[1] | Kurtzman CP, Fell JW, Boekhout T, editors (2011) The yeasts, a taxonomy study. Amsterdam: Elseveir xxii +1–289, xv +290–1335, xvi +1336–2080 p.
|
[2] | Jeffries TW, Kurtzman CP (1994) Strain selection, taxonomy, and genetics of close-fermenting yeasts. Enzyme Microb Tech 16: 922–932.
|
[3] | Hahn-Hagerdal B, Karhumaa K, Jeppsson M, Gorwa-Grauslund MF (2007) Metabolic engineering for pentose utilization in Saccharomyces cerevisiae. Adv Biochem Eng Biotechnol 108: 147–177.
|
[4] | Hahn-Hagerdal B, Karhumaa K, Fonseca C, Spencer-Martins I, Gorwa-Grauslund MF (2007) Towards industrial pentose-fermenting yeast strains. Appl Microbiol Biotechnol 74: 937–953.
|
[5] | Jeffries TW, Shi NQ (1999) Genetic engineering for improved xylose fermentation by yeasts. Adv Biochem Eng Biotechnol 65: 117–161.
|
[6] | Shi NQ, Davis B, Sherman F, Cruz J, Jeffries TW (1999) Disruption of the cytochrome c gene in xylose-utilizing yeast Pichia stipitis leads to higher ethanol production. Yeast 15: 1021–1030.
|
[7] | Hamacher T, Becker J, Gardonyi M, Hahn-Hagerdal B, Boles E (2002) Characterization of the xylose-transporting properties of yeast hexose transporters and their influence on xylose utilization. Microbiology 148: 2783–2788.
|
[8] | Jin YS, Ni H, Laplaza JM, Jeffries TW (2003) Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate D-xylulokinase activity. Appl Environ Microbiol 69: 495–503.
|
[9] | Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25: 319–326.
|
[10] | Karhumaa K, Sanchez RG, Hahn-Hagerdal B, Gorwa-Grauslund MF (2007) Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant Saccharomyces cerevisiae. Microb Cell Fact 6: 5.
|
[11] | Karhumaa K, Fromanger R, Hahn-Hagerdal B, Gorwa-Grauslund MF (2007) High activity of xylose reductase and xylitol dehydrogenase improves xylose fermentation by recombinant Saccharomyces cerevisiae. Appl Microbiol Biotechnol 73: 1039–1046.
|
[12] | Hughes SR, Sterner DE, Bischoff KM, Hector RE, Dowd PF, et al. (2009) Engineered Saccharomyces cerevisiae strain for improved xylose utilization with a three-plasmid SUMO yeast expression system. Plasmid 61: 22–38.
|
[13] | Hector RE, Qureshi N, Hughes SR, Cotta MA (2008) Expression of a heterologous xylose transporter in a Saccharomyces cerevisiae strain engineered to utilize xylose improves aerobic xylose consumption. Appl Microbiol Biotechnol 80: 675–684.
|
[14] | Kumar S, Gummadi SN (2011) Metabolism of glucose and xylose as single and mixed feed in Debaryomyces nepalensis NCYC 3413: production of industrially important metabolites. Appl Microbiol Biotechnol 89: 1405–1415.
|
[15] | Shi NQ, Cruz J, Sherman F, Jeffries TW (2002) SHAM-sensitive alternative respiration in the xylose-metabolizing yeast Pichia stipitis. Yeast 19: 1203–1220.
|
[16] | Jeffries TW (2006) Engineering yeasts for xylose metabolism. Curr Opin Biotechnol 17: 320–326.
|
[17] | Van Vleet JH, Jeffries TW, Olsson L (2008) Deleting the para-nitrophenyl phosphatase (pNPPase), PHO13, in recombinant Saccharomyces cerevisiae improves growth and ethanol production on D-xylose. Metab Eng 10: 360–369.
|
[18] | Nguyen NH, Suh SO, Marshall CJ, Blackwell M (2006) Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov. Mycol Res 110: 1232–1241.
|
[19] | Cadete RM, Santos RO, Melo MA, Mouro A, Goncalves DL, et al. (2009) Spathaspora arborariae sp. nov., a D-xylose-fermenting yeast species isolated from rotting wood in Brazil. FEMS Yeast Res 9: 1338–1342.
|
[20] | Cadete RM, Melo MA, Lopes MR, Pereira GM, et al. (2011) Candida amazonensis sp. nov., an ascomycetous yeast isolated from rotting wood in Amazonian Forest, Brazil. Int J Syst Evol Microbiol. (In press).
|
[21] | Suh SO, Marshall CJ, McHugh JV, Blackwell M (2003) Wood ingestion by passalid beetles in the presence of xylose-fermenting gut yeasts. Mol Ecol 12: 3137–3145.
|
[22] | Grunwald S, Pilhofer M, Holl W (2010) Microbial associations in gut systems of wood- and bark-inhabiting longhorned beetles [Coleoptera: Cerambycidae]. Syst Appl Microbiol 33: 25–34.
|
[23] | Tanahashi M, Kubota K, Matsushita N, Togashi K (2010) Discovery of mycangia and the associated xylose-fermenting yeasts in stag beetles (Coleoptera: Lucanidae). Naturwissenschaften 97: 311–317.
|
[24] | Suh SO, Blackwell M, Kurtzman CP, Lachance MA (2006) Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 98: 1006–1017.
|
[25] | Toivola A, Yarrow D, van den Bosch E, van Dijken JP, Scheffers WA (1984) Alcoholic fermentation of D-xylose by yeasts. Appl Environ Microbiol 47: 1221–1223.
|
[26] | Delgenes JP, Moletta R, Navarro JM (1989) Fermentation of D-xylose, D-glucose, L-arabinose mixture by Pichia stipitis: Effect of the oxygen transfer rate on fermentation performance. Biotechnol Bioeng 34: 398–402.
|
[27] | Delgenes JP, Moletta R, Navarro JM (1986) The effect of aeration on D-xylose fermentation by Pachysolen tannophilus, Pichia stipitis, Kluyveromyces marxianus and Candida shehatae. Biotechnol Lett 8: 897–900.
|
[28] | Du Preez JC, Bosch M, Prior BA (1986) Xylose fermentation by Candida shehatae and Pichia stipitis, effects of pH, temperature and substrate concentration. Enzyme Microb Tech 8: 360–364.
|
[29] | Parekh SR, Yu S, Wayman M (1986) Adaptation of Candida shehatae and Pichia stipitis to wood hydrolysates for increased ethanol production. Appl Microbiol Biotechnol 25: 300–304.
|
[30] | Parekh S, Wayman M (1986) Fermentation of cellobiose and wood sugars to ethanol by Candida shehatae and Pichia stipitis. Biotechnol Lett 8: 597–600.
|
[31] | Sreenath HK, Chapman TW, Jeffries TW (1986) Ethanol production from D-xylose in batch fermentations with Candida shehatae: Process variables. Appl Microbiol Biotechnol 24: 294–299.
|
[32] | Alexander MA, Chapman TW, Jeffries TW (1988) Xylose metabolism by Candida shehatae in continuous culture. Appl Microbiol Biotechnol 28: 478–486.
|
[33] | Alexander MA, Chapman TW, Jeffries TW (1987) Continuous ethanol production from D-xylose by Candida shehatae. Biotechnol Bioeng 30: 685–691.
|
[34] | Prior BA, Alexander MA, Yang V, Jeffries TW (1988) The role of alcohol-dehydrogenase in the fermentation of D-xylose by Candida shehatae ATCC-22984. Biotechnol Lett 10: 37–42.
|
[35] | Ho NW, Lin FP, Huang S, Andrews PC, Tsao GT (1990) Purification, characterization, and amino terminal sequence of xylose reductase from Candida shehatae. Enzyme Microb Tech 12: 33–39.
|
[36] | Palnitkar S, Lachke A (1992) Effect of nitrogen sources on oxidoreductive enzymes and ethanol production during D-xylose fermentation by Candida shehatae. Can J Microbiol 38: 258–260.
|
[37] | Palnitkar SS, Lachke AH (1990) Efficient simultaneous saccharification and fermentation of agricultural residues by Saccharomyces cerevisiae and Candida shehatae. The D-xylose fermenting yeast. Appl Biochem Biotechnol 26: 151–158.
|
[38] | Agbogbo FK, Wenger KS (2007) Production of ethanol from corn stover hemicellulose hydrolyzate using Pichia stipitis. J Ind Microbiol Biotechnol 34: 723–727.
|
[39] | Agbogbo FK, Coward-Kelly G (2008) Cellulosic ethanol production using the naturally occurring xylose-fermenting yeast, Pichia stipitis. Biotechnol Lett 30: 1515–1524.
|
[40] | Agbogbo FK, Haagensen FD, Milam D, Wenger KS (2008) Fermentation of acid-pretreated corn stover to ethanol without detoxification using Pichia stipitis. Appl Biochem Biotechnol 145: 53–58.
|
[41] | Agbogbo FK, Wenger KS (2006) Effect of pretreatment chemicals on xylose fermentation by Pichia stipitis. Biotechnol Lett 28: 2065–2069.
|
[42] | Jeffries TW (1986) Regulation of the xylose fermentation in Candida shehatae and Pachysolen tannophilus. Abstr Pap Am Chem S 192: 51–BTEC.
|
[43] | Jeffries TW, Van VleetJR (2009) Pichia stipitis genomics, transcriptomics, and gene clusters. FEMS Yeast Res 9: 793–807.
|
[44] | Lee JW, Zhu JY, Scordia D, Jeffries TW (2011) Evaluation of ethanol production from corncob using Scheffersomyces (Pichia) stipitis CBS 6054 by volumetric scale-up. Appl Biochem Biotechnol 165: 814–822.
|
[45] | Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, et al. (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A 108: 13212–13217.
|
[46] | Jeppsson M, Bengtsson O, Franke K, Lee H, Hahn-Hagerdal B, et al. (2006) The expression of a Pichia stipitis xylose reductase mutant with higher K(M) for NADPH increases ethanol production from xylose in recombinant Saccharomyces cerevisiae. Biotechnol Bioeng 93: 665–673.
|
[47] | Fromanger R, Guillouet SE, Uribelarrea JL, Molina-Jouve C, Cameleyre X (2010) Effect of controlled oxygen limitation on Candida shehatae physiology for ethanol production from xylose and glucose. J Ind Microbiol Biotechnol 37: 437–445.
|
[48] | Zhang J, Yang M, Tian S, Zhang Y, Yang X (2010) Co-expression of xylose reductase gene from Candida shehatae and endogenous xylitol dehydrogenase gene in Saccharomyces cerevisiae and the effect of metabolizing xylose to ethanol. Prikl Biokhim Mikrobiol 46: 456–461.
|
[49] | Bajwa PK, Phaenark C, Grant N, Zhang X, Paice M, et al. (2011) Ethanol production from selected lignocellulosic hydrolysates by genome shuffled strains of Scheffersomyces stipitis. Bioresour Technol 102: 9965–9969.
|
[50] | Khattab SM, Watanabe S, Saimura M, Kodaki T (2011) A novel strictly NADPH-dependent Pichia stipitis xylose reductase constructed by site-directed mutagenesis. Biochem Biophys Res Commun 404: 634–637.
|
[51] | Hughes SR, Gibbons WR, Bang SS, Pinkelman R, Bischoff KM, et al. (2012) Random UV-C mutagenesis of Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars. J Ind Microbiol Biotechnol 39: 163–173.
|
[52] | Kreger-van Rij NJW (1970) Pichia Hansen. In: Lodder J, editor. pp. 455–554. Amsterdam: North-Holland.
|
[53] | Vaughan-Martini A (1984) Comparazione dei genomi del lievito Pichia stipitis e di alcune specie imperfette affini. Ann. Fac. Agrar. Univ. Perugia 38: 331–335.
|
[54] | Kurtzman CP, Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek 73: 331–371.
|
[55] | Kurtzman CP, Suzuki M (2010) Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces. Mycoscience 51: 2–14.
|
[56] | Suh SO, White MM, Nguyen NH, Blackwell M (2004) The status and characterization of Enteroramus dimorphus: a xylose-fermenting yeast attached to the gut of beetles. Mycologia 96: 756–760.
|
[57] | Passoth V, Hansen M, Klinner U, Emeis CC (1992) The electrophoretic banding pattern of the chromosomes of Pichia stipitis and Candida shehatae. Curr Genet 22: 429–431.
|
[58] | Kurtzman CP (1990) Candida shehatae genetic diversity and phylogenetic relationships with other xylose-fermenting yeasts. Antonie Van Leeuwenhoek 57: 215–222.
|
[59] | Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, the Barcoding Consortium (2012) The internal transcribed spacer as a universal DNA barcode marker for Fungi. Fungal Barcoding Consortium. Proc Natl Acad Sci U S A 109: 6241–6246.
|
[60] | Suh SO, McHugh JV, Blackwell M (2004) Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles. Int J Syst Evol Microbiol 54: 2409–2429.
|
[61] | White TJ, Bruns TD, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. pp. 315–322. San Diego: Academic Press.
|
[62] | Hibbett DS (1996) Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi. Mol Biol Evol 13: 903–917.
|
[63] | Matheny PB, Liu YJJ, Ammirati JF, Hall BD (2002) Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89: 688–698.
|
[64] | Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J (2004) Molecular phylogeny of Zygomycota based on EF-1 alpha and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol Phylogenet Evol 30: 438–449.
|
[65] | Sullivan DJ, Westerneng TJ, Haynes KA, Bennett DE, Coleman DC (1995) Candida dubliniensis sp. nov.: phenotypic and molecular characterization of a novel species associated with oral candidosis in HIV-infected individuals. Microbiology 141 (Pt 7): 1507–1521.
|
[66] | Fadda ME, Mossa V, Pisano MB, Deplano M, Cosentino S (2004) Occurrence and characterization of yeasts isolated from artisanal Fiore Sardo cheese. Int J Food Microbiol 95: 51–59.
|
[67] | Fadda ME, Viale S, Deplano M, Pisano MB, Cosentino S (2010) Characterization of yeast population and molecular fingerprinting of Candida zeylanoides isolated from goat's milk collected in Sardinia. Int J Food Microbiol 136: 376–380.
|
[68] | Fuentefria AM, Suh SO, Landell MF, Faganello J, Schrank A, et al. (2008) Trichosporon insectorum sp. nov., a new anamorphic basidiomycetous killer yeast. Mycol Res 112: 93–99.
|
[69] | Yarrow D (1998) Methods for the isolation, maintenance and identification of yeasts. In: Kurtzman CP, Fell JW, editors. pp. 77–100. Amsterdam: Elsevier.
|
[70] | Barnett JA, Payne RW, Yarrow D (2000) Yeasts: Characteristics and identification. Cambridge: Cambridge University Press. x+1139 p.
|
[71] | Maddison W, Maddison D (2005) Mesquite: A modular system for evolutionary analysis. Evolution 62: 1103–1118.
|
[72] | Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, et al. (2012) SATe-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol 61: 90–106.
|
[73] | Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.
|
[74] | Ohama T, Suzuki T, Mori M, Osawa S, Ueda T, et al. (1993) Non-universal decoding of the leucine codon CUG in several Candida species. Nucleic Acids Res 21: 4039–4045.
|
[75] | Muller T, Vingron M (2000) Modeling amino acid replacement. J Comput Biol 7: 761–776.
|
[76] | Milan EP, Kallas EG, Costa PR, da Matta DA, Lopes Colombo A (2001) Oral colonization by Candida spp. among AIDS household contacts. Mycoses 44: 273–277.
|
[77] | Knapp S, McNeill J, Turland NJ (2011) Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne: What does e-publication mean for you? Taxon 60: 1498–1501.
|
[78] | Chu BC, Lee H, et al. (2006) Investigation of the role of a conserved glycine motif in the Saccharomyces cerevisiae xylose reductase. Curr Microbiol 53: 118–123.
|
[79] | Zhang Q, Shirley NJ, Burton RA, Lahnstein J, Hrmova M (2010) The genetics, transcriptional profiles, and catalytic properties of UDP-alpha-D-xylose 4-epimerases from barley. Plant Physiol 153: 555–568.
|
[80] | Kurtzman CP, Robnett CJ (2007) Multigene phylogenetic analysis of the Trichomonascus, Wickerhamiella and Zygoascus yeast clades, and the proposal of Sugiyamaella gen. nov. and 14 new species combinations. FEMS Yeast Res 7: 141–151.
|
[81] | Houseknecht JL, Hart EL, Suh SO, Zhou JJ (2011) Yeasts in the Sugiyamaella clade associated with wood-ingesting beetles and the proposal of Candida bullrunensis sp. nov. Int J Syst Evol Microbiol 61: 1751–1756.
|
[82] | Zhang N, Suh SO, Blackwell M (2003) Microorganisms in the gut of beetles: evidence from molecular cloning. J Invertebr Pathol 84: 226–233.
|
[83] | Gaster PF (2006) Yeast and invertebrate associations. In: Rosa CA, Gabor P, editors. pp. 303–370. Berlin: Springer-Verlag.
|
[84] | Nardi JB, Bee CM, Miller LA, Nguyen NH, Suh SO, et al. (2006) Communities of microbes that inhabit the changing hindgut landscape of a subsocial beetle. Arthropod Struct Dev 35: 57–68.
|
[85] | Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798–804.
|
[86] | Cadez N, Raspor P, Smith MT (2006) Phylogenetic placement of Hanseniaspora-Kloeckera species using multigene sequence analysis with taxonomic implications: descriptions of Hanseniaspora pseudoguilliermondii sp. nov. and Hanseniaspora occidentalis var. citrica var. nov. Int J Syst Evol Microbiol 56: 1157–1165.
|
[87] | Liti G, Barton DB, Louis EJ (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839–850.
|
[88] | Lachance MA, Dobson J, Wijayanayaka DN, Smith AM (2010) The use of parsimony network analysis for the formal delineation of phylogenetic species of yeasts: Candida apicola, Candida azyma, and Candida parazyma sp. nov., cosmopolitan yeasts associated with floricolous insects. Antonie Van Leeuwenhoek 97: 155–170.
|
[89] | Robbertse B, Reeves JB, Schoch CL, Spatafora JW (2006) A phylogenomic analysis of the Ascomycota. Fungal Genet Biol 43: 715–725.
|
[90] | Schoch CL, Sung GH, Lopez-Giraldez F, Townsend JP, Miadlikowska J, et al. (2009) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol 58: 224–239.
|
[91] | Chang CF, Yao CH, Young SS, Limtong S, Kaewwichian R, et al. (2011) Candida gosingica sp. nov., an anamorphic ascomycetous yeast closely related to Scheffersomyces spartinae. Int J Syst Evol Microbiol 61: 690–694.
|
[92] | Ryabova OB, Chmil OM, Sibirny AA (2003) Xylose and cellobiose fermentation to ethanol by the thermotolerant methylotrophic yeast Hansenula polymorpha. FEMS Yeast Res 4: 157–164.
|
[93] | Han JH, Park JY, Yoo KS, Kang HW, Choi GW, et al. (2011) Effect of glucose on xylose utilization in Saccharomyces cerevisiae harboring the xylose reductase gene. Arch Microbiol 193: 335–340.
|