Adaptive laboratory evolution of microorganisms: methods and applications in biotechnology

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Рұқсат ақылы немесе тек жазылушылар үшін

Аннотация

The article discusses the key mechanisms, methods, and achievements of adaptive laboratory evolution. The term «adaptive evolution» is commonly understood as a selection-based process in which the fittest organisms have genetic changes (the occurrence of point mutations, transfer, duplication, insertion and deletion, acquisition and loss of individual genes) that contribute to survival in certain conditions. The factors influencing the adaptation of microorganisms are analyzed, including population size, frequency and variability of alleles, selection conditions and interaction with other species. The main stages of adaptive evolution are described: the occurrence of mutations and their consolidation in the population. Special attention is paid to modern methods of genomics, sequencing and bioinformatics, which make it possible to study the dynamics of evolutionary changes and identify genetic adaptations. Conclusions about the prospects of using adaptive laboratory evolution in biotechnology and fundamental research are presented.

Авторлар туралы

V. Chernova

Peter the Great St. Petersburg Polytechnic University

Email: chernova_ve@bk.ru
St. Petersburg, Russia

E. Aronova

Peter the Great St. Petersburg Polytechnic University

Email: chernova_ve@bk.ru
St. Petersburg, Russia

E. Buslaeva

Pharm Holding

Email: chernova_ve@bk.ru
Saint Petersburg, Russia

T. Mukhina

Pharm Holding

Email: chernova_ve@bk.ru
Saint Petersburg, Russia

E. Yevreiskaia

Pharm Holding

Email: chernova_ve@bk.ru
Saint Petersburg, Russia

Z. Khasanshina

Pharm Holding; ITMO University

Хат алмасуға жауапты Автор.
Email: chernova_ve@bk.ru
Saint Petersburg, Russia; Saint Petersburg, Russia

Әдебиет тізімі

  1. Ахметова Д.И., Бердыгулова Ж.А., Евтыхова Е.Б., Шустов А.В. Сальмонеллы: молекулярные механизмы приспособленности и факторы вирулентности // Биотехнология. Теория и практика. 2012. № 1. С. 3–24.
  2. Захарова И.Б., Викторов Д.В. Интегративные конъюгативные элементы микроорганизмов (ICEs) // Мол. генет. микробиол. вирусол. 2015. № 3. С. 9–16.
  3. Мустафин Р.Н. Роль мобильных генетических элементов в возникновении жизни // Успехи физиол. наук. 2019. Т. 50 (3). С. 45–64.
  4. Шестаков С.В., Карбышева Е.А. Эволюция систем горизонтального переноса генов у бактерий // Новые информационные технологии в медицине, биологии, фармакологии и экологии / Мат. междунар. конф. 2017. С. 14–19.
  5. Юрченко Н.Н., Коваленко Л.В., Захаров И.К. Мобильные генетические элементы: нестабильность генов и геномов // Вавиловский журн. генетики и селекции. 2011. Т. 15 (2). С. 261–270.
  6. Alcantara-Diaz D., Brena-Valle M., Serment-Guerrero J. Divergent adaptation of Escherichia coli to cyclic ultraviolet light exposures // Mutagenesis. 2004. V. 19 (5). P. 349–354.
  7. Alibayov B., Baba-Moussa L., Sina H. et al. Staphylococcus aureus mobile genetic elements // Mol. Biol. Rep. 2014. V. 41 (8). P. 5005–5018.
  8. Bailey J.A., Liu G., Eichler E.E. An Alu transposition model for the origin and expansion of human segmental duplications // Am. J. Hum. Genet. 2003. V. 73 (4). P. 823–834.
  9. Bailey S.F., Blanquart F., Bataillon T., Kassen R. What drives parallel evolution? How population size and mutational variation contribute to repeated evolution // BioEssays. 2017. V. 39 (1). P. 1–9.
  10. Bailey S.F., Rodrigue N., Kassen R. The effect of selection environment on the probability of parallel evolution // Mol. Biol. Evol. 2015. V. 32 (6). P. 1436–1448.
  11. Bala S., Garg D., Phutela U.G. et al. Oscillatoria sancta cultivation using fruit and vegetable waste formulated media and its potential as a functional food: assessment of cultivation optimization // Mol. Biotechnol. 2023. P. 1–19.
  12. Ballester S., Lopez P., Espinosa M. et al. Plasmid structural instability associated with pC194 replication functions // J. Bacteriol. 1989. V. 171 (5). P. 2271–2277.
  13. Barrick J.E., Lenski R.E. Genome dynamics during experimental evolution // Nat. Rev. Genet. 2013. V. 14 (12). P. 827–839.
  14. Bellanger X., Payot S., Leblond-Bourget N., Guedon, G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity // FEMS Microbiol. Rev. 2014. V. 38 (4). P. 720–760.
  15. Benner P., Meier L., Pfeffer A. et al. Lab-scale photobioreactor systems: principles, applications, and scalability // Bioproc. Biosyst. Engin. 2022. V. 45 (5). P. 791–813.
  16. Bergthorsson U., Andersson D.I., Roth J.R. Ohno’s dilemma: evolution of new genes under continuous selection // PNAS USA. 2007. V. 104 (43). P. 17004–17009.
  17. Biener R., Horn T., Komitakis A. et al. High-cell-density cultivation of Vibrio natriegens in a low-chloride chemically defined medium // Appl. Microbiol. Biotechnol. 2023. V. 107 (23). P. 7043–7054.
  18. Billington S.J., Jost B.H. Multiple genetic elements carry the tetracycline resistance gene tet(W) in the animal pathogen Arcanobacterium pyogenes // Antimicrob. Agents Chemother. 2006. V. 50 (11). P. 3580–3587.
  19. Blaby I.K., Lyons B.J., Wroclawska-Hughes E. et al. Experimental evolution of a facultative thermophile from a mesophilic ancestor // Appl. Environ. Microbiol. 2012. V. 78 (1). P. 144–155.
  20. Boecker S., Schulze P., Klamt, S. Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli // Biotechnol. Biofuels Bioprod. 2023. V. 16 (1). P. 1–13.
  21. Borodovich T., Shkoporov A.N., Ross R.P., Hill C. Phage-mediated horizontal gene transfer and its implications for the human gut microbiome // Gastroenterol. Rep. 2022. V. 10. P. goac012.
  22. Botelho J., Cazares A., Schulenburg, H. The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements // Nucl. Acids Res. 2023. V. 51 (1). P. 236–252.
  23. Brimacombe C.A., Ding H., Johnson J.A., Thomas Beatty J. Homologues of genetic transformation DNA import genes are required for Rhodobacter capsulatus gene transfer agent recipient capability regulated by the response regulator CtrA // J. Bacteriol. 2015. V. 197 (16). P. 2653–2663.
  24. Calos M. The phiC31 integrase system for gene therapy // Curr. Gene Therap. 2006. V. 6 (6). P. 633–645.
  25. Cao M., Gao M., Suastegui M. et al. Building microbial factories for the production of aromatic amino acid pathway derivatives: from commodity chemicals to plant-sourced natural products // Metab. Engin. 2020. V. 58. P. 94–132.
  26. Carraro N., Rivard N., Ceccarelli D. et al. IncA/C conjugative plasmids mobilize a new family of multidrug resistance islands in clinical Vibrio cholerae Non-O1/Non-O139 isolates from Haiti // mBio. 2016. V. 7 (4). P. e00509-16.
  27. Caryl J.A., O’Neill A.J. Complete nucleotide sequence of pGO1, the prototype conjugative plasmid from the Staphylococci // Plasmid. 2009. V. 62 (1). P. 35–38.
  28. Choudhury D., Saini S. Evolution of Escherichia coli in different carbon environments for 2,000 generations // J. Evol. Biol. 2019. V. 32 (12). P. 1331–1341.
  29. Chu H.Y., Sprouffske K., Wagner A. The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient // J. Evol. Biol. 2017. V. 30 (9). P. 1692–1711.
  30. Colavecchio A., Cadieux B., Lo A., Goodridge L.D. Bacteriophages contribute to the spread of antibiotic resistance genes among foodborne pathogens of the Enterobacteriaceae family - a review // Front. Microbiol. 2017. V. 8. P. 1108.
  31. Cooke M.B., Herman C. Conjugation’s toolkit: the roles of nonstructural proteins in bacterial sex // J. Bacteriol. 2023. V. 205 (3). P. e0043822.
  32. Cooper V.S., Bennett A.F., Lenski R.E. Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment // Evolution. 2001. V. 55 (5). P. 889–896.
  33. Crow K.D., Wagner G.P. What is the role of genome duplication in the evolution of complexity and diversity? // Mol. Biol. Evol. 2006. V. 23 (5). P. 887–892.
  34. De La Cruz F., Frost L.S., Meyer R.J., Zechner E.L. Conjugative DNA metabolism in gram-negative bacteria // FEMS Microbiol. Rev. 2010. V. 34 (1). P. 18–40.
  35. Deatherage D.E., Kepner J.L., Bennett A.F., et al. Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures // PNAS USA. 2017. V. 114 (10). P. E1904–E1912.
  36. Dekel E., Alon U. Optimality and evolutionary tuning of the expression level of a protein // Nature. 2005. V. 436 (7050). P. 588–592.
  37. DeSalle R. Adaptive evolution of genes and genomes // Heredity. 2000. V. 85 (3). P. 303–303.
  38. Douarre P.E., Sauvage E., Poyart C., Glaser P. Host specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus // J. Antimicrob. Chemother. 2015. V. 70 (12). P. 3205–3213.
  39. Dragosits M., Mattanovich D. Adaptive laboratory evolution – principles and applications for biotechnology // Microb. Cell Fact. 2013. V. 12 (1). P. 64.
  40. Dubois V., Poirel L., Marie C. et al. Molecular characterization of a novel class 1 integron containing bla(GES-1) and a fused product of aac3-Ib/aac6’-Ib’ gene cassettes in Pseudomonas aeruginosa // Antimicrob. Agents Chemother. 2002. V. 46 (3). P. 638–645.
  41. Elena S.F., Lenski R.E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation // Nat. Rev. Genet. 2003. V. 4 (6). P. 457–469.
  42. Feiner R., Argov T., Rabinovich L. et al. A new perspective on lysogeny: prophages as active regulatory switches of bacteria // Nat. Rev. Microbiol. 2015. V. 13 (10). P. 641–650.
  43. Fletcher E., Feizi A., Bisschops M.M.M. et al. Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments // Metab. Engin. 2017. V. 39. P. 19–28.
  44. Force A., Lynch M., Pickett F.B. et al. Preservation of duplicate genes by complementary, degenerative mutations // Genetics. 1999. V. 151 (4). P. 1531–1545.
  45. Fordham S.M.E., Mantzouratou A., Sheridan E. Prevalence of insertion sequence elements in plasmids relating to mgrB gene disruption causing colistin resistance in Klebsiella pneumoniae // MicrobiologyOpen. 2022. V. 11 (1).
  46. Frost L.S., Leplae R., Summers A.O., Toussaint, A. Mobile genetic elements: the agents of open source evolution // Nat. Rev. Microbiol. 2005. V. 3 (9). P. 722–732.
  47. Gan Y., Bai M., Lin X., et al. Improvement of macrolactins production by the genetic adaptation of Bacillus siamensis A72 to saline stress via adaptive laboratory evolution // Microb. Cell Fact. 2022. V. 21 (1). P. 1–15.
  48. Gao D. Introduction of plant transposon annotation for beginners // Biology. 2023. V. 26 (12).
  49. Gao Y., Wu Y., Huan T., et al. The application of oncolytic viruses in cancer therapy // Biotechnol. Lett. 2021. V. 43 (10). P. 1945–1954.
  50. Gillings M.R. Integrons: past, present, and future // Microbiol. Mol. Biol. Rev. 2014. V. 78 (2). P. 257–277.
  51. Gresham D., Hong J. The functional basis of adaptive evolution in chemostats // FEMS Microbiol. Rev. 2015. V. 39 (1). P. 2–16.
  52. Grobe C., Kohl T.A., Niemann S. et al. Loss of mobile genomic islands in metal-resistant, hydrogen-oxidizing Cupriavidus metallidurans // Appl. Environ. Microbiol. 2022. V. 88 (4).
  53. Guedon G., Libante V., Coluzzi C. et al. The obscure world of integrative and mobilizable elements, highly widespread elements that pirate bacterial conjugative systems // Genes. 2017. V. 8 (11).
  54. Hamidkhani A., Asgarani E., Saboora A. et al. Ethanol as a carotenoid production stimulator in Dunaliella salina CCAP 19/18 // Folia Microbiol. 2023. V. 68 (6). P. 925–937.
  55. Han H.J., Eom G.T. Production of lactobionic acid at high salt concentrations by Acinetobacter halotolerans isolated from seaside soil // Bioproc. Biosyst. Engin. 2022. V. 45 (10). P. 1683–1691.
  56. Haniford D.B., Ellis M.J. Transposons Tn10 and Tn5 // Microbiol. Spectrum. 2015. V. 3 (1).
  57. Harmer C.J., Hamidian M., Hall R.M. pIP40a, a type 1 IncC plasmid from 1969 carries the integrative element GIsul2 and a novel class II mercury resistance transposon // Plasmid. 2017. V. 92. P. 17–25.
  58. Hastings P.J., Bull H.J., Klump J.R., Rosenberg S.M. Adaptive amplification: an inducible chromosomal instability mechanism // Cell. 2000. V. 103 (5). P. 723–731.
  59. Hirasawa T., Maeda T. Adaptive laboratory evolution of microorganisms: methodology and application for bioproduction // Microorganisms. 2022. V. 11 (1).
  60. Hirose J., Watanabe T., Futagami T. et al. A new iceclc subfamily integrative and conjugative element responsible for horizontal transfer of biphenyl and salicylic acid catabolic pathway in the pcb-degrading strain Pseudomonas stutzeri kf716 // Microorganisms. 2021. V. 9 (12).
  61. Hollants J., Leliaert F., Verbruggen H. et al. Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis // Mol. Phylogenet. Evol. 2013. V. 67 (3). P. 608–614.
  62. Hu Q., Chen L. Virulence and antibiotic and heavy metal resistance of Vibrio parahaemolyticus isolated from crustaceans and shellfish in Shanghai, China // J. Food Protect. 2016. V. 79 (8). P. 1371–1377.
  63. Ishihama A. Building a complete image of genome regulation in the model organism Escherichia coli // J. Gen. Appl. Microbiol. 2018. V. 63 (6). P. 311–324.
  64. Janzen D.H. When is it coevolution? // Evolution. 1980. V. 34 (3). P. 611–612.
  65. Johnsborg O., Eldholm V., Havarstein L.S. Natural genetic transformation: prevalence, mechanisms and function // Res. Microbiol. 2007. V. 158 (10). P. 767–778.
  66. Kawakubo S., Kim H., Takeshita M., Masuta C. Host-specific adaptation drove the coevolution of leek yellow stripe virus and Allium plants // Microbiol. Spectrum. 2023. V. 11 (5).
  67. Kuzmin E., Vandersluis B., Ba A.N.N. et al. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis // Science. 2020. V. 368 (6498).
  68. Lang A.S., Beatty J.T. Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus // PNAS USA. 2000. V. 97 (2). P. 859–864.
  69. Lavrentyeva E.V., Erdyneeva E.B., Dunaevskii Y.E. et al. Extracellular, highly stable, alkaline peptidases of the alkalophilic bacteria Alkalicaulis satelles G-192t and Aliidiomarina sp. P-156 and their possible use in the composition of detergents // Appl. Biochem. Microbiol. 2021. V. 57 (6). P. 725–731.
  70. Lee H., Popodi E., Tang H., Foster P.L. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing // PNAS USA. 2012. V. 109 (41).
  71. Lei C.W., Chen Y.P., Kang Z.Z. et al. Characterization of a novel SXT/R391 integrative and conjugative element carrying cfr, blaCTX-M-65, fosA3, and aac(6’)-Ib-cr in Proteus mirabilis // Antimicrob. Agents Chemother. 2018. V. 62 (9).
  72. Lenski R.E., Wiser M.J., Ribeck N. et al. Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli // Proc. Biol. Sci. 2015. V. 282 (1821).
  73. Leon-Velarde C.G., Happonen L., Pajunen M., et al. Yersinia enterocolitica-specific infection by bacteriophages TG1 and ϕR1-RT is dependent on temperature-regulated expression of the phage host receptor OmpF // Appl. Environ. Microbiol. 2016. V. 82 (17). P. 5340–5353.
  74. Levin B.R., Bergstrom C.T. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes // PNAS USA. 2000. V. 97 (13). P. 6981–6985.
  75. Lima-Mendez G., Alvarenga D.O., Ross K. et al. Toxin-antitoxin gene pairs found in Tn 3 family transposons appear to be an integral part of the transposition module // mBio. 2020. V. 11 (2).
  76. Liu Y., Jia K., Chen H. et al. Cold-adapted enzymes: mechanisms, engineering and biotechnological application // Bioproc. Biosyst. Engin. 2023. V. 46 (10). P. 1399–1410.
  77. Martens J.H., Barg H., Warren M., Jahn D. Microbial production of vitamin B12 // Appl. Microbiol. Biotechnol. 2002. V. 58 (3). P. 275–285.
  78. Mayer C., Boos W. Hexose/pentose and hexitol/pentitol metabolism // EcoSal Plus. 2005. V. 1 (2).
  79. McCarlie S.J., Boucher C.E., Bragg R.R. Genomic islands identified in highly resistant Serratia sp. HRI: a pathway to discover new disinfectant resistance elements // Microorganisms. 2023. V. 11 (2).
  80. Millan C., Pena C., Flores C. et al. Improving glucose and xylose assimilation in Azotobacter vinelandii by adaptive laboratory evolution // World J. Microbiol. Biotechnol. 2020. V. 36 (3). P. 1–11.
  81. Modi S.R., Lee H.H., Spina C.S., Collins J.J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome // Nature. 2013. V. 499 (7457). P. 219–222.
  82. Nepal S., Bonn F., Grasso S. et al. An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae // Virulence. 2018. V. 9 (1). P. 1377–1389.
  83. Nutzmann H.W., Reyes-Dominguez Y., Scherlach K. et al. Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation // PNAS USA. 2011. V. 108 (34). P. 14282–14287.
  84. Olson-Manning C.F., Wagner M.R., Mitchell-Olds T. Adaptive evolution: evaluating empirical support for theoretical predictions // Nat. Rev. Genetics. 2012. V. 13 (12). P. 867–877.
  85. Orr H.A. The probability of parallel evolution // Evolution. 2005. V. 59 (1). P. 216–220.
  86. Park H.J., Bae J.H., Ko H.J. et al. Low-pH production of d-lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7 // Biotechnol. Bioengin. 2018. V. 115 (9). P. 2232–2242.
  87. Park J., Kerner A., Burns M.A., Lin X.N. Microdroplet-enabled highly parallel co-cultivation of microbial communities // PLoS One. 2011. V. 6 (2).
  88. Patel A., Rantzos C., Krikigianni E. et al. A bioprocess engineering approach for the production of hydrocarbons and fatty acids from green microalga under high cobalt concentration as the feedstock of high-grade biofuels // Biotechnol. Biofuel. Bioprod. 2024. V. 17 (1). P. 1–25.
  89. Ponder R.G., Fonville N.C., Rosenberg S.M. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation // Mol. Cell. 2005. V. 19 (6). P. 791–804.
  90. Pontrelli S., Fricke R.C.B., Sakurai S.S.M. et al. Directed strain evolution restructures metabolism for 1-butanol production in minimal media // Metab. Engin. 2018. V. 49. P. 153–163.
  91. Rajabi H., Salimizand H., Khodabandehloo M. et al. Prevalence of algD, pslD, pelF, Ppgl, and PAPI-1 genes involved in biofilm formation in clinical Pseudomonas aeruginosa strains // BioMed Res. Int. 2022.
  92. Ram Y., Hadany L. Stress-induced mutagenesis and complex adaptation // Proc. Biol. Sci. 2014. V. 281 (1792).
  93. Rasul F., You D., Jiang Y. et al. Thermophilic cyanobacteria—exciting, yet challenging biotechnological chassis // Appl. Microbiol. Biotechnol. 2024. V. 108 (1). P. 1–15.
  94. Sauer U. Evolutionary engineering of industrially important microbial phenotypes // Adv. Biochem. Engin. Biotechnol. 2001. V. 73. P. 129–169.
  95. Schonknecht G., Weber A.P.M., Lercher M.J. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution // BioEssays News Rev. Mol. Cell. Dev. Biol. 2014. V. 36 (1). P. 9–20.
  96. Schoustra S.E., Bataillon T., Gifford D.R., Kassen R. The properties of adaptive walks in evolving populations of fungus // PLoS Biol. 2009. V. 7 (11). P. e1000250.
  97. Schroder G., Lanka E. The mating pair formation system of conjugative plasmids-A versatile secretion machinery for transfer of proteins and DNA // Plasmid. 2005. V. 54 (1). P. 1–25.
  98. Schroeckh V., Scherlach K., Nutzmann H.W. et al. Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans // PNAS USA. 2009. V. 106 (34). P. 14558–14563.
  99. Sharavin D.Y., Belyaeva P.G. Biotechnological potential of psychrotolerant methylobacteria isolated from biotopes of Antarctic oases // Arch. Microbiol. 2024. V. 206 (7). P. 1–16.
  100. Smillie C., Garcillan-Barcia M.P., Francia M.V. et al. Mobility of plasmids // Microbiol. Mol. Biol. Rev. 2010. V. 74 (3). P. 434–452.
  101. Stanton T.B. Prophage-like gene transfer agents-novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species // Anaerobe. 2007. V. 13 (2). P. 43–49.
  102. Stevens M.J.A., Nuesch-Inderbinen M., Horlbog J.A. et al. Sucrose-fermenting Salmonella Typhimurium N23-2364: a challenge for the diagnostic laboratory // Diagn. Microbiol. Infect. Dis. 2024. V. 109 (2). P. 116280.
  103. Stokes H.W., O’Gorman D.B., Recchia G.D. et al. Structure and function of 59-base element recombination sites associated with mobile gene cassettes // Mol. Microbiol. 1997. V. 26 (4). P. 731–745.
  104. Strauss S.Y., Irwin R.E. Ecological and evolutionary consequences of multispecies plant-animal interactions // Ann. Rev. Ecol. Evol. Syst. 2004. V. 35. P. 435–466.
  105. The H.C., Thanh D.P., Holt K.E. et al. The genomic signatures of Shigella evolution, adaptation and geographical spread // Nat. Rev. Microbiol. 2016. V. 14 (4). P. 235–250.
  106. Thorpe H.M., Smith M.C.M. In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family // PNAS USA. 1998. V. 95 (10). P. 5505–5510.
  107. Tilloy V., Ortiz-Julien A., Dequin S. Reduction of ethanol yield and improvement of glycerol formation by adaptive evolution of the wine yeast Saccharomyces cerevisiae under hyperosmotic conditions // Appl. Environ. Microbiol. 2014. V. 80 (8). P. 2623–2632.
  108. Traxler M.F., Watrous J.D., Alexandrov T. et al. Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome // mBio. 2013. V. 4 (4).
  109. von Wintersdorff C.J.H., Penders J., Van Niekerk J.M. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer // Front.Microbiol. 2016. V. 7.
  110. Wagner A. Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein // Nat. Commun. 2023. V. 14 (1).
  111. Wang J., Dong X., Shao Y. et al. Genome adaptive evolution of Lactobacillus casei under long-term antibiotic selection pressures // BMC Genomics. 2017. V. 18 (1). P. 1–8.
  112. Wang X., Khushk I., Xiao Y. et al. Tolerance improvement of Corynebacterium glutamicum on lignocellulose derived inhibitors by adaptive evolution // Appl. Microbiol. Biotechnol. 2018. V. 102 (1). P. 377–388.
  113. Weil J., Signer E.R. Recombination in bacteriophage lambda II. Site-specific recombination promoted by the integration system // J. Mol. Biol. 1968. V. 34 (2). P. 273–279.
  114. Weisberg A.J., Chang J.H. Mobile genetic element flexibility as an underlying principle to bacterial evolution // Ann. Rev. Microbiol. 2023. V. 77. P. 603–624.
  115. Wright B.E. A biochemical mechanism for nonrandom mutations and evolution // J. Bacteriol. 2000. V. 182 (11). P. 2993–3001.
  116. Wright B.E. Stress-directed adaptive mutations and evolution // Mol. Microbiol. 2004. V. 52 (3). P. 643–650.
  117. Xu C., Sun T., Li S. et al. Adaptive laboratory evolution of cadmium tolerance in Synechocystis sp. PCC 6803 // Biotechnol. Biofuel. 2018. V. 11 (1).
  118. Zhang J. Evolution by gene duplication: an update // Trends Ecol. Evol. 2003. V. 18 (6). P. 292–298.
  119. Zorraquino-Salvo V., Quinones-Soto S., Kim M. et al. Deciphering the genetic and transcriptional basis of cross-stress responses in Escherichia coli under complex evolutionary scenarios // bioRxiv. 2014. V. 56. P. 1–16.

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