Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses

intergeneric-chromosomal-transfer-in-yeast-results-in-improved-phenotypes-and-widespread-transcriptional-responses
Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses

References

  1. Soucy, S. M., Huang, J. & Gogarten, J. P. Horizontal gene transfer: building the web of life. Nat. Rev. Genet. 16, 472–482 (2015).

    Google Scholar 

  2. Steensels, J., Gallone, B. & Verstrepen, K. J. Interspecific hybridization as a driver of fungal evolution and adaptation. Nat. Rev. Microbiol. 19, 485–500 (2021).

    Google Scholar 

  3. Stegemann, S., Keuthe, M., Greiner, S. & Bock, R. Horizontal transfer of chloroplast genomes between plant species. Proc. Natl. Acad. Sci. 109, 2434–2438 (2012).

    Google Scholar 

  4. Ma, L.-J. et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367–373 (2010).

    Google Scholar 

  5. Gibson, B. & Liti, G. Saccharomyces pastorianus: genomic insights inspiring innovation for industry. Yeast Chichester Engl. 32, 17–27 (2015).

    Google Scholar 

  6. Mergoum, M. et al. Triticale: A “New” Crop with Old Challenges. 267–287 (Handbook of Plant Breeding, vol 3. Springer, New York, 2009).

  7. Chen, Z. J. Genomic and epigenetic insights into the molecular bases of heterosis. Nat. Rev. Genet. 14, 471–482 (2013).

    Google Scholar 

  8. Landry, C. R., Hartl, D. L. & Ranz, J. M. Genome clashes in hybrids: insights from gene expression. Heredity 99, 483–493 (2007).

    Google Scholar 

  9. Signor, S. A. & Nuzhdin, S. V. The Evolution of Gene Expression in cis and trans. Trends Genet. 34, 532–544 (2018).

    Google Scholar 

  10. Gombert, A. K., Madeira, J. V., Cerdán, M.-E. & González-Siso, M.-I. Kluyveromyces marxianus as a host for heterologous protein synthesis. Appl. Microbiol. Biotechnol. 100, 6193–6208 (2016).

    Google Scholar 

  11. Bilal, M. et al. Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology. Front. Bioeng. Biotechnol. 10, 851768 (2022).

    Google Scholar 

  12. Groeneveld, P., Stouthamer, A. H. & Westerhoff, H. V. Super life – how and why ‘cell selection’ leads to the fastest-growing eukaryote. FEBS J. 276, 254–270 (2009).

    Google Scholar 

  13. Lertwattanasakul, N. et al. Utilization capability of sucrose, raffinose and inulin and its less-sensitiveness to glucose repression in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042. AMB Express 1, 20 (2011).

    Google Scholar 

  14. Rodrussamee, N. et al. Growth and ethanol fermentation ability on hexose and pentose sugars and glucose effect under various conditions in thermotolerant yeast Kluyveromyces marxianus. Appl. Microbiol. Biotechnol. 90, 1573–1586 (2011).

    Google Scholar 

  15. Fisk, D. G. et al. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23, 857–865 (2006).

    Google Scholar 

  16. Witte, V., Grossmann, B. & Emeis, C. C. Molecular probes for the detection of Kluyveromyces marxianus chromosomal DNA in electrophoretic karyotypes of intergeneric protoplast fusion products. Arch. Microbiol. 152, 441–446 (1989).

    Google Scholar 

  17. Albonico, F., B, E., G, P. H. & B, D. New Saccharomyces cerevisiaeKluyveromyces marxianus fusant shows enhanced alcoholic fermentation performance. World J. Microbiol. Biotechnol. 38, 251 (2022).

    Google Scholar 

  18. Fournier, R. E. & Ruddle, F. H. Microcell-mediated transfer of murine chromosomes into mouse, Chinese hamster, and human somatic cells. Proc. Natl. Acad. Sci. 74, 319–323 (1977).

    Google Scholar 

  19. Fukagawa, T. et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat. Cell Biol. 6, 784–791 (2004).

    Google Scholar 

  20. O’Doherty, A. et al. An aneuploid mouse strain carrying human chromosome 21 with Down syndrome phenotypes. Science 309, 2033–2037 (2005).

    Google Scholar 

  21. Wilson, M. D. et al. Species-specific transcription in mice carrying human chromosome 21. Science 322, 434–438 (2008).

    Google Scholar 

  22. Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632–638 (2007).

    Google Scholar 

  23. Shen, X.-X. et al. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell 175, 1533–1545.e20 (2018).

    Google Scholar 

  24. Kitaoka, M., Smith, O. K., Straight, A. F. & Heald, R. Molecular conflicts disrupting centromere maintenance contribute to Xenopus hybrid inviability. Curr. Biol. 32, 3939–3951.e6 (2022).

    Google Scholar 

  25. Kitano, J. & Okude, G. Causative genes of intrinsic hybrid incompatibility in animals and plants: what we have learned about speciation from the molecular perspective. Evol. J. Linn. Soc. 3, kzae022 (2024).

    Google Scholar 

  26. Lartigue, C. et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693–1696 (2009).

    Google Scholar 

  27. Nieduszynski, C. A., Knox, Y. & Donaldson, A. D. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 20, 1874–1879 (2006).

    Google Scholar 

  28. Theis, J. F. & Newlon, C. S. The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl. Acad. Sci. 94, 10786–10791 (1997).

    Google Scholar 

  29. Iborra, F. & Ball, M. M. Kluyveromyces marxianus small DNA fragments contain both autonomous replicative and centromeric elements that also function in Kluyveromyces lactis. Yeast Chichester Engl. 10, 1621–1629 (1994).

    Google Scholar 

  30. Ball, M. M., Raynal, A., Guérineau, M. & Iborra, F. Construction of efficient centromeric, multicopy and expression vectors for the yeast Kluyveromyces marxianus using homologous elements and the promoter of a purine-cytosine-like permease. J. Mol. Microbiol. Biotechnol. 1, 347–353 (1999).

    Google Scholar 

  31. Rajkumar, A. S., Varela, J. A., Juergens, H., Daran, J.-M. G., and Morrissey, J. P. Biological Parts for Kluyveromyces marxianus Synthetic Biology. Front. Bioeng. Biotechnol. 7 (2019).

  32. Abdel-Banat, B. M. A., Hoshida, H. & Akada, R. Various short autonomously replicating sequences from the yeast Kluyveromyces marxianus seemingly without canonical consensus. Curr. Res. Microb. Sci. 2, 100053 (2021).

    Google Scholar 

  33. Hegemann, J. H. & Fleig, U. N. The centromere of budding yeast. BioEssays 15, 451–460 (1993).

    Google Scholar 

  34. Ren, H. et al. Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus. Microorganisms 10, 1240 (2022).

    Google Scholar 

  35. Sikorski, R. S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27 (1989).

    Google Scholar 

  36. Gnügge, R. & Rudolf, F. Saccharomyces cerevisiae Shuttle vectors. Yeast Chichester Engl. 34, 205–221 (2017).

    Google Scholar 

  37. Bitoun, R. & Zamir, A. Spontaneous amplification of yeast CEN ARS plasmids. Mol. Gen. Genet. 204, 98–102 (1986).

    Google Scholar 

  38. Zhou, H. et al. Efficient and markerless gene integration with SlugCas9-HF in Kluyveromyces marxianus. Commun. Biol. 7, 797 (2024).

    Google Scholar 

  39. Peska, V. et al. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Sci. Rep. 11, 12784 (2021).

    Google Scholar 

  40. Shao, Y. et al. Creating a functional single-chromosome yeast. Nature 560, 331–335 (2018).

    Google Scholar 

  41. Noskov, V. N. et al. Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies. Nat. Protoc. 6, 89–96 (2011).

    Google Scholar 

  42. Lyu, Y., Wu, P., Zhou, J., Yu, Y. & Lu, H. Protoplast transformation of Kluyveromyces marxianus. Biotechnol. J. 16, e2100122 (2021).

    Google Scholar 

  43. Tschumper, G. & Carbon, J. High frequency excision of Ty elements during transformation of yeast. Nucleic Acids Res. 14, 2989–3001 (1986).

    Google Scholar 

  44. Wu, P. et al. Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus. mLife 3, 129–142 (2024).

    Google Scholar 

  45. Travesa, A. & Wittenberg, C. Turned on by genotoxic stress. Cell Cycle 11, 3145–3146 (2012).

    Google Scholar 

  46. Walker, G. M. & Basso, T. O. Mitigating stress in industrial yeasts. Fungal Biol. 124, 387–397 (2020).

    Google Scholar 

  47. Chakrabortee, S. et al. Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. Cell 167, 369–381.e12 (2016).

    Google Scholar 

  48. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

    Google Scholar 

  49. Coluccio, A. et al. Morphogenetic pathway of spore wall assembly in Saccharomyces cerevisiae. Eukaryot. Cell 3, 1464–1475 (2004).

    Google Scholar 

  50. Nguyen, T. H., Fleet, G. H. & Rogers, P. L. Composition of the cell walls of several yeast species. Appl. Microbiol. Biotechnol. 50, 206–212 (1998).

    Google Scholar 

  51. Soares, E. V. Flocculation in Saccharomyces cerevisiae: a review. J. Appl. Microbiol. 110, 1–18 (2011).

    Google Scholar 

  52. Teunissen, A. W. & Steensma, H. Y. Review: the dominant flocculation genes of Saccharomyces cerevisiae constitute a new subtelomeric gene family. Yeast Chichester Engl. 11, 1001–1013 (1995).

    Google Scholar 

  53. Nonklang, S. et al. Construction of flocculent Kluyveromyces marxianus strains suitable for high-temperature ethanol fermentation. Biosci. Biotechnol. Biochem. 73, 1090–1095 (2009).

    Google Scholar 

  54. Brothers, M. & Rine, J. Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae. eLife 11, e75653 (2022).

    Google Scholar 

  55. Sjöstrand, J. O. O., Kegel, A. & Aström, S. U. Functional diversity of silencers in budding yeasts. Eukaryot. Cell 1, 548–557 (2002).

    Google Scholar 

  56. Aström, S. U., Kegel, A., Sjöstrand, J. O. & Rine, J. Kluyveromyces lactis Sir2p regulates cation sensitivity and maintains a specialized chromatin structure at the cryptic alpha-locus. Genetics 156, 81–91 (2000).

    Google Scholar 

  57. De Boer, C. G. & Hughes, T. R. YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res. 40, 169–179 (2012).

    Google Scholar 

  58. Wittkopp, P. J. Contributions of mutation and selection to regulatory variation: lessons from the Saccharomyces cerevisiae TDH3 gene. Philos. Trans. R. Soc. B Biol. Sci. 378, 20220057 (2023).

    Google Scholar 

  59. Metzger, B. P. H., Wittkopp, P. J. & Coolon, J. D. Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species. Genome Biol. Evol. 9, 843–854 (2017).

    Google Scholar 

  60. Guerrero, R. F., Posto, A. L., Moyle, L. C. & Hahn, M. W. Genome-wide patterns of regulatory divergence revealed by introgression lines. Evol. Int. J. Org. Evol. 70, 696–706 (2016).

    Google Scholar 

  61. Gordon, K. L. & Ruvinsky, I. Tempo and Mode in Evolution of Transcriptional Regulation. PLoS Genet. 8, e1002432 (2012).

    Google Scholar 

  62. Tirosh, I., Reikhav, S., Levy, A. A. & Barkai, N. A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation. Science 324, 659–662 (2009).

    Google Scholar 

  63. Landry, C. R. et al. Compensatory cistrans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171, 1813–1822 (2005).

    Google Scholar 

  64. Barrière, A., Gordon, K. L. & Ruvinsky, I. Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLOS Genet. 8, e1002961 (2012).

    Google Scholar 

  65. Steensels, J. et al. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol. Rev. 38, 947–995 (2014).

    Google Scholar 

  66. Pobiega, S. & Marcand, S. Dicentric breakage at telomere fusions. Genes Dev. 24, 720–733 (2010).

    Google Scholar 

  67. Postma, E. D. et al. A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae. Nucleic Acids Res. 49, 1769–1783 (2021).

    Google Scholar 

  68. Zhou, J. et al. Exogenous artificial DNA forms chromatin structure with active transcription in yeast. Sci. China Life Sci. 65, 851–860 (2022).

    Google Scholar 

  69. Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).

    Google Scholar 

  70. Peris, D. et al. Synthetic hybrids of six yeast species. Nat. Commun. 11, 2085 (2020).

    Google Scholar 

  71. Zhang, W. & Geng, A. Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method. Biotechnol. Biofuels 5, 46 (2012).

    Google Scholar 

  72. Stojiljković, M. et al. Whole-genome transformation of yeast promotes rare host mutations with a single causative snp enhancing acetic acid tolerance. Mol. Cell. Biol. 42, e0056021 (2022).

    Google Scholar 

  73. Ho, C. H., et al. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat. Biotechnol. 27, https://doi.org/10.1038/nbt.1534 (2009).

  74. Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).

    Google Scholar 

  75. Venetz, J. E. et al. Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc. Natl. Acad. Sci. USA. 116, 8070–8079 (2019).

    Google Scholar 

  76. Meneu, L. et al. Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus. Science 387, eadm9466 (2025).

    Google Scholar 

  77. Carroll, S. B. Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution. Cell 134, 25–36 (2008).

    Google Scholar 

  78. Stern, D. L. & Orgogozo, V. The loci of evolution: how predictable is genetic evolution? Evolution 62, 2155–2177 (2008).

    Google Scholar 

  79. McManus, C. J. et al. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res. 20, 816–825 (2010).

    Google Scholar 

  80. Díaz, F., Wolf, J. & de Brito, R. A. Transcriptional Misexpression in Hybrids between Species Linked by Gene Flow Is Associated With Patterns of Sequence Divergence. Genome Biol. Evol. 15, evad071 (2023).

    Google Scholar 

  81. Bullard, J. H., Mostovoy, Y., Dudoit, S. & Brem, R. B. Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc. Natl. Acad. Sci. USA. 107, 5058–5063 (2010).

    Google Scholar 

  82. Li, X. C. & Fay, J. C. Cis-regulatory divergence in gene expression between two thermally divergent yeast species. Genome Biol. Evol. 9, 1120–1129 (2017).

    Google Scholar 

  83. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003).

    Google Scholar 

  84. Krieger, G., Lupo, O., Levy, A. A. & Barkai, N. Independent evolution of transcript abundance and gene regulatory dynamics. Genome Res. 30, 1000–1011 (2020).

    Google Scholar 

  85. Zhou, J., Zhu, P., Hu, X., Lu, H. & Yu, Y. Improved secretory expression of lignocellulolytic enzymes in Kluyveromyces marxianus by promoter and signal sequence engineering. Biotechnol. Biofuels 11, 235 (2018).

    Google Scholar 

  86. Amberg, D. C., Burke, D., Strathern, J. N., and Burke, D. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual 2005 ed. (Cold Spring Harbor Laboratory Press, 2005).

  87. Antunes, D. F., de Souza Junior, C. G. & de Morais Junior, M. A. A simple and rapid method for lithium acetate-mediated transformation of Kluyveromyces marxianus cells. World J. Microbiol. Biotechnol. 16, 653–654 (2000).

    Google Scholar 

  88. Gietz, R. D. & Schiestl, R. H. Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 38–41 (2007).

    Google Scholar 

  89. Shi, T., Zeng, J., Zhou, J., Yu, Y. & Lu, H. Correlation Between Improved Mating Efficiency and Weakened Scaffold-Kinase Interaction in the Mating Pheromone Response Pathway Revealed by Interspecies Complementation. Front. Microbiol. 13, 865829 (2022).

    Google Scholar 

  90. Shao, Y., Lu, N., Qin, Z. & Xue, X. CRISPR-Cas9 Facilitated Multiple-Chromosome Fusion in Saccharomyces cerevisiae. ACS Synth. Biol. 7, 2706–2708 (2018).

    Google Scholar 

  91. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinforma. Oxf. Engl. 25, 1754–1760 (2009).

    Google Scholar 

  92. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Google Scholar 

  93. Yu, Y. et al. Comparative genomic and transcriptomic analysis reveals specific features of gene regulation in Kluyveromyces marxianus. Front. Microbiol. 12, 598060 (2021).

    Google Scholar 

  94. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    Google Scholar 

  95. Wagih, O. & Parts, L. gitter: a robust and accurate method for quantification of colony sizes from plate images. G3 Bethesda 4, 547–552 (2014).

    Google Scholar 

  96. Matheson, K., Parsons, L. & Gammie, A. Whole-genome sequence and variant analysis of w303, a widely-used strain of Saccharomyces cerevisiae. G3 Bethesda 7, 2219–2226 (2017).

    Google Scholar 

  97. Miao, Z. et al. ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel. Nucleic Acids Res. 53, D852–D863 (2025).

    Google Scholar 

  98. Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

    Google Scholar 

  99. Anders, S., Pyl, P. T. & Huber, W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

    Google Scholar 

  100. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Google Scholar 

  101. Stephens, M. False discovery rates: a new deal. Biostat. Oxf. Engl. 18, 275–294 (2017).

    Google Scholar 

  102. Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).

    Google Scholar 

  103. Emerson, J. J. et al. Natural selection on cis and trans regulation in yeasts. Genome Res. 20, 826–836 (2010).

    Google Scholar 

  104. Fraser, H. B. et al. Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity. Genome Res. 22, 1930–1939 (2012).

    Google Scholar 

  105. Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

    Google Scholar 

Download references