GFAJ-1
GFAJ-1 is a
Discovery
The GFAJ-1 bacterium was discovered by
Taxonomy and phylogeny
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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
In the Science journal article, GFAJ-1 is referred to as a
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]
When the researcher, Joseph Tolle added
Arsenate ester stability
Arsenate
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 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,
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
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[update], the paper had not been retracted.[1]
See also
- Arsenic biochemistry
- Arsenate-reducing bacteria
- Arsenic poisoning
- Arsenic toxicity
- Hypothetical types of biochemistry
- Nucleic acid analogues
- Organoarsenic chemistry
- Prebiotic arsenic
References
- ^ S2CID 51834091.
- ^ . Retrieved 2 December 2010.
- ^ "Arsenic-loving bacteria may help in hunt for alien life". BBC News. 2 December 2010. Retrieved 2 December 2010.
- ^ "Studies refute arsenic bug claim". BBC News. 9 July 2012. Retrieved 10 July 2012.
- S2CID 20229329.
- ^ RRResearch By Rosie Redfield. 16 January 2012
- PMID 22773140.
- ^ Bortman, Henry (5 October 2009). "Searching for Alien Life, on Earth". Astrobiology Magazine (NASA). Retrieved 2 December 2010.
- Wall Street Journal. Retrieved 5 December 2010.
- ^ a b c d e f Bortman, Henry (2 December 2010). "Thriving on arsenic". Astrobiology Magazine (NASA). Retrieved 11 December 2010.
- S2CID 16828951. Archived from the original(PDF) on 20 December 2010.
- ^ S2CID 51834091.
- S2CID 2575554.
- ^ "Halomonas sp. GFAJ-1". U.S. National Library of Medicine. Retrieved 11 December 2011.
- PMID 17911321.
- ^ 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.
- PMID 21089234.
- ^ 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.
- S2CID 30010282.
- S2CID 84276654.
- ^ "GTDB - GCF_002966495.1". gtdb.ecogenomic.org.
- ^ 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.
- ^ Rosie Redfield. "RRResearch: Two mistakes discovered".
- ^ Rosie Redfield. "RRResearch: Growth of GFAJ-1 in arsenate".
- ^ Rosie Redfield (16 January 2012). "The CsCl/mass spectrometry data". rrresearch.fieldofscience.com.
- PMID 2434996. Archived from the original(PDF) on 16 June 2011.
- PMID 6324859.
- PMID 21268588.
- .
- hdl:11336/45869.
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- ^ Opinion (8 December 2010). "Curb your enthusiasm for aliens, NASA". New Scientist. No. 2790. p. 5. Retrieved 9 December 2010.
- ^ "MEDIA ADVISORY : M10-167, NASA Sets News Conference on Astrobiology Discovery; Science Journal Has Embargoed Details". 29 November 2010.
- .
- ^ a b Zimmer, Carl (7 December 2010). "Scientists see fatal flaws in the NASA study of arsenic-based life". Slate. Retrieved 7 December 2010.
- ^ Zimmer, Carl (27 May 2011). "The Discovery of Arsenic-Based Twitter". Slate. Retrieved 29 May 2011.
- ^ Redfield, Rosemary (4 December 2010). "Arsenic-associated bacteria (NASA's claims)". RR Research blog]. Retrieved 4 December 2010.
- ^ Redfield, Rosemary (8 December 2010). "My Letter to Science". RR Research blog. Retrieved 9 December 2010.
- ^ 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.
- ^ 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.
- ^ "NASA Science Seminar: Arsenic and the Meaning of Life". 21 December 2010. Retrieved 30 January 2010.
- ^ S2CID 95731255.
- ^ 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.
- PMID 21622705.
- PMID 21622706.
- PMID 21622707.
- PMID 21622708.
- PMID 21622711.
- PMID 21622712.
- PMID 21622713.
- PMID 21622709.
- ^ Hamilton, Jon (30 May 2011). "Study of Arsenic-Eating Microbe Finds Doubters". NPR. Retrieved 30 May 2011.
- S2CID 95731255.
- S2CID 220093358.
- PMID 21387349.
- S2CID 211729481. Retrieved 20 January 2012.
- ^ Sheridan, Kerry (9 July 2012). "Scientists say NASA's 'new arsenic form of life' was untrue". phys.org. Retrieved 22 January 2024.
- PMID 22798070.
- ^ David Sanders (9 July 2012). "Despite refutation, Science arsenic life paper deserves retraction, scientist argues". Retraction Watch. Retrieved 9 July 2012.
- ^ Sanders, David (21 January 2021). "Why one biologist says it's not too late to retract the "arsenic life" paper".
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