Xenobiology: An expanded semantical review

  • Adhityo WICAKSONO Division of Biotechnology, Genbinesia Foundation, Jl. Swadaya Barat no. 4, Gresik 61171, East Java (ID) https://orcid.org/0000-0003-3298-3577
  • Ghea P. CRISTY Division of Biotechnology, Genbinesia Foundation, Jl. Swadaya Barat no. 4, Gresik 61171, East Java (ID)
Keywords: estranged life, origin of life, shadow biosphere, speculative biology, synthetic life

Abstract

The definition of “xenobiology” has gradually shifted from the study of the foreign, estranged life forms potentially existing in outer space to the study where the natural and synthetic life are involved. The natural concept of xenobiology governs the unseen, hypothetical life on the outer space, and the hidden life with completely different biochemistry on Earth. The life on the outer space might possess different way to harvest energy from the one on Earth. The hidden life on Earth, or the “Shadow Biosphere” might rose from completely different way of creation and evolution on Earth, which lead to its complete difference from the known biosphere. The newest concept of xenobiology involves synthetic life, built with unnatural base pair of the nucleic acid, with analogous or xeno nucleic acid (XNA), has a synthetic genome which capable of self-replicating or enables the synthetic cell to self-replicate, or even possesses a synthetic physiological pathway. By understanding the broad spectrum of xenobiology, in both natural and synthetic concepts, we can expand our view on how life might develop into a completely estranged system, which is different from anthropocentric view of life available around us on Earth. From these perspectives, we might understand how life evolved by evolving it synthetically.

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References

Antonovsky N, Gleizer S, Noor E, Zohar Y, Herz E, Barenholz U, … Milo R (2016). Sugar synthesis from CO2 in Escherichia coli. Cell 166(1):115-125. https://doi.org/10.1016/j.cell.2016.05.064

Ambrogelly A, Palioura S, Söll D (2007). Natural expansion of the genetic code. Nature Chemical Biology 3(1):29-35. https://doi.org/10.1038/nchembio847

Budisa N, Kubyshkin V, Schmidt M (2020). Xenobiology: A Journey towards parallel life forms. Chemistry Europe 2228-2231. https://doi.org/10.1002/cbic.202000141

Chaput JC, Herdewijn P (2019). What Is XNA? Angewandte Chemie International Edition 58(34):2-5. https://doi.org/10.1002/anie.201905999

Clément G, Slenzka K (2006). Fundamentals of space biology: research on cells, animals, and plants in space (Vol. 18). Springer Science & Business Media, Heidelberg, Germany.

Cleland CE, Copley SD (2005). The possibility of alternative microbial life on Earth. International Journal of Astrobiology 4(3-4):165-173. https://doi.org/10.1017/S147355040500279X

Csibra E, Renders M, Pinheiro VB (2020). Towards XNA molecular biology: Bacterial cell display as a robust and versatile platform for the engineering of low affinity ligands and enzymes. bioRxiv.

Cui K, Shoemaker SP (2018). Public perception of genetically-modified (GM) food: A nationwide Chinese consumer study. Science of Food 2(1):1-8. https://doi.org/10.1038/s41538-018-0018-4

Dadachova E, Bryan RA, Huang X, Moadel T, Schweitzer AD, Aisen P, Nosanchuk JD, Casadevall A (2007). Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi. PloS One 2(5):457. https://doi.org/10.1371/journal.pone.0000457

Dadachova E, Casadevall A (2008). Ionizing radiation: how fungi cope, adapt, and exploit with the help of melanin. Current Opinion in Microbiology 11(6):525-531. https://doi.org/10.1016/j.mib.2008.09.013

Darling D, Schulze-Makuch D (2016). The extraterrestrial encyclopedia. First Edition Design Publishing, New York.

Davies PC, Lineweaver CH (2005). Finding a second sample of life on Earth. Astrobiology 5(2):154-163. https://doi.org/10.1089/ast.2005.5.154

Davies PC, Benner SA, Cleland CE, Lineweaver CH, McKay CP, Wolfe-Simon F (2009). Signatures of a shadow biosphere. Astrobiology 9(2):241-249. https://doi.org/10.1089/ast.2008.0251

Editors of the American Heritage Dictionaries (2011). The American Heritage Dictionary of the English Language. 5th ed. Houghton Mifflin Harcourt, Boston, Massachusetts, USA.

Erb TJ, Kiefer P, Hattendorf B, Günther D, Vorholt JA (2012). GFAJ-1 is an arsenate-resistant, phosphate-dependent organism. Science 337(6093):467-470. https://doi.org/10.1126/science.1218455

Galindo-Murillo R, Barroso-Flores J (2017). Structural and dynamical instability of DNA caused by high occurrence of d5SICS and dNaM unnatural nucleotides. Physical Chemistry Chemical Physics 19(16):10571-10580. https://doi.org/10.1039/C7CP01477E

Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, … Merryman C (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329(5987):52-56. https://doi.org/10.1126/science.1190719

Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, …Milo R (2019). Conversion of Escherichia coli to generate all biomass carbon from CO2. Cell 179(6):1255-1263. https://doi.org/10.1016/j.cell.2019.11.009

Gutmann A (2011). The ethics of synthetic biology: guiding principles for emerging technologies. Hastings Center Report 41(4):17-22. https://doi.org/10.1002/j.1552-146X.2011.tb00118.x

Hanson R (1998). The great filter: Are we almost past it? Retrieved 2021 June 01 from https://web.archive.org/web/20100507074729/http://hanson.gmu.edu/greatfilter.html

Haque RU, Paradisi F, Allers T (2020). Haloferax volcanii for biotechnology applications: challenges, current state and perspectives. Applied Microbiology and Biotechnology 104(4):1371-1382. https://doi.org/10.1007/s00253-019-10314-2

Hawking S (1996). Life in the universe. Retrieved 2021 June 01 from https://www.hawking.org.uk/in-words/lectures/life-in-the-universe

Herdewijn P, Marlière P (2009). Toward safe genetically modified organisms through the chemical diversification of nucleic acids. Chemistry & Biodiversity 6(6):791-808. https://doi.org/10.1002/cbdv.200900083

Hielscher S, Pies I, Valentinov V, Chatalova L (2016). Rationalizing the GMO debate: The ordonomic approach to addressing agricultural myths. International Journal of Environmental Research and Public Health 13(5):476. http://dx.doi.org/10.3390/ijerph13050476

Horneck G, Rettberg P, Reitz G, Wehner J, Eschweiler U, Strauch K, … Baumstark-Khan C (2001). Protection of bacterial spores in space, a contribution to the discussion on panspermia. Origins of Life and Evolution of the Biosphere 31(6):527-547. https://doi.org/10.1023/A:1012746130771

Hugill A (2012). Pataphysics: a useless guide. MIT Press, Massachusetts, USA.

Impey C (2011). The living cosmos: our search for life in the universe. Cambridge University Press, Cambridge, UK, pp 189.

Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, … Soukal P (2016). A eukaryote without a mitochondrial organelle. Current Biology 26(10):1274-1284. https://doi.org/10.1016/j.cub.2016.03.053

Karalis DT, Karalis T, Karalis S, Kleisiari AS (2020). Genetically modified products: perspectives and challenges. Cureus 12(3):e7306. https://doi.org/10.7759/cureus.7306

Kim JI, Cox MM (2002). The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proceedings of the National Academy of Sciences USA 99(12):7917-7921. https://doi.org/10.1073/pnas.122218499

Krzmarzick MJ, Taylor DK, Fu X, McCutchan AL (2018). Diversity and niche of archaea in bioremediation. Archaea 2018:3194108. https://doi.org/10.1155/2018/3194108

Kubyshkin V, Budisa N (2017). Synthetic alienation of microbial organisms by using genetic code engineering: Why and how? Biotechnology Journal 12(8):1600097. https://doi.org/10.1002/biot.201600097

Kuntz M (2014). The GMO case in France: politics, lawlessness and postmodernism. GM Crops & Food 5(3):163-169. https://doi.org/10.4161/21645698.2014.945882

Kuznetsov SI (1956). Possibility of radiosynthesis. Mikrobiologiia 25(2):195-199.

Kvenvolden K, Lawless J, Pering K, Peterson E, Flores J, Ponnamperuma C, Kaplan IR, Moore C (1970). Evidence for extra-terrestrial amino-acids and hydrocarbons in the Murchison meteorite. Nature 228(5275):923-926. https://doi.org/10.1038/228923a0

Lodders K (2010). Exoplanet chemistry. In: Barnes R (Ed). Formation and Evolution of Exoplanets. Glasgow, John Wiley & Sons, pp 169.

Malo ME, Dadachova E (2019) Melanin as an energy transducer and a radioprotector in black fungi. In: Tiquia-Arashiro S, Grube M (Eds). Fungi in Extreme Environments: Ecological Role and Biotechnological Significance. Springer, Cham. https://doi.org/10.1007/978-3-030-19030-9_10

Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR, Romesberg FE (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature 509(7500):385-388. https://doi.org/10.1038/nature13314

Marris C (2001). Public views on GMOs: deconstructing the myths. Stakeholders in the GMO debate often describe public opinion as irrational. But do they really understand the public?. EMBO Reports 2(7):545-548. https://doi.org/10.1093/embo-reports/kve142

Martins Z, Botta O, Fogel ML, Sephton MA, Glavin DP, Watson JS, … Ehrenfreund P (2008). Extra-terrestrial nucleobases in the Murchison meteorite. Earth and Planetary Science Letters 270(1-2):130-136. https://doi.org/10.1016/j.epsl.2008.03.026

Mix LJ (2009). Life in space: astrobiology for everyone. Harvard University Press, Massachusetts, USA pp 4-5.

Miller TE, Beneyton T, Schwander T, Diehl C, Girault M, McLean R, … Erb TJ (2020). Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts. Science 368(6491):649-654. https://doi.org/10.1126/science.aaz6802

Muller AW, Schulze-Makuch D (2006). Thermal energy and the origin of life. Origins of Life and Evolution of Biospheres 36(2):177-189. https://doi.org/10.1007/s11084-005-9003-4

Mursidawati S, Wicaksono A, Teixeira da Silva JAT (2019). Development of the endophytic parasite, Rafflesia patma Blume, among host plant (Tetrastigma leucostaphylum (Dennst.) Alston) vascular cambium tissue. South African Journal of Botany 123:382-386. https://doi.org/10.1016/j.sajb.2019.03.028

Nikolov LA, Tomlinson PB, Manickam S, Endress PK, Kramer EM, Davis CC (2014). Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world's largest flowers. Annals of Botany 114(2):233-242. https://doi.org/10.1093/aob/mcu114

Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, … Herdewijn P (2012). Synthetic genetic polymers capable of heredity and evolution. Science 336(6079):341-344. https://doi.org/10.1126/science.1217622

Popa R (2010). Necessity, futility and the possibility of defining life are all embedded in its origin as a punctuated-gradualism. Origins of Life and Evolution of Biospheres 40(2):183-190. https://doi.org/10.1007/s11084-010-9198-x

Reaves ML, Sinha S, Rabinowitz JD, Kruglyak L, Redfield RJ (2012). Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science 337(6093):470-473. https://doi.org/10.1126/science.1219861

Richardson SM, Patron NJ (2016). Synthia: playing god in a sandbox. Retrieved 2020 August 20 from https://microbiologysociety.org/publication/past-issues/what-is-life/article/synthia-playing-god-in-a-sandbox-what-is-life.html

Rzymski P, Królczyk A (2016). Attitudes toward genetically modified organisms in Poland: to GMO or not to GMO?. Food Security 8:689-697. https://doi.org/10.1007/s12571-016-0572-z

Sagan C, Salpeter EE (1976). Particles, environments, and possible ecologies in the Jovian atmosphere. The Astrophysical Journal Supplement Series 32:737-755.

Schmidt M (2010). Xenobiology: a new form of life as the ultimate biosafety tool. Bioessays 32(4):322-331. https://doi.org/10.1002/bies.200900147

Schmitt-Kopplin P, Gabelica Z, Gougeon RD, Fekete A, Kanawati B, Harir M, Gebefuegi I, … Hertkorn N (2010). High molecular diversity of extra-terrestrial organic matter in Murchison meteorite revealed 40 years after its fall. Proceedings of the National Academy of Sciences USA 107(7):2763-2768. https://doi.org/10.1073/pnas.0912157107

Schmitt FJ, Frielingsdorf S, Friedrich T, Budisa N (2021). Courses based on iGEM/BIOMOD competitions are the ideal format for research‐based learning of xenobiology. Chemistry Europe 22(5):818-825. https://doi.org/10.1002/cbic.202000614

Schulze-Makuch D, Irwin LN (2002). Energy cycling and hypothetical organisms in Europa's ocean. Astrobiology 2(1):105-121. https://doi.org/10.1089/153110702753621385

Schulze-Makuch D, Irwin LN (2018). Life in the universe: Expectations and Constraints 3rd ed. Springer Science & Business Media, Heidelberg, Germany.

Stavropoulos DN, Hornby AS (2008). Oxford English-Greek Learner's Dictionary. 2nd ed. Oxford University Press, Oxford, UK.

Stoeckenius W (1981). Walsby's square bacterium: fine structure of an orthogonal procaryote. Journal of Bacteriology 148(1):352-360.

Taylor AI, Holliger P (2015). Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers. Nature Protocols 10(1):1625-1642. https://doi.org/10.1038/nprot.2015.104

Taylor AI, Pinheiro VB, Smola MJ, Morgunov AS, Peak-Chew S, Cozens C, … Holliger P (2015). Catalysts from synthetic genetic polymers. Nature 518(7539):427-430. https://doi.org/10.1038/nature13982

Wagner I, Musso H (1983). New naturally occurring amino acids. Angewandte Chemie International Edition in English 22(11):816-828. https://doi.org/10.1002/anie.198308161

Walton, D. (2010). Space rock contains organic molecular feasts. Retrieved 2021 May 31 from https://web.archive.org/web/20100216052616/http://news.bbc.co.uk/2/hi/science/nature/8516319.stm

Wang F, Zhang W (2019). Synthetic biology: recent progress, biosafety and biosecurity concerns, and possible solutions. Journal of Biosafety and Biosecurity 1(1):22-30. https://doi.org/10.1016/j.jobb.2018.12.003

Ward P, Brownlee D (2000). Rare earth: why complex life is uncommon in the universe. Copernicus Book, New York, USA.

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, … Anbar AD (2011). A bacterium that can grow by using arsenic instead of phosphorus. Science 332(6034):1163-1166. https://doi.org/10.1126/science.1197258

Yahalomi D, Atkinson SD, Neuhof M, Chang ES, Philippe H, Cartwright P, … Huchon D (2020). A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome. Proceedings of the National Academy of Sciences USA 117(10):5358-5363. https://doi.org/10.1073/pnas.1909907117

Zhdanova NN, Vasilevskaya AI, Artyshkova LV, Sadovnikov YS, Lashko TN, Gavrilyuk VI, Dighton J (1994). Changes in micromycete communities in soil in response to pollution by long-lived radionuclides emitted in the Chernobyl accident. Mycological Research 98(7):789-795. https://doi.org/10.1016/S0953-7562(09)81057-5

Zhdanova NN, Tugay T, Dighton J, Zheltonozhsky V, Mcdermott P (2004). Ionizing radiation attracts soil fungi. Mycological Research 108(9):1089-1096. https://doi.org/10.1017/S0953756204000966

Published
2021-06-23
How to Cite
WICAKSONO, A., & CRISTY, G. P. (2021). Xenobiology: An expanded semantical review. Notulae Scientia Biologicae, 13(2), 10929. https://doi.org/10.15835/nsb13210929
Section
Review articles
CITATION
DOI: 10.15835/nsb13210929