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May 04, 2022;13 (17): 4838-4853.

An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions.

Aayush Arya, Jessica Ray, Siddhant Sharma, Romulo Cruz Simbron, Alejandro Lozano, Harrison B Smith, Jakob Lykke Andersen, Huan Chen, Markus Meringer, Henderson James Cleaves
Author Information
  1. Aayush Arya: Department of Physics, Lovely Professional University Jalandhar Delhi-GT Road Phagwara Punjab 144411 India. ORCID
  2. Jessica Ray: Blue Marble Space Institute of Science Seattle Washington 98104 USA.
  3. Siddhant Sharma: Blue Marble Space Institute of Science Seattle Washington 98104 USA. ORCID
  4. Romulo Cruz Simbron: Blue Marble Space Institute of Science Seattle Washington 98104 USA. ORCID
  5. Alejandro Lozano: Blue Marble Space Institute of Science Seattle Washington 98104 USA.
  6. Harrison B Smith: Earth-Life Science Institute, Tokyo Institute of Technology Tokyo Japan hcleaves@elsi.jp. ORCID
  7. Jakob Lykke Andersen: Department of Mathematics and Computer Science, University of Southern Denmark Campusvej 55 5230 Odense M Denmark.
  8. Huan Chen: National High Magnetic Field Laboratory Tallahassee Florida 32310 USA. ORCID
  9. Markus Meringer: German Aerospace Center (DLR) 82234 Oberpfaffenhofen Wessling Germany. ORCID
  10. Henderson James Cleaves: Blue Marble Space Institute of Science Seattle Washington 98104 USA. ORCID
PMID: 35655880 DOI: 10.1039/d2sc00256f

Abstract

A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes over others. Some degree of molecular complexity likely had to be supplied by environmental processes to produce entailed self-replicating processes. The origin of entailment, therefore, must connect to fundamental chemistry that builds molecular complexity. We present here an open-source chemoinformatic workflow to model abiological chemistry to discover such entailment. This pipeline automates generation of chemical reaction networks and their analysis to discover novel compounds and autocatalytic processes. We demonstrate this pipeline's capabilities against a well-studied model system by vetting it against experimental data. This workflow can enable rapid identification of products of complex chemistries and their underlying synthetic relationships to help identify autocatalysis, and potentially self-organization, in such systems. The algorithms used in this study are open-source and reconfigurable by other user-developed workflows.

References

  1. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25230-25236 [PMID: 32989134]
  2. Orig Life Evol Biosph. 1991;21(2):59-111 [PMID: 1758688]
  3. Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109): [PMID: 29133447]
  4. Life (Basel). 2021 Mar 12;11(3): [PMID: 33809046]
  5. Life (Basel). 2021 May 29;11(6): [PMID: 34072344]
  6. Astrobiology. 2004 Spring;4(1):1-9 [PMID: 15104899]
  7. Orig Life. 1984;14(1-4):565-70 [PMID: 6462692]
  8. Orig Life Evol Biosph. 2017 Sep;47(3):249-260 [PMID: 28078499]
  9. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501 [PMID: 26481353]
  10. J Mol Evol. 2021 Feb;89(1-2):2-11 [PMID: 33427903]
  11. Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5387-5392 [PMID: 30842280]
  12. BMC Bioinformatics. 2007 Mar 27;8:105 [PMID: 17389044]
  13. Nat Chem. 2020 Nov;12(11):1016-1022 [PMID: 33046840]
  14. Phys Rev Lett. 1985 Sep 30;55(14):1530-1533 [PMID: 10031847]
  15. Arch Biochem Biophys. 1961 Aug;94:217-27 [PMID: 13731263]
  16. Meteorit Planet Sci. 2020 Nov;55(11):2422-2439 [PMID: 33536738]
  17. Life (Basel). 2021 Oct 26;11(11): [PMID: 34833016]
  18. Proc Natl Acad Sci U S A. 1972 Apr;69(4):809-11 [PMID: 16591973]
  19. J Chem Inf Model. 2019 Oct 28;59(10):4266-4277 [PMID: 31498614]
  20. Orig Life Evol Biosph. 1998 Feb;28(1):91-6 [PMID: 11536858]
  21. Life (Basel). 2021 Apr 01;11(4): [PMID: 33916135]
  22. Nature. 2012 Nov 1;491(7422):72-7 [PMID: 23075853]
  23. Carbohydr Res. 2000 Nov 3;329(2):359-65 [PMID: 11117319]
  24. Sci Am. 2007 Jun;296(6):46-53 [PMID: 17663224]
  25. Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):15830-15835 [PMID: 31332006]
  26. Angew Chem Int Ed Engl. 2013 Dec 2;52(49):12800-26 [PMID: 24127341]
  27. Proc Natl Acad Sci U S A. 2016 Jun 14;113(24):E3322-31 [PMID: 27247410]
  28. Chem Rev. 2014 Jan 8;114(1):285-366 [PMID: 24171674]
  29. Anal Chem. 2004 May 1;76(9):2511-6 [PMID: 15117191]
  30. Life (Basel). 2013 Apr 29;3(2):331-45 [PMID: 25369745]
  31. Chem Biodivers. 2007 Apr;4(4):554-73 [PMID: 17443871]
  32. Nucleic Acids Res. 2022 Jan 7;50(D1):D603-D609 [PMID: 34850162]
  33. Orig Life Evol Biosph. 2016 Jun;46(2-3):149-69 [PMID: 26508401]
  34. J Agric Food Chem. 2012 Mar 28;60(12):3266-74 [PMID: 22375847]
  35. Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617 [PMID: 29140435]
  36. ACS Cent Sci. 2017 May 24;3(5):434-443 [PMID: 28573205]
  37. Cold Spring Harb Perspect Biol. 2010 Mar;2(3):a002105 [PMID: 20300213]
  38. Commun Chem. 2021 Feb 2;4(1):11 [PMID: 36697508]
  39. Science. 2020 Sep 25;369(6511): [PMID: 32973002]
  40. J Mol Evol. 2021 Apr;89(3):183-188 [PMID: 33506330]
  41. J Food Sci Technol. 2014 Sep;51(9):1686-96 [PMID: 25190825]
  42. Anal Chem. 2001 Oct 1;73(19):4676-81 [PMID: 11605846]
  43. Nat Commun. 2021 Jun 10;12(1):3538 [PMID: 34112800]
  44. Proc Natl Acad Sci U S A. 2021 Jan 19;118(3): [PMID: 33431670]
  45. Biosystems. 1975 Jul;7(1):15-21 [PMID: 1156666]
  46. Nat Commun. 2018 Dec 12;9(1):5177 [PMID: 30538226]
  47. Orig Life Evol Biosph. 2000 Feb;30(1):33-43 [PMID: 10836263]
  48. Anal Chem. 2008 Dec 1;80(23):8908-19 [PMID: 19551926]
  49. Nature. 1995 Apr 13;374(6523):594-5 [PMID: 7536302]
  50. Plant Physiol. 1992 Sep;100(1):1-6 [PMID: 16652929]
  51. Chem Soc Rev. 2010 Jan;39(1):301-12 [PMID: 20023854]
  52. Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
  53. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2763-8 [PMID: 20160129]
  54. Nature. 1990 Nov 1;348(6296):47-9 [PMID: 11536470]
  55. Entropy (Basel). 2020 Nov 16;22(11): [PMID: 33287069]
  56. J Am Chem Soc. 2021 Nov 17;143(45):18820-18826 [PMID: 34727496]
  57. Chem Soc Rev. 2012 Aug 21;41(16):5394-403 [PMID: 22508108]
  58. Orig Life Evol Biosph. 2005 Dec;35(6):523-36 [PMID: 16254690]
  59. Science. 1973 Nov 23;182(4114):781-90 [PMID: 17772148]
  60. J Theor Biol. 1986 Mar 7;119(1):1-24 [PMID: 3713221]
  61. Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109): [PMID: 29133444]
Journal Article
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