1887

Abstract

The yeast Kluyveromyces marxianus possesses advantageous traits like rapid growth, GRAS (generally regarded as safe) status and thermotolerance that make it very suitable for diverse biotechnological applications. Although physiological studies demonstrate wide phenotypic variation within the species, there is only limited information available on the genetic diversity of K. marxianus. The aim of this work was to develop a multilocus sequence typing (MLST) method for K. marxianus to improve strain classification and selection. Analysis of housekeeping genes in a number of sequenced strains led to the selection of five genes, IPP1, TFC1, GPH1, GSY2 and SGA1, with sufficient polymorphic sites to allow MLST analysis. These loci were sequenced in an additional 76 strains and used to develop the MLST. This revealed wide diversity in the species and separation of the culture collection and wild strains into multiple distinct clades. Two subsets of strains that shared sources of origin were subjected to MLST and split decomposition analysis. The latter revealed evidence of recombination, indicating that this yeast undergoes mating in the wild. A public access web-based portal was established to allow expansion of the database and application of MLST to additional K. marxianus strains. This will aid understanding of the genetic diversity of the yeast and facilitate biotechnological exploitation.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000153
2018-01-18
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/mgen/4/2/mgen000153.html?itemId=/content/journal/mgen/10.1099/mgen.0.000153&mimeType=html&fmt=ahah

References

  1. Arrizon J, Morel S, Gschaedler A, Monsan P. Fructanase and fructosyltransferase activity of non-Saccharomyces yeasts isolated from fermenting musts of Mezcal. Bioresour Technol 2012; 110:560–565 [View Article][PubMed]
    [Google Scholar]
  2. Lane MM, Morrissey JP. Kluyveromyces marxianus: a yeast emerging from its sister's shadow. Fungal Biol Rev 2010; 24:17–26 [View Article]
    [Google Scholar]
  3. Lachance MA. Kluyveromyces van der Walt (1971). In The Yeasts: A Taxonomic Study, 5th ed. Amsterdam: NHPC; 2011 pp. 471–481
    [Google Scholar]
  4. Mayoral MB, Martín R, Sanz A, Hernández PE, González I et al. Detection of Kluyveromyces marxianus and other spoilage yeasts in yoghurt using a PCR-culture technique. Int J Food Microbiol 2005; 105:27–34 [View Article][PubMed]
    [Google Scholar]
  5. Amaya-Delgado L, Herrera-López EJ, Arrizon J, Arellano-Plaza M, Gschaedler A. Performance evaluation of Pichia kluyveri, Kluyveromyces marxianus and Saccharomyces cerevisiae in industrial tequila fermentation. World J Microbiol Biotechnol 2013; 29:875–881 [View Article][PubMed]
    [Google Scholar]
  6. Gethins L, Rea MC, Stanton C, Ross RP, Kilcawley K et al. Acquisition of the yeast Kluyveromyces marxianus from unpasteurised milk by a kefir grain enhances kefir quality. FEMS Microbiol Lett 2016; 363:fnw165 [View Article][PubMed]
    [Google Scholar]
  7. Coloretti F, Chiavari C, Luise D, Tofalo R, Fasoli G et al. Detection and identification of yeasts in natural whey starter for Parmigiano Reggiano cheese-making. Int Dairy J 2017; 66:13–17 [View Article]
    [Google Scholar]
  8. Fonseca GG, Heinzle E, Wittmann C, Gombert AK. The yeast Kluyveromyces marxianus and its biotechnological potential. Appl Microbiol Biotechnol 2008; 79:339–354 [View Article][PubMed]
    [Google Scholar]
  9. Morrissey JP, Etschmann MM, Schrader J, de Billerbeck GM. Cell factory applications of the yeast Kluyveromyces marxianus for the biotechnological production of natural flavour and fragrance molecules. Yeast 2015; 32:3–16 [View Article][PubMed]
    [Google Scholar]
  10. Rocha SN, Abrahão-Neto J, Gombert AK. Physiological diversity within the Kluyveromyces marxianus species. Antonie van Leeuwenhoek 2011; 100:619–630 [View Article][PubMed]
    [Google Scholar]
  11. Kurtzman CP, Robnett CJ. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res 2003; 3:417–432 [View Article][PubMed]
    [Google Scholar]
  12. Pérez-Brito D, Tapia-Tussell R, Quijano-Ramayo A, Larqué-Saavedra A, Lappe P. Molecular characterization of Kluyveromyces marxianus strains isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico. Mol Biotechnol 2007; 37:181–186 [View Article][PubMed]
    [Google Scholar]
  13. Tofalo R, Fasoli G, Schirone M, Perpetuini G, Pepe A et al. The predominance, biodiversity and biotechnological properties of Kluyveromyces marxianus in the production of Pecorino di Farindola cheese. Int J Food Microbiol 2014; 187:41–49 [View Article][PubMed]
    [Google Scholar]
  14. Lopandic K, Zelger S, Bánszky LK, Eliskases-Lechner F, Prillinger H. Identification of yeasts associated with milk products using traditional and molecular techniques. Food Microbiol 2006; 23:341–350 [View Article][PubMed]
    [Google Scholar]
  15. Suzzi G, Lombardi A, Lanorte MT, Caruso M, Andrighetto C et al. Phenotypic and genotypic diversity of yeasts isolated from water-buffalo mozzarella cheese. J Appl Microbiol 2000; 88:117–123 [View Article][PubMed]
    [Google Scholar]
  16. Sohier D, Le Dizes A-S, Thuault D, Neuveglise C, Coton E et al. Important genetic diversity revealed by inter-LTR PCR fingerprinting of Kluyveromyces marxianus and Debaryomyces hansenii strains from French traditional cheeses. Dairy Sci Technol 2009; 89:569–581 [View Article]
    [Google Scholar]
  17. Belloch C, Barrio E, García MD, Querol A. Inter- and intraspecific chromosome pattern variation in the yeast genus Kluyveromyces . Yeast 1998; 14:1341–1354 [View Article][PubMed]
    [Google Scholar]
  18. Fasoli G, Tofalo R, Lanciotti R, Schirone M, Patrignani F et al. Chromosome arrangement, differentiation of growth kinetics and volatile molecule profiles in Kluyveromyces marxianus strains from Italian cheeses. Int J Food Microbiol 2015; 214:151–158 [View Article][PubMed]
    [Google Scholar]
  19. Lane MM, Burke N, Karreman R, Wolfe KH, O'Byrne CP et al. Physiological and metabolic diversity in the yeast Kluyveromyces marxianus . Antonie van Leeuwenhoek 2011; 100:507–519 [View Article][PubMed]
    [Google Scholar]
  20. Belloch C, Barrio E, Uruburu F, Garcia MD, Querol A. Characterisation of four species of the genus Kluyveromyces by mitochondrial DNA restriction analysis. Syst Appl Microbiol 1997; 20:397–408 [View Article]
    [Google Scholar]
  21. Masneuf-Pomarede I, Salin F, Börlin M, Coton E, Coton M et al. Microsatellite analysis of Saccharomyces uvarum diversity. FEMS Yeast Res 2016; 16:fow002 [View Article][PubMed]
    [Google Scholar]
  22. Hennequin C, Thierry A, Richard GF, Lecointre G, Nguyen HV et al. Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J Clin Microbiol 2001; 39:551–559 [View Article][PubMed]
    [Google Scholar]
  23. Pérez-Brito D, Tapia-Tussell R, Quijano-Ramayo A, Larqué-Saavedra A, Lappe P. Molecular characterization of Kluyveromyces marxianus strains isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico. Mol Biotechnol 2007; 37:181–186 [View Article][PubMed]
    [Google Scholar]
  24. Cooper JE, Feil EJ. Multilocus sequence typing – what is resolved?. Trends Microbiol 2004; 12:373–377 [View Article][PubMed]
    [Google Scholar]
  25. Taylor JW, Fisher MC. Fungal multilocus sequence typing – it’s not just for bacteria. Curr Opin Microbiol 2003; 64:351–356
    [Google Scholar]
  26. Maiden MC. Multilocus sequence typing of bacteria. Annu Rev Microbiol 2006; 60:561–588 [View Article][PubMed]
    [Google Scholar]
  27. Fay JC, Benavides JA. Evidence for domesticated and wild populations of Saccharomyces cerevisiae . PLoS Genet 2005; 1:e571 [View Article][PubMed]
    [Google Scholar]
  28. Fay JC, Benavides JA. Hypervariable noncoding sequences in Saccharomyces cerevisiae . Genetics 2005; 170:1575–1587 [View Article][PubMed]
    [Google Scholar]
  29. Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW et al. Population structure and gene evolution in Saccharomyces cerevisiae . FEMS Yeast Res 2006; 6:702–715 [View Article][PubMed]
    [Google Scholar]
  30. Bougnoux ME, Morand S, D'Enfert C. Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans . J Clin Microbiol 2002; 40:1290–1297 [View Article][PubMed]
    [Google Scholar]
  31. Bougnoux ME, Tavanti A, Bouchier C, Gow NA, Magnier A et al. Collaborative consensus for optimized multilocus sequence typing of Candida albicans . J Clin Microbiol 2003; 41:5265–5266 [View Article][PubMed]
    [Google Scholar]
  32. Tavanti A, Gow NA, Senesi S, Maiden MC, Odds FC. Optimization and validation of multilocus sequence typing for Candida albicans . J Clin Microbiol 2003; 41:3765–3776 [View Article][PubMed]
    [Google Scholar]
  33. Fasoli G, Barrio E, Tofalo R, Suzzi G, Belloch C. Multilocus analysis reveals large genetic diversity in Kluyveromyces marxianus strains isolated from Parmigiano Reggiano and Pecorino di Farindola cheeses. Int J Food Microbiol 2016; 233:1–10 [View Article][PubMed]
    [Google Scholar]
  34. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  35. Okonechnikov K, Golosova O, Fursov M. UGENE team Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article][PubMed]
    [Google Scholar]
  36. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  37. Odds FC, Jacobsen MD. Multilocus sequence typing of pathogenic Candida species. Eukaryot Cell 2008; 7:1075–1084 [View Article][PubMed]
    [Google Scholar]
  38. Jolley KA, Feil EJ, Chan MS, Maiden MC. Sequence type analysis and recombinational tests (START). Bioinformatics 2001; 17:1230–1231 [View Article][PubMed]
    [Google Scholar]
  39. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006; 23:254–267 [View Article][PubMed]
    [Google Scholar]
  40. Smith JM, Smith NH, O'Rourke M, Spratt BG. How clonal are bacteria?. Proc Natl Acad Sci USA 1993; 90:4384–4388 [View Article][PubMed]
    [Google Scholar]
  41. Haubold B, Hudson RR. LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage analysis. Bioinformatics 2000; 16:847–849 [View Article][PubMed]
    [Google Scholar]
  42. Saghrouni F, Ben Abdeljelil J, Boukadida J, Ben Said M. Molecular methods for strain typing of Candida albicans: a review. J Appl Microbiol 2013; 114:1559–1574 [View Article][PubMed]
    [Google Scholar]
  43. Pérez MA, Gallego FJ, Hidalgo P. Evaluation of molecular techniques for the genetic characterization of Saccharomyces cerevisiae strains. FEMS Microbiol Lett 2001; 205:375–378 [View Article][PubMed]
    [Google Scholar]
  44. Teste MA, Duquenne M, François JM, Parrou JL. Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae . BMC Mol Biol 2009; 10:99 [View Article][PubMed]
    [Google Scholar]
  45. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 1998; 95:3140–3145 [View Article][PubMed]
    [Google Scholar]
  46. Yarimizu T, Nonklang S, Nakamura J, Tokuda S, Nakagawa T et al. Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non-homologous end joining-mediated integrative transformation with genes from Saccharomyces cerevisiae . Yeast 2013; 30:485–500 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000153
Loading
/content/journal/mgen/10.1099/mgen.0.000153
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error