PMID   21622709.
  52. ↑ Hamilton, Jon (30 May 2011). "Study of Arsenic-Eating Microbe Finds Doubters". NPR . Retrieved 30 May 2011.
  53. ↑ Wolfe-Simon, F.; Blum, J. S.; Kulp, T. R.; Gordon, G. W.; Hoeft, S. E.; Pett-Ridge, J.; Stolz, J. F.; Webb, S. M.; et al. (2011). "Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus"" (PDF). Science. 332 (6034): 1149. Bibcode:2011Sci...332.1149W. doi: 10.1126/science.1202098 . S2CID   95731255.
  54. ↑ Alberts, B. (2011). "Editor's Note". Science. 332 (6034): 1149. doi:10.1126/science.1208877. PMID   21622710. S2CID   220093358.
  55. ↑ Rosen, Barry P.; Ajees, A. Abdul; McDermott, Timothy R. (2011). "Life and death with arsenic". BioEssays. 33 (5): 350–357. doi:10.1002/bies.201100012. PMC   3801090 . PMID   21387349.
  56. ↑ Hayden, Erika Check (20 January 2012). "Study challenges existence of arsenic-based life". Nature News . doi:10.1038/nature.2012.9861. S2CID   211729481 . Retrieved 20 January 2012.
  57. ↑ Sheridan, Kerry (9 July 2012). "Scientists say NASA's 'new arsenic form of life' was untrue". phys.org. Retrieved 22 January 2024.
  58. ↑ Basturea GN, Harris TK and Deutscher MP (17 August 2012). "Growth of a bacterium that apparently uses arsenic instead of phosphorus is a consequence of massive ribosome breakdown". J Biol Chem. 287 (34): 28816–9. doi: 10.1074/jbc.C112.394403 . PMC   3436571 . PMID   22798070.
  59. ↑ David Sanders (9 July 2012). "Despite refutation, Science arsenic life paper deserves retraction, scientist argues". Retraction Watch. Retrieved 9 July 2012.
  60. ↑ Sanders, David (21 January 2021). "Why one biologist says it's not too late to retract the "arsenic life" paper".
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.