Practical Successes of Laboratory Evolution

Capa

Citar

Texto integral

Acesso aberto Acesso aberto
Acesso é fechado Acesso está concedido
Acesso é fechado Somente assinantes

Resumo

Adaptive Laboratory Evolution (ALE) represents a novel methodology for the generation of microbial strains with desired characteristics and the production of value-added products. Additionally, ALE is employed as a means of enhancing comprehension of the genetic and/or metabolic pathways of evolution. The objective of this review is to analyze the results of studies that elucidate and demonstrate the potential of microorganisms as model objects for laboratory evolutionary experiments. These experiments are becoming increasingly prevalent in the study of adaptation, the evaluation of evolutionary dynamics, and the testing of various evolutionary hypotheses. Concurrently, ALE has demonstrated itself to be a promising and efficacious methodology, which, when employed for biotechnological applications, has already resulted in the generation of novel and useful microbial strains. It is important to note that the current successes not only demonstrate the power and versatility of this approach but also highlight a number of unanswered questions. The conclusions drawn on the basis of ALE require a cautious interpretation of the results obtained.

Texto integral

Acesso é fechado

Sobre autores

Y. Dunaevsky

Lomonosov Moscow State University

Autor responsável pela correspondência
Email: dun@belozersky.msu.ru

Belozersky Institute of Physico-Chemical Biology

Rússia, Moscow, 119991

O. Kudryavtseva

Lomonosov Moscow State University

Email: dun@belozersky.msu.ru

Biological Faculty

Rússia, Moscow, 119991

S. Agroskin

Lomonosov Moscow State University

Email: dun@belozersky.msu.ru

Biological Faculty

Rússia, Moscow, 119991

A. Gasparyan

Lomonosov Moscow State University

Email: dun@belozersky.msu.ru

Biological Faculty

Rússia, Moscow, 119991

M. Belozersky

Lomonosov Moscow State University

Email: dun@belozersky.msu.ru

Belozersky Institute of Physico-Chemical Biology

Rússia, Moscow, 119991

Bibliografia

  1. Sandberg T.E., Salazar M.J., Weng L.L., Palsson B.O., Feist A.M. // Metab. Eng. 2019. V. 56. P. 1–16.
  2. Kumar R., Kumar P. // Front. Microbiol. 2017. V. 8. P. 450. https://doi.org/10.3389/fmicb.2017.00450
  3. Adegboye M.F., Ojuederie O.B., Talia P.M., Babalola О.О. // Biotechnol. Biofuels. 2021. V. 14. P. 5. https://doi.org/10.1186/s13068-020-01853-2
  4. Cho J.S., Kim G.B., Eun H., Moon C.W., Lee S.Y. // JACS Au 2022. V. 2. P. 1781–1799.
  5. Sanchez-Garcia L., Martín L., Mangues R., Ferrer-Miralles N., Vázquez E., Villaverde A. // Microb. Cell Fact. 2016. V. 15. P. 33. https://doi.org/10.1186/s12934-016-0437-3
  6. Martinez R.J., Liu L., Petranovic D., Nielsen J. // Curr. Opin. Biotechnol. 2012. V. 23. P. 965–971.
  7. Rai A.K., Pandey A., Sahoo D. // Trends Food Sci. Technol. 2019. V. 83. P. 129–137.
  8. Elena S.F., Lenski R.E. // Nat. Rev. 2003. V. 4. P. 457–469.
  9. Cakar Z.P., Turanli-Yildiz B., Alkim C., Yilmaz U. // FEMS Yeast Res. 2012. V. 12. P. 171–182.
  10. Dragosits M., Mattanovich D. // Microb. Cell Fact. 2013. V. 12. P. 64. https://doi.org/10.1186/1475-2859-12-64
  11. Hirasawa T, Maeda T. // Microorganisms 2022. V. 11. P. 92. https://doi.org/10.3390/microorganisms11010092
  12. LaCroix R.A., Sandberg T.E., O’Brien E.J., Utrilla J., Ebrahim A., Guzman G.I. et al. // Appl. Environ. Microbiol. 2015. V. 81. P. 17–30.
  13. Ibarra R., Edwards J., Palsson B. // Nature. 2002. V. 420. P. 186–189.
  14. Kim K., Hou C.Y., Choe D., Kang M., Cho S., Sung B.H. et al. // Metab. Eng. 2022. V. 69. P. 59–72.
  15. Fong S.S., Marciniak J.Y., Palsson B. // J. Bacteriol. 2003. V. 185. P. 6400–6408.
  16. Sánchez-Adriá I.E., Sanmartín G., Prieto J.A., Estruch F., Fortis E., Randez-Gil F. // LWT-Food Sci. Technol. 2023. V. 184. P. 114957. https://doi.org/10.1016/j.lwt.2023.114957
  17. Hong K.K., Vongsangnak W., Vemuri G.N., Nielsen J. // Proc. Natl. Acad. Sci. USA. 2011. V. 108. P. 12179–12184.
  18. Almeida J.R.M., Modig T., Petersson A., Hähn-Hägerdal B., Lidén G., Gorwa-Grauslund M.F. // J. Chem. Technol. Biotechnol. 2007. V. 82. P. 340–349.
  19. Mavrommati M., Papanikolaou S., Aggelis G. //Process Biochem. 2023. V. 124. P. 280–289.
  20. Tekarslan-Sahin S.H. // Fermentation 2022. V. 8. P. 372. https://doi.org/10.3390/fermentation8080372
  21. Voordeckers K., Kominek J., Das A., Espinosa-Cantú A., De Maeyer D., Arslan A. et al. // PLoS Genet. 2015. V. 11. P. e1005635. https://doi.org/10.1371/journal.pgen.1005635
  22. Krogerus K., Holmström S., Gibson. B. // Appl. Environ. Microbiol. 2018. V. 84. P. e02302-17. https://doi.org/10.1128/AEM.02302-17
  23. Ekberg J., Rautio J., Mattinen L., Vidgren V., Londesborough J., Gibson B.R. // FEMS Yeast Res. 2013. V. 13. P. 335–349.
  24. Swamy K.B.S., Zhou N. // Appl. Microbiol. Biotechnol. 2019. V. 103. P. 2067–2077.
  25. Brickwedde A., Van den Broek M., Geertman J.A., Magalhães F., Kuijpers N.G.A., Gibson B. et al. // Front. Microbiol. 2017. V. 8. P. 1690. https://doi.org/10.3389/fmicb.2017.01690
  26. Iattici F., Catallo M., Solieri L. // Beverages 2020. V. 6. P. 3. https://doi.org/10.3390/beverages6010003
  27. Gibson B., Vidgren V., Peddinti G., Krogerus K. // J. Ind. Microbiol. Biotechnol. 2018. V. 45. P. 1103–1112.
  28. Blount Z., Borland C., Lenski R. // Proc. Natl. Acad. Sci. USA. 2008. V. 105. P. 7899–7906.
  29. Lee D.H., Palsson B. // Appl. Environ. Microbiol. 2010. V. 76. P. 4158–4168.
  30. Veeravalli K., Boyd D., Iverson B.L., Beckwith J., Georgiou G. // Nat. Chem. Biol. 2011. V. 7. P. 101–105.
  31. Dev C., Jilani S.B., Yazdani S.S. // Microb. Cell Fact. 2022. V. 21. P. 154. https://doi.org/10.1186/s12934-022-01879-1
  32. Seong W., Han G.H., Lim H.S., Baek J.I., Kim S.J., Kim D. et al. // Metab. Eng. Commun. 2020. V. 62. P. 249–259.
  33. Lee Y., Sathesh-Prabu C., Kwak G.H., Bang I., Jung H.W., Kim D., Lee S.K. // Biotechnol. J. 2022. V. 17. P. e2000416. https://doi.org/10.1002/biot.202000416
  34. Jin C., Hou W., Yao R., Zhou P., Zhang H., Bao J. // Bioresour. Technol. 2019. V. 289. P. 121623. https://doi.org/10.1016/j.biortech.2019.121623
  35. Sarkar P., Mukherjee M., Goswami G., Das D. // J. Ind. Microbiol. Biotechnol. 2020. V. 47. P. 329–341.
  36. Hemansi H., Patel A.K., Saini J.K., Singhania R.R. // Bioresour. Technol. 2022. V. 344(Pt B). P. 126247. https://doi.org/10.1016/j.biortech.2021.126247
  37. Millán C., Peña C., Flores C., Espín G., Galindo E., Castillo T. // World J. Microbiol. Biotechnol. 2020. V. 36. P. 46. https://doi.org/10.1007/s11274-020-02822-5
  38. Zhang J., Jin B., Fu J., Wang Z., Chen T. // Molecules 2022. V. 27. P. 22. https://doi.org/10.3390/molecules2709302
  39. Catrileo D., Acuña-Fontecilla A., Godoy L. //Front. Microbiol. 2020. V. 11. P. 1–13.
  40. Godara A., Kao K.C. // Microb. Cell Fact. 2021. V. 20. P. 106. https://doi.org/10.1186/s12934-021-01598-z
  41. Zhu C., You X., Wu T., Li W., Chen H., Cha Y. et al. // Green Chem. 2022. V. 24. P. 4614–4627.
  42. Klimacek M., Kirl E., Krahulec S., Longus K., Novy V., Nidetzky B. // Microb. Cell Fact. 2014. V. 13. P. 37. https://doi.org/10.1186/1475-2859-13-37
  43. Hughes B.S., Cullum A.J., Bennett A.F. // Evolution 2007. V. 61. P. 1725–1734.
  44. Kishimoto T., Iijima L., Tatsumi M., Ono N., Oyake A., Hashimoto T. et al. // PLoS Genet. 2010. V. 6. P. e1001164. https://doi.org/10.1371/journal.pgen.1001164
  45. Royce L.A., Yoon J.M., Chen Y., Rickenbach E., Shanks J.V., Jarboe L.R. // Metab. Eng. 2015. V. 29. P. 180–188.
  46. Tilloy V., Ortiz-Julien A., Dequin S. // Appl. Environ. Microbiol. 2014. V. 80. P. 2623-2632.
  47. Caspeta L., Chen Y., Ghiaci P., Feizi A., Buskov S., Hallström B.M. et al. // Science 2014. V. 346. P. 75–78.
  48. Wallace-Salinas V., Gorwa-Grauslund M.F. // Biotechnol. Biofuels 2013. V. 6. P. 151. https://doi.org/10.1186/1754-6834-6-151
  49. Horinouchi T., Tamaoka K., Furusawa C., Ono N., Suzuki S., Hirasawa T. et al. // BMC Genomics 2010. V. 11. P. 579. https://doi.org/10.1186/1471-2164-11-579
  50. Atsumi S., Wu T.Y., Machado I.M., Huang W.C., Chen P.Y., Pellegrini M. et al. // Mol. Syst. Biol. 2010. V. 6. P. 449. https://doi.org/10.1038/msb.2010.98
  51. Hartono S., Meijerink M.F.A., Abee T., Smid E.J., van Mastrigt O. // New Biotechnol. 2023. V. 78. P. 123–130.
  52. Becker J., Wittmann C. // Curr. Opin. Biotechnol. 2012. V. 23. P. 718–726.
  53. Mundhada H., Seoane J.M., Schneider K., Koza A., Christensen H.B., Klein T. et al. // Metab. Eng. 2017. V. 39. P. 141–150.
  54. Creamer K.E., Ditmars F.S., Basting P.J., Kunka K.S., Hamdallah I.N., Bush S.P. et al. // Appl. Environ. Microbiol. 2017. V. 83. P. e02736-16. https://doi.org/10.1128/AEM.02736-16
  55. Niu F.X., He X., Wu Y.Q., Liu J.Z. // Front. Microbiol. 2018. V. 9. P. 1623. https://doi.org/10.3389/fmicb.2018.01623
  56. Matson M.M., Cepeda M.M., Zhang A., Case A.E., Kavvas E.S., Wang X. et al. // Metab. Eng. 2022. V. 69. P. 50–58.
  57. Rychel K., Tan J., Patel A., Lamoureux C., Hefner Y., Szubin R. et al. // Cell Rep. 2023. V. 42. P. 113105. https://doi.org/10.1016/j.celrep.2023.113105
  58. Cavero-Olguin V.H., Rahimpour F., Dishisha T., Alvarez-Aliaga M.T., Hatti-Kaul R. // Process Biochem. 2021. V. 110. P. 223–230.
  59. Zhang W., Tao Y., Wu M., Xin F., Dong W., Zhou J., et al. // Process Biochem. 2020. V. 98. P. 76–82.
  60. Ghoshal M., Bechtel T.D., Gibbons J.G., McLandsborough L. // Front. Microbiol. 2023. V. 14. P. 1285421. https://doi.org/10.3389/fmicb.2023.1285421
  61. Kim Y.Y., Kim J.C., Kim S., Yang J.E., Kim H.M., Park H.W. // Food Res. Int. 2024.V. 175. P. 113731. https://doi.org/10.1016/j.foodres.2023.113731 Xia H., Kang Y., Ma Z., Hu C., Yang Q., Zhang X., et al. // Microb. Cell Fact. 2022. V. 21. P. 269. https://doi.org/10.1186/s12934-022-01996-x
  62. Gong A., Liu W., Lin Y., Huang L., Xie Z. // Microbiol. Spectr. 2023. V. 11. P. e0132623. https://doi.org/10.1128/spectrum.01326-23
  63. Yao L., Jia Y., Zhang Q., Zheng X., Yang H., Dai J. et al. // Front. Microbiol. 2024. V. 14. P. 1333777. https://doi.org/10.3389/fmicb.2023.1333777
  64. Friedman L., Alder J.D., Silverman J.A. // Antimicrob. Agents Chemother. 2006. V. 50. P. 2137–2145.
  65. Charusanti P., Fong N.L., Nagarajan H., Pereira A.R., Li H.J., Abate E.A., et al. // PLoS One 2012. V. 7. P. e33727. https://doi.org/10.1371/journal.pone.0033727
  66. Çakar Z.P., Seker U.O.S., Tamerler C., Sonderegger M., Sauer U. // FEMS Yeast Res. 2005. V. 5. P. 569–578.
  67. Sauer U. // Eng. Biotechnol. 2001. V. 73. P. 130–166.
  68. Portnoy V.A., Bezdan D., Zengler K. // Curr. Opin. Biotechnol. 2011. V. 22. P. 590–594.
  69. Choe D., Lee J.H., Yoo M., Hwang S., Sung B.H., Cho S. et al. // Nat. Commun. 2019. V. 10. P. 935. https://doi.org/10.1038/s41467-019-08888-6
  70. Dunham M.J. // Methods Enzymol. 2010. V. 470. P. 487-507.
  71. Giannakou K., Cotterrell M., Delneri D. // Front. Genet. 2020. V. 11 P. 916. https://doi.org/10.3389/fgene.2020.00916
  72. Gassler T., Baumschabl M., Sallaberger J., Egermeier M., Mattanovich D. // Metab. Eng. 2022. V. 69. P. 112–121.
  73. Liu Z., Radi M., Mohamed E.T. T., Feist A.M., Dragone G., Mussatto S.I. // Bioresour. Technol. 2021. V. 333. P. 125171. https://doi.org/10.1016/j.biortech.2021.125171
  74. Semumu T., Gamero A., Boekhout T., Zhou N. // World J. Microbiol. Biotechnol. 2022. V. 38. P. 48. https://doi.org/10.1007/s11274-021-03226-9
  75. Fernandes T., Osório C., Sousa M.J., Franco-Duarte R. // J. Fungi 2023. V. 9. P. 186. https://doi.org/10.3390/jof9020186
  76. Dolpatcha S., Phong H.X., Thanonkeo S., Klanrit P., Yamada M., Thanonkeo P. // Sci. Rep. 2023. V. 13. P. 21000. https://doi.org/10.1038/s41598-023-48408-7
  77. Bodinaku I., Shaffer J., Connors A.B., Steenwyk J.L., Biango-Daniels M.N., Kastman E.K. et al. // Мbio 2019. V. 10. P. e02445-19. https://doi.org/10.1128/mBio.02445-19
  78. Du Z.-Y., Zienkiewicz K., Pol N.V., Ostrom N.E., Benning C., Bonito G.M. // Elife 2019. V. 8. P. e47815. https://doi.org/10.7554/eLife.47815
  79. Kale S.P., Bhatnagar D., Bennett J.W. // Mycol. Res. 1994. V. 98. P. 645–652.
  80. Horn B.W., Dorner J.W. // Mycologia 2002. V. 94. P. 741–751.
  81. Voyles J., Johnson L.R., Rohr J., Kelly R., Barron C., Miller D. et al. // Oecologia 2017. V. 184. P. 363–373.
  82. Valero-Jiménez C.A., van Kan J.A.L., Koenraadt C.J.M., Zwaan B.J., Schoustra S.E. // Evol. Appl. 2017. V. 10. P. 433–443.
  83. de Crecy E., Jaronski S., Lyons B., Lyons T.J., Keyhani N.O. // BMC Biotechnol. 2009. V. 9. P. 74. https://doi.org/10.1186/1472-6750-9-74
  84. Han J.O., Naeger N.L., Hopkins B.K., Sumerlin D., Stamets P.E., Carris L.M. et al. // Sci. Rep. 2021. V. 11. P. 10582. https://doi.org/10.1038/s41598-021-89811-2
  85. Wang G., Li Q., Zhang Z., Yin X., Wang B., Yang X. // J. Ind. Microbiol. Biotechnol. 2023. V. 50. P. kuac023. https://doi.org/10.1093/jimb/kuac023

Arquivos suplementares

Arquivos suplementares
Ação
1. JATS XML
Baixar

Declaração de direitos autorais © Russian Academy of Sciences, 2025