Saccharomyces sensu stricto: Systematics, genetic diversity and evolution

Journal of Bioscience and Bioengineering

Volumn 96, Issue 1, 2003, Pages 1-9

  Rainieri, Sandra ^a   Zambonelli, Carlo ^b   Kaneko, Yoshinobu ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Evolution; Genetic variation; Saccharomyces sensu stricto; Systematics

Indexed keywords

BIODIVERSITY; FERMENTATION;

TAXONOMY;

YEAST;

FUNGAL DNA; MITOCHONDRIAL DNA;

EVOLUTION; FERMENTATION; FUNGUS CULTURE; GENETIC VARIABILITY; LIFE CYCLE; NONHUMAN; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SACCHAROMYCES; SACCHAROMYCES SENSU; SPECIES DIFFERENTIATION; STRAIN DIFFERENCE; TAXONOMY; YEAST;

FUNGI; SACCHAROMYCES; SACCHAROMYCES BAYANUS; SACCHAROMYCES PASTORIANUS;

EID: 0042420600     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1263/jbb.96.1     Document Type: Review

References (86)

1. Vaughan-Martini, A. and Martini, A.: Facts, myths and legends on the prime industrial microorganism. J. Ind. Microbiol., 14, 514-522 (1995).
2. Mortimer, R. K.: Evolution and variation of the yeast (Saccharomyces) genome. Genome Res., 10, 403-409 (2000).
3. Reess, M.: Botanische Untersuchungen über die Alkoholgärungspilze. Felix, Leipzig (1870).
4. Hansen, E. C.: Undersøgelser over alkoholgjaesvamenes fysiologi og morfologi. II. Om askosporedannelsen hos slaegent Saccharomyces. Medd. Carlsberg Lab., 2, 29-86 (1883).
5. Guilliermond, A.: Les Levures. Octave Doin et Fils, Paris (1912).
6. Stellin-Dekker, L. M.: Die sporogenen Hefen. Afd. Natuurkunde, Sect. II. Verh. Kon. Akad. Wetenschap, Amsterdam (1931).
7. Lodder, J. and Kreger van Rij, N. J. W.: The yeasts, a taxonomic study. North Holland Publishing Company, Amsterdam (1952).
8. Kudriavtzev, V. I.: Sistematica Drozhzhei. Akademii Nauk SSSR, Moskow (1954).
9. Kudriavtzev, V. I.: Die Systematik der Helen. Akademie Verlag, Berlin (1960).
10. Lodder, J.: The yeasts, a taxonomic study, 2nd ed. North Holland Publishing Company, Amsterdam (1970).
11. Barnett, J. A., Payne, R. W., and Yarrow, D.: Yeasts: characteristics and identification. Cambridge University Press, Cambridge (1983).
12. Kreger van Rij, N. J. W.: The yeasts, a taxonomic study, 3rd ed. Elsevier Science Publisher, Amsterdam (1984).
13. Barnett, J. A., Payne, R. W., and Yarrow, D.: Yeasts: characteristics and identification, 2nd ed. Cambridge University Press, Cambridge (1990).
14. Kurtzman, C. P. and Fell, J. W.: The yeasts, a taxonomic study, 4th ed. Elsevier Science, Amsterdam (1998).
15. van der Walt, J. P.: Genus 16 Saccharomyces Meyen emend. Rees, p. 555-718. In Lodder, J. (ed.), The yeasts, a taxonomic study, 2nd ed. North Holland Publishing Company, Amsterdam (1970).
16. Vaughan-Martini, A. and Martini, A.: Saccharomyces Meyen ex Rees, p. 358-371. In Kurtzman, C.P. and Fell, J.W. (ed.), The yeasts, a taxonomic study, 4th ed. Elsevier Science, Amsterdam (1998).
17. Naumov, G. I., James, S. A., Naumova, E. S., Louis, E. J., and Roberts, I. N.: Three new species in the Saccharomyces sensu stricto complex. Int. J. Syst. Evol. Microbiol., 50, 1931-1942 (2000).
18. Nguyen, H-V. and Gaillardin, C.: Two subgroups within the Saccharomyces bayanus species evidenced by PCR amplification and restriction polymorphism of the non-transcribed spacer 2 in the ribosomal DNA unit. Syst. Appl. Microbiol., 20, 286-294 (1997).
19. Rainieri, S., Zambonelli, C., Hallsworth, J. E., Pulvirenti, A., and Giudici, P.: Saccharomyces uvarum: a distinct group within Saccharomyces sensu stricto. FEMS Microbiol. Lett., 177, 177-185 (1999).
20. Yamagishi, H. and Ogata, T.: Chromosomal structures of bottom fermenting yeasts. Syst. Appl. Microbiol., 22, 341-353 (1999).
21. Nguyen, H-V., Lepingle, A., and Gaillardin, C.: Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus type strain CBS 380. Syst. Appl. Microbiol., 23, 71-85 (2000).
22. Naumov, G. I.: Genetic identification of biologlcal species in the Saccharomyces sensu stricto complex. J. Ind. Microbiol., 17, 295-302 (1992).
23. Vaughan-Martini, A. and Kurtzman, C. P.: Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto. Int. J. Syst. Bacteriol., 35, 508-511 (1985).
24. Sebastiani, F., Barberio, C., Casalone, E., Cavalieri, D., and Polsinelli, M.: Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids. Res. Microbiol., 153, 53-58 (2002).
25. Hunter, N., Chambers, S. R., Louis, E. J., and Borts, R. H.: The mismatch repair system contributes to meiotic sterility in an interspecific yeast hybrid. EMBO J., 15, 1726-1733 (1996).
26. Kurtzman, C. P.: Molecular taxonomy of fungi, p. 35-56. In Barnet, J. W. and Lasure, L. L. (ed.), Gene manipulation in fungi. Academic Press, New York (1985).
27. Price, C. W., Fuson, G. B., and Phaff, H. J.: Genome comparison in yeast systematic delimitation of species within the genera Scwanniomyces, Saccharomyces, Debaryomyces, and Pichia. Microbiol. Rev., 42, 161-193 (1978).
28. Johnston, J. R. and Mortimer, R. K.: Electrophoretic karyotyping of laboratory and commercial strains of Saccharomyces and other yeasts. Int. J. Syst. Bacteriol., 36, 569-572 (1986).
29. Guilliamon, J. M., Barrio, E., Huerta, T., and Querol, A.: Rapid characterization of four species of the Saccharomyces sensu stricto complex according to mitochondrial DNA patterns. Int. J. System. Bacteriol., 44, 708-714 (1994).
30. de Barros Lopes, M., Soden, A., Martens, A. L., Henschke, P. A., and Langridge, P.: Differentiation and species identification of yeasts using PCR. Int. J. Syst. Bacteriol., 48, 279-286 (1998).
31. Ryu, S.-L., Mikata, K., Murooka, Y., and Kaneko, Y.: A simple PCR method for distinguishing Saccharomyces cerevisiae from its sibling species by amplification of the RPL2 region. J. Ferment. Bioeng., 86, 249-252 (1998).
32. de Barros Lopes, M., Rainieri, S., Henschke, P. A., and Langridge, P.: AFLP fingerprinting for analysis of yeast genetic variation. Int. J. Syst. Bacteriol., 49, 915-924 (1999).
33. Azumi, M. and Goto-Yamamoto, N.: AFLP analysis of type strains and laboratory and industrial strains of Saccharomyces sensu stricto and its application to phenetic clustering. Yeast, 18, 1145-1154 (2001).
34. Valente, P., Ramos, J. P., and Leoncini, O.: Sequencing as a tool in yeast molecular taxonomy. Can. J. Microbiol., 45, 949-958 (1999).
35. Giudici, P. and Pulvirenti, A.: Molecular methods for identification of wine yeasts, p. 35-52. In Biodiversity and biotechnology of wine yeast. Managing Editor Research, India (2002).
36. Petersen, R. F., Marinoni, G., Nielsen, M. L., and Piskur, J.: Molecular approaches for analyzing diversity and phylogeny among yeast species. Contrib. Microbiol., 5, 15-35 (2000).
37. Olsen, G. J. and Woese, C.: Ribosomal RNA: a key to phylogeny. FASEB J., 7, 113-123 (1993).
38. Kurtzman, C. P. and Robnett, C. J.: Phylogenetic relationships among species of Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces determined from partial ribosomal RNA sequences. Yeast, 7, 61-72 (1991).
39. James, S. A., Collins, M. D., and Roberts, I. N.: Use of an rRNA internal transcribed spacer region to distinguish phylogenetically closely related species of the genera Zygosaccharomyces and Torulaspora. Int. J. Syst. Bacteriol., 46, 189-194 (1996).
40. Oda, Y., Yabuki, M., Tonomura, K., and Fukunaga, M.: A phylogenetic analysis of the Saccharomyces species by the sequence of 18S-28S rRNA spacer regions. Yeast, 13, 1243-1250 (1997).
41. James, S. A., Cai, J., Roberts, I. N., and Collins, M. D.: A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov. Int. J. Syst. Bacteriol., 47, 453-460 (1997).
42. Naumov, G. I., Naumova, E., and Gaillardin, G.: Genetic and karyotypic identification of wine Saccharomyces bayanus yeasts isolated in France and Italy. Syst. Appl. Microbiol., 16, 274-279 (1993).
43. Naumov, G. I., Masneuf, I., Naumova, E. S., Aisle, M., and Dubourdieu, D.: Association of Saccharomyces bayanus var. uvarum with some French wines: genetic analysis of yeast populations. Res. Microbiol., 151, 683-691 (2000).
44. Naumov, G. I., Nguyen, H-V., Naumova, E. S., Michel, A., Aisle, M., and Gaillardin, C.: Genetic identification of Saccharomyces bayanus var. uvarum, a cider-fermenting yeast. Int. J. Food Microbiol., 65, 163-171 (2001).
45. Sipiczk, M., Romano, P., Lipani, G., Miklos, I., and Antunovics, Z.: Analysis of yeasts derived from natural fermentation in a Tokaj winery. Antoine van Leeuwenhoek, 79, 97-105 (2001).
46. Giudici, P., Cassia, C., Pulvirenti, A., and Restuccia, C.: Cryotolerant Saccharomyces strains and spoilage of refrigerated musts. Ann. Microbiol. Enzymol., 49, 155-161 (1999).
47. Walsh, R. M. and Martin, P. A.: Growth of Saccharomyces cerevisiae and Saccharomyces uvarum in a gradient temperature incubator. J. Inst. Brew., 83, 169-172 (1977).
48. Vaughan-Martini, A. and Martini, A.: A taxonomic key for the genus Saccharomyces. Syst. Appl. Microbiol., 16, 113-119 (1993).
49. Rodrigues de Sousa, H., Madeira-Lopes, A., and Spencer-Martins, I.: The significance of active fructose transport and maximum temperature for growth in the taxonomy of Saccharomyces sensu stricto. Syst. Appl. Microbiol., 18, 44-51 (1995).
50. Pulvirenti, A., Nguyen, H-V., Cassia, C., Giudici, P., Rainieri, S., and Zambonelli, C.: Saccharomyces uvarum, a proper species within Saccharomyces sensu stricto. FEMS Microbiol. Lett., 192, 191-196 (2000).
51. Naumov, G. I.: Saccharomyces bayanus var. uvarum comb. nov., a new variety established by genetic analysis. Microbiology, 69, 338-342 (2000).
52. Casaregola, S., Nguyen, H-V., Lapathitis, G., Kotyk, A., and Gaillardin, C.: Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int. J. Syst. Evol. Microbiol., 51, 1607-1618 (2001).
53. Joubert, R., Brignon, P., Lehmann, C., Monribot, C., Gendre, F., and Boucherie, H.: Two-dimensional gel analysis of the proteome of lager brewing yeasts. Yeast, 16, 511-522 (2000).
54. Tamai, Y., Tanaka, K., Umemoto, N., Tomizuka, K., and Kaneko, Y.: Diversity of the HO gene encoding an endonuclease for mating-type conversion in the bottom fermenting yeast Saccharomyces pastorianus. Yeast, 16, 1335-1343 (2000).
55. Kodama, Y., Omura, F., and Ashikari, T.: Isolation and characterization of a gene specific to lager brewing yeast that encodes a branched-chained amino acid permease. Appl. Environ. Microbiol., 67, 3455-3462 (2001).
56. Herskowitz, I.: Mating type determination and mating type interconversion in Saccharomyces cerevisiae, p. 583-656. In Jones, E. W., Pringle, J. R., and Broach, J. R. (ed.), The molecular and cellular biology of the yeast Saccharomyces: gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1992).
57. Pretorius, I. S.: Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking. Yeast, 16, 675-729 (2000).
58. Benitez, T., Martinez, P., and Codon, A. C.: Genetic constitution of industrial yeast. Microbiologia, 12, 371-384 (1996).
59. Monch, J. and Stahl, U.: Polymorphism of industrial strains of Saccharomyces yeasts: genotypic and phenotypic features. Food Biotechnol., 14, 113-146 (2000).
60. Mortimer, R. K., Romano, P., Suzzi, G., and Polsinelli, M.: Genome renewal: a new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast, 10, 1543-1552 (1994).
61. Puig, S., Querol, A., Barrio, E., and Perez-Ortin, J. E.: Mitotic recombination and genetic change in Saccharomyces cerevisiae during wine fermentation. Appl. Environ. Microbiol., 66, 2057-2061 (2000).
62. Marinoni, G., Manuel, M., Petersen, P. F., Hvidtfeldt, J., Sulo, P., and Piskur, J.: Horizontal transfer of genetic material among Saccharomyces yeasts. J. Bacteriol., 181, 6488-6496 (1999).
63. Rainieri, S. and Pretorius, I. S.: Selection and improvement of wine yeasts. Ann. Microbiol., 50, 15-31 (2000).
64. Benitez, T., Gasent-Ramirez, J. M., Castrejon, F., and Codon, A. C.: Development of new strains for the food industry. Biotechnol. Progress, 12, 149-163 (1996).
65. de Barros Lopes, M., Bellon, J. R., Shirley, N. J., and Ganter, P. F.: Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. FEMS Yeast Res., 1, 323-331 (2002).
66. Pedersen, M. B.: DNA sequence polymorphism in the genus Saccharomyces 111. Restriction endonuclease fragment patterns of chromosomal regions in brewing and other yeast strains. Carlsberg Res. Commun., 51, 163-183 (1986).
67. Hansen, J. and Kielland-Brandt, M. C.: Saccharomyces carlsbergensis contains two functional MET2 alleles similar to homologues from S. cerevisiae and S. monacensis. Gene, 140, 33-40 (1995).
68. Tamai, Y., Momma, T., Yoshimoto, H., and Kaneko, Y.: Co-existence of two types of chromosome in the bottom fermenting yeast, Saccharomyces pastorianus. Yeast, 14, 923-933 (1998).
69. Yoshimoto, H., Fujiwara, D., Momma, T., Ito, C., Sone, H., Kaneko, Y., and Tamai, Y.: Characterization of the ATF1 and Lg-ATF1 genes encoding alcohol acetyltransferases in the bottom fermenting yeast Saccharomyces pastorianus. J. Ferment. Bioeng., 86, 15-20 (1998).
70. Masneuf, I., Hansen, J., Groth, C., Piskur, J., and Dubourdieu, D.: New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl. Environ. Microbiol., 64, 3887-3892 (1998).
71. Naumov, G. I., Naumova, E. S., Masneuf, I., Aisle, M., Kondratieva, V. I., and Dubourdieu, D.: Natural polyploidization of some cultured yeast Saccharomyces sensu stricto: auto- and allotetraploidy. Syst. Appl. Microbiol., 23, 442-449 (2000).
72. Groth, C., Hansen, H., and Piskur, J.: A natural chimeric yeast containing genetic material from three species. Int. J. Syst. Bacteriol., 49, 1933-1938 (1999).
73. Zambonelli, C.: Microbiologia e biotecnologia dei vini. Edgricole, Bologna (2002).
74. Pulvirenti, A., Zambonelli, C., Todaro, A., and Giudici, P.: Interspecific hybridisation by digestive tract of invertebrates as a source of environmental biodiversity within the Saccharomyces cerevisiae species. Ann. Microbiol., 52, 245-255 (2002).
75. Wolfe, K. H. and Shields, D. C.: Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708-713 (1997).
76. Ryu, S.-L., Murooka, Y., and Kaneko, Y.: Genomic reorganization between two sibling yeast species, Saccharomyces bayanus and Saccharomyces cerevisiae. Yeast, 12, 757-764 (1996).
77. Ryu, S.-L., Murooka, Y., and Kaneko, Y.: Reciprocal translocation at duplicated RPL2 loci might cause speciation of Saccharomyces bayanus and Saccharomyces cerevisiae. Curr. Genet., 33, 345-351 (1998).
78. Perez-Ortin, J. E., Querol, A., Puig, S., and Barrio, E.: Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains. Genome Res., 12, 1533-1539 (2002).
79. Fisher, G., James, S. A., Roberts, I. N., Oliver, S. G., and Louis, E. J.: Chromosomal evolution in Saccharomyces. Nature, 405, 451-454 (2000).
80. Groth, C., Petersen, R. F., and Piskur, J.: Diversity in organization and the origin of gene orders in the mitochondrial DNA molecules of the genus Saccharomyces. Mol. Biol. Evol., 17, 1833-1841 (2000).
81. Langkjaer, R. B., Nielsen, M. L., Daugaard, P. R., Liu, W., and Piskur, J.: Yeast chromosomes have been significantly reshaped during their evolutionary history. J. Mol. Biol., 304, 271-288 (2000).
82. Bon, E., Neuveglise, C., Casaregola, S., Artiguenave, F., Wineker, P., Aigle, M., and Durrens, P.: Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum. FEBS Lett., 487, 37-41 (2000).
83. Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R. W., and 10 other authors: Prevalence of small inversions in yeast gene order evolution. Proc. Natl. Acad. Sci. USA, 97, 14433-14437 (2000).
84. Souciet, J-L., Aigle, M., Artiguenave, F., Blandin, G., Bolotin-Fukuhara, M., Bon, E., Brottier, P., Casaregola, S., de Montigny, J., Dujon, B., and 14 other authors: Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett., 487, 3-12 (2000).
85. Fisher, G., Neuveglise, C., Durrens, P., Gaillardin, C., and Dujon, B.: Evolution of gene order in the genomes of two related yeast species. Genome Res., 11, 2009-2019 (2001).
86. Wong, S., Butler, G., and Wolfe, K. H.: Gene order evolution and paleoploydy in hemiascomycete yeasts. Proc. Natl. Acad. Sci. USA, 99, 9272-9277 (2002).