Skip to main content
SpringerLink
Log in

Synthetic Biology in the Candida (CTG) Clade

  • Chapter
  • First Online:
Synthetic Biology of Yeasts

  • 1278 Accesses

Abstract

The continuous bio-race to find an ideal microbial chassis opens the path toward the Candida CTG clade to enter the competition. Unexpectedly, this unique CUG-serine coding clade successfully mastered the production of various nutraceutical, commercial, and pharmaceutical valuable compounds. The following chapter aims to snapshot the Candida CTG clade’s bioengineering properties and their biotechnological applications in synthetic biology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbas CA, Sibirny AA (2011) Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 75(2):321–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Agirman B, Erten H (2020) Biocontrol ability and action mechanisms of Aureobasidium pullulans GE17 and Meyerozyma guilliermondii KL3 against Penicillium digitatum DSM2750 and Penicillium expansum DSM62841 causing postharvest diseases. Yeast 37(9–10):437–448

    Article  CAS  PubMed  Google Scholar 

  • Anastassiadis S, Wandrey C, Rehm HJ (2005) Continuous citric acid fermentation by Candida oleophila under nitrogen limitation at constant C/N ratio. World J Microbiol Biotechnol 21(5):695–705

    Article  CAS  Google Scholar 

  • Andreieva Y, Petrovska Y, Lyzak O, Liu W, Kang Y, Dmytruk K et al (2020) Role of the regulatory genes SEF1, VMA1 and SFU1 in riboflavin synthesis in the flavinogenic yeast Candida famata (Candida flareri). Yeast (chichester, England) 37(9–10):497–504

    Article  CAS  Google Scholar 

  • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S et al (2018) KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 36(7):566–569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Asadzadeh M, Dashti M, Ahmad S (2020) Whole genome and targeted-amplicon sequencing of fluconazole-susceptible and -resistant Candida parapsilosis isolates from Kuwait reveals a previously undescribed N1132D polymorphism in CDR1. Antimicrob Agents Chemother

    Google Scholar 

  • Austin S, Ziese M, Sternberg N (1981) A novel role for site-specific recombination in maintenance of bacterial replicons. Cell 25(3):729–736

    Article  CAS  PubMed  Google Scholar 

  • Awad A, El Khoury P, Wex B, Khalaf RA (2018) Proteomic analysis of a Candida albicans pga1 Null Strain. EuPA Open Proteom 18:1–6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babar MM, Afzaal H, Pothineni VR, Zaidi N-u-SS, Ali Z, Zahid MA et al (2018) Omics approaches in industrial biotechnology and bioprocess engineering ((Chap 14)). In: Barh D, Azevedo V (eds) Omics technologies and bio-engineering. Academic Press, pp 251–69

    Google Scholar 

  • Babbal, Adivitiya, Khasa YP (2017) Microbes as biocontrol Agents. In: Kumar V, Kumar M, Sharma S, Prasad R (eds) Probiotics and plant health. Springer, Singapore, pp 507–552

    Google Scholar 

  • Bahafid W, Tahri Joutey N, Sayel H, Boularab I, Ghachtouli N (2013) Bioaugmentation of chromium-polluted soil microcosms with Candida tropicalis diminishes phytoavailable chromium. J Appl Microbiol 115(3):727–734

    Google Scholar 

  • Bassler BL, Losick R (2006) Bacterially speaking. Cell 125(2):237–246

    Article  CAS  PubMed  Google Scholar 

  • Basso LR Jr, Bartiss A, Mao Y, Gast CE, Coelho PSR, Snyder M et al (2010) Transformation of Candida albicans with a synthetic hygromycin B resistance gene. Yeast (chichester, England) 27(12):1039–1048

    Article  CAS  Google Scholar 

  • Beckerman J, Chibana H, Turner J, Magee PT (2001) Single-copy IMH3 allele is sufficient to confer resistance to mycophenolic acid in Candida albicans and to mediate transformation of clinical Candida species. Infect Immun 69(1):108–114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berens C, Hillen W (2004) Gene regulation by tetracyclines. Genet Eng (NY) 26:255–277

    CAS  Google Scholar 

  • Bhatia S, Bhatia R, Choi Y-K, Kane E, Kim Y-G, Yanga Y-H (2018) Biotechnological potential of microbial consortia and future perspective. Crit Rev Biotechnol 38

    Google Scholar 

  • Bijlani S, Nahar AS, Ganesan K (2018) Improved Tet-On and Tet-Off systems for tetracycline-regulated expression of genes in Candida. Curr Genet 64(1):303–316

    Article  CAS  PubMed  Google Scholar 

  • Blazeck J, Alper H (2010) Systems metabolic engineering: genome-scale models and beyond. Biotechnol J 5(7):647–659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bratiichuk D, Kurylenko O, Vasylyshyn R, Zuo M, Kang Y, Dmytruk K et al (2020) Development of new dominant selectable markers for the nonconventional yeasts Ogataea polymorpha and Candida famata. Yeast 37(9–10):505–513

    Article  CAS  PubMed  Google Scholar 

  • Brenner K, You L, Arnold FH (2008) Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 26(9):483–489

    Article  CAS  PubMed  Google Scholar 

  • Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA et al (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459(7247):657–662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cabrera Z, Gutarra MLE, Guisan JM, Palomo JM (2010) Highly enantioselective biocatalysts by coating immobilized lipases with polyethyleneimine. Catal Commun 11(11):964–967

    Article  CAS  Google Scholar 

  • Campa D, Tavanti A, Gemignani F, Mogavero CS, Bellini I, Bottari F et al (2008) DNA microarray based on arrayed-primer extension technique for identification of pathogenic fungi responsible for invasive and superficial mycoses. J Clin Microbiol 46(3):909–915

    Article  CAS  PubMed  Google Scholar 

  • Cao M, Seetharam AS, Severin AJ, Shao Z (2017a) Rapid isolation of centromeres from Scheffersomyces stipitis. ACS Synth Biol 6(11):2028–2034

    Article  CAS  PubMed  Google Scholar 

  • Cao M, Gao M, Lopez-Garcia CL, Wu Y, Seetharam AS, Severin AJ et al (2017b) Centromeric DNA facilitates nonconventional yeast genetic engineering. ACS Synth Biol 6(8):1545–1553

    Article  CAS  PubMed  Google Scholar 

  • Castellan A, Bart JCJ, Cavallaro S (1991) Industrial production and use of adipic acid. Catal Today 9(3):237–254

    Article  CAS  Google Scholar 

  • Chandrasegaran S, Carroll D (2016) Origins of programmable nucleases for genome engineering. J Mol Biol 428(5 Pt B):963–89

    Google Scholar 

  • Chang W, Zhang M, Li Y, Lou H (2015) Flow cytometry-based method to detect persisters in Candida albicans. Antimicrob Agents Chemother 59(8):5044–5048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chattopadhyay A, Gupta A, Maiti MK (2020) Engineering an oleaginous yeast Candida tropicalis SY005 for enhanced lipid production. Appl Microbiol Biotechnol 104(19):8399–8411

    Article  CAS  PubMed  Google Scholar 

  • Chen YC, Eisner JD, Kattar MM, Rassoulian-Barrett SL, LaFe K, Yarfitz SL et al (2000) Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA genes. J Clin Microbiol 38(6):2302–2310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen H, Wang Z, Cai H, Zhou C (2016) Progress in the microbial production of S-adenosyl-L-methionine. World J Microbiol Biotechnol 32(9):153

    Article  CAS  PubMed  Google Scholar 

  • Cheng Z (2016) The spatial correlation and interaction between manufacturing agglomeration and environmental pollution. Ecol Ind 61:1024–1032

    Article  Google Scholar 

  • Christen S, Sauer U (2011) Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics. FEMS Yeast Res 11(3):263–272

    Article  CAS  PubMed  Google Scholar 

  • Clark DP, Pazdernik NJ, McGehee MR (2019) Analysis of gene expression (Chap 21). In: Clark DP, Pazdernik NJ, McGehee MR (eds) Molecular biology, 3rd ed. Academic Cell, pp 654–90

    Google Scholar 

  • Coimbra CD, Rufino RD, Luna JM, Sarubbo LA (2009) Studies of the cell surface properties of Candida species and relation to the production of biosurfactants for environmental applications. Curr Microbiol 58(3):245–251

    Article  CAS  PubMed  Google Scholar 

  • Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173(1):33–38

    Article  CAS  PubMed  Google Scholar 

  • Cormack BP, Bertram G, Egerton M, Gow NA, Falkow S, Brown AJ (1997) Yeast-enhanced green fluorescent protein (yEGFP): a reporter of gene expression in Candida albicans. Microbiology 143(2):303–311

    Article  CAS  PubMed  Google Scholar 

  • Cortez DV, Mussatto SI, Roberto IC (2016) Improvement on D-xylose to xylitol biotransformation by Candida guilliermondii using cells permeabilized with triton X-100 and selected process conditions. Appl Biochem Biotechnol 180(5):969–979

    Article  CAS  PubMed  Google Scholar 

  • Courdavault V, Millerioux Y, Clastre M, Simkin AJ, Marais E, Crèche J et al (2011) Fluorescent protein fusions in Candida guilliermondii. Fungal Genet Biol 48(11):1004–1011

    Article  CAS  PubMed  Google Scholar 

  • Dangi AK, Sharma B, Hill RT, Shukla P (2019) Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 39(1):79–98

    Article  CAS  PubMed  Google Scholar 

  • Dashtban M, Wen X, Bajwa PK, Ho CY, Lee H (2015) Deletion of hxk1 gene results in derepression of xylose utilization in Scheffersomyces stipitis. J Ind Microbiol Biotechnol 42(6):889–896

    Article  CAS  PubMed  Google Scholar 

  • Defosse TA, Courdavault V, Coste AT, Clastre M, de Bernonville TD, Godon C et al (2018a) A standardized toolkit for genetic engineering of CTG clade yeasts. J Microbiol Methods 144:152–156

    Article  CAS  PubMed  Google Scholar 

  • Defosse TA, Le Govic Y, Courdavault V, Clastre M, Vandeputte P, Chabasse D et al (2018b) Les levures du clade CTG (clade Candida): biologie, incidence en santé humaine et applications en biotechnologie. Med Mycol J 28(2):257–268

    Article  CAS  Google Scholar 

  • Defosse TA, Mélin C, Clastre M, Besseau S, Lanoue A, Glévarec G et al (2016) An additional Meyerozyma guilliermondii IMH3 gene confers mycophenolic acid resistance in fungal CTG clade species. FEMS Yeast Res 16(6)

    Google Scholar 

  • Dennison PM, Ramsdale M, Manson CL, Brown AJ (2005) Gene disruption in Candida albicans using a synthetic, codon-optimised Cre-loxP system. Fungal Genet Biol 42(9):737–748

    Article  CAS  PubMed  Google Scholar 

  • DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41(7):4336–4343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding C, Butler G (2007) Development of a gene knockout system in Candida parapsilosis reveals a conserved role for BCR1 in biofilm formation. Eukaryot Cell 6(8):1310–1319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dmytruk KV, Yatsyshyn VY, Sybirna NO, Fedorovych DV, Sibirny AA (2011) Metabolic engineering and classic selection of the yeast Candida famata (Candida flareri) for construction of strains with enhanced riboflavin production. Metab Eng 13(1):82–88

    Article  CAS  PubMed  Google Scholar 

  • Dmytruk K, Lyzak O, Yatsyshyn V, Kluz M, Sibirny V, Puchalski C et al (2014) Construction and fed-batch cultivation of Candida famata with enhanced riboflavin production. J Biotechnol 172:11–17

    Article  CAS  PubMed  Google Scholar 

  • Doyle TC, Nawotka KA, Purchio AF, Akin AR, Francis KP, Contag PR (2006a) Expression of firefly luciferase in Candida albicans and its use in the selection of stable transformants. Microb Pathog 40(2):69–81

    Article  CAS  PubMed  Google Scholar 

  • Doyle TC, Nawotka KA, Kawahara CB, Francis KP, Contag PR (2006b) Visualizing fungal infections in living mice using bioluminescent pathogenic Candida albicans strains transformed with the firefly luciferase gene. Microb Pathog 40(2):82–90

    Article  CAS  PubMed  Google Scholar 

  • Du C, Li Y, Zhao X, Pei X, Yuan W, Bai F et al (2019) The production of ethanol from lignocellulosic biomass by Kluyveromyces marxianus CICC 1727–5 and Spathaspora passalidarum ATCC MYA-4345. Appl Microbiol Biotechnol 103(6):2845–2855

    Article  CAS  PubMed  Google Scholar 

  • Dujon BA, Louis EJ (2017) Genome diversity and evolution in the budding yeasts (Saccharomycotina). Genetics 206(2):717–750

    Article  PubMed  PubMed Central  Google Scholar 

  • Enjalbert B, Rachini A, Vediyappan G, Pietrella D, Spaccapelo R, Vecchiarelli A et al (2009) A multifunctional, synthetic Gaussia princeps luciferase reporter for live imaging of Candida albicans infections. Infect Immun 77(11):4847–4858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Expression G, Sundaresan G, Gambhir SS (2002) Radionuclide imaging of reporter gene expression (Chap 29). In: Toga AW, Mazziotta JC (eds) Brain mapping: the methods, 2nd edn. Academic Press, San Diego, pp 799–818

    Chapter  Google Scholar 

  • Feng X, Page L, Rubens J, Chircus L, Colletti P, Pakrasi H et al (2010) Bridging the gap between fluxomics and industrial biotechnology. J Biomed Biotechnol 2010:460717

    Google Scholar 

  • Fitzpatrick DA, Logue ME, Stajich JE, Butler G (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 6(1):99

    Article  PubMed  PubMed Central  Google Scholar 

  • Foureau E, Courdavault V, Navarro Gallón SM, Besseau S, Simkin AJ, Crèche J et al (2013) Characterization of an autonomously replicating sequence in Candida guilliermondii. Microbiol Res 168(9):580–588

    Article  CAS  PubMed  Google Scholar 

  • Freimoser FM, Rueda-Mejia MP, Tilocca B, Migheli Q (2019) Biocontrol yeasts: mechanisms and applications. World J Microbiol Biotechnol 35(10):154

    Article  PubMed  PubMed Central  Google Scholar 

  • Gabriel F, Accoceberry I, Bessoule JJ, Salin B, Lucas-Guérin M, Manon S et al (2014) A Fox2-dependent fatty acid ß-oxidation pathway coexists both in peroxisomes and mitochondria of the ascomycete yeast Candida lusitaniae. PLoS One 9(12):e114531

    Google Scholar 

  • Gácser A, Trofa D, Schäfer W, Nosanchuk JD (2007) Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence. J Clin Invest 117(10):3049–3058

    Article  PubMed  PubMed Central  Google Scholar 

  • Gao M, Cao M, Suástegui M, Walker J, Rodriguez Quiroz N, Wu Y et al (2017) Innovating a nonconventional yeast platform for producing shikimate as the building block of high-value aromatics. ACS Synth Biol 6(1):29–38

    Article  CAS  PubMed  Google Scholar 

  • García-Béjar B, Arévalo-Villena M, Guisantes-Batan E, Rodríguez-Flores J, Briones A (2020) Study of the bioremediatory capacity of wild yeasts. Sci Rep 10(1):11265

    Article  PubMed  PubMed Central  Google Scholar 

  • Gerami-Nejad M, Berman J, Gale CA (2001) Cassettes for PCR-mediated construction of green, yellow, and cyan fluorescent protein fusions in Candida albicans. Yeast 18(9):859–864

    Article  CAS  PubMed  Google Scholar 

  • Gerami-Nejad M, Dulmage K, Berman J (2009) Additional cassettes for epitope and fluorescent fusion proteins in Candida albicans. Yeast 26(7):399–406

    Article  CAS  PubMed  Google Scholar 

  • Gordon ZB, Soltysiak MPM, Leichthammer C, Therrien JA, Meaney RS, Lauzon C et al (2019) Development of a transformation method for Metschnikowia borealis and other CUG-Serine Yeasts. Genes (Basel) 10(2)

    Google Scholar 

  • Grahl N, Demers EG, Crocker AW, Hogan DA (2017) Use of RNA-protein complexes for genome editing in non-albicans Candida species. mSphere 2(3)

    Google Scholar 

  • Gräslund S, Sagemark J, Berglund H, Dahlgren LG, Flores A, Hammarström M et al (2008) The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins. Protein Expr Purif 58(2):210–221

    Article  PubMed  Google Scholar 

  • Griffith F (1928) The significance of pneumococcal types. J Hyg 27(2):113–159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guerrero V, Guigón-López C, Berlanga D, Ojeda-Barrios D (2014) Complete control of Penicillium expansum on apple fruit using a combination of antagonistic yeast Candida oleophila. Chilean J Agric Res 74:427–431

    Article  Google Scholar 

  • Han T-l, Cannon RD, Villas-Bôas SG (2012) Metabolome analysis during the morphological transition of Candida albicans. Metabolomics 8(6):1204–1217

    Google Scholar 

  • Hara A, Arie M, Kanai T, Matsui T, Matsuda H, Furuhashi K et al (2001) Novel and convenient methods for Candida tropicalis gene disruption using a mutated hygromycin B resistance gene. Arch Microbiol 176(5):364–369

    Article  CAS  PubMed  Google Scholar 

  • Hasin Y, Seldin M, Lusis A (2017) Multi-omics approaches to disease. Genome Biol 18(1):83

    Article  PubMed  PubMed Central  Google Scholar 

  • Heidari R, Shaw DM, Elger BS (2017) CRISPR and the rebirth of synthetic biology. Sci Eng Ethics 23(2):351–363

    Article  PubMed  Google Scholar 

  • Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92(5):1792–1805

    Article  CAS  PubMed  Google Scholar 

  • Herrgård M, Panagiotou G (2012) Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”. Comput Struct Biotechnol J 3(4):e201210012

    Google Scholar 

  • Herrgård M, Fong S, Palsson B (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2:e72

    Google Scholar 

  • Hinchliffe E, Kenny E (1993) Yeast as a vehicle for the expression of heterologous genes (Chap 9). In: Rose AH, Stuart Harrison J (eds) The yeasts, 2nd edn. Academic Press, San Diego, pp 325–356

    Chapter  Google Scholar 

  • Hirata Y, Ryu M, Oda Y, Igarashi K, Nagatsuka A, Furuta T et al (2009) Novel characteristics of sophorolipids, yeast glycolipid biosurfactants, as biodegradable low-foaming surfactants. J Biosci Bioeng 108(2):142–146

    Article  CAS  PubMed  Google Scholar 

  • Holkers M, Vries AAFd, Gonçalves MAFV (2006) Modular and excisable molecular switch for the induction of gene expression by the yeast FLP recombinase. BioTech 41(6):711–713

    Google Scholar 

  • Horgan RP, Kenny LC (2011) ‘Omic’ technologies: genomics, transcriptomics, proteomics and metabolomics. Obstet Gynaecol 13(3):189–195

    Article  Google Scholar 

  • Huang C, Luo M-T, Chen X-F, Qi G-X, Xiong L, Lin X-Q et al (2017) Combined “de novo” and “ex novo” lipid fermentation in a mix-medium of corncob acid hydrolysate and soybean oil by Trichosporon dermatis. Biotechnol Biofuels 10(1):147

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang MY, Mitchell AP (2017) Marker recycling in Candida albicans through CRISPR-Cas9-induced marker excision. mSphere 2(2):e00050-17

    Google Scholar 

  • Ilmén M, Koivuranta K, Ruohonen L, Suominen P, Penttilä M (2007) Efficient production of lactic acid from Xylose by Pichia stipitis. Appl Environ Microbiol 73(1):117–123

    Article  PubMed  Google Scholar 

  • Ishchuk O, Dmytruk K, Rohulya O, Voronovsky A, Abbas C, Sibirny A (2008) Development of a promoter assay system for the flavinogenic yeast Candida famata based on the Kluyveromyces lactis β-galactosidase LAC4 reporter gene. Enzyme Microb Technol 42:208–215

    Article  CAS  Google Scholar 

  • Jenior ML, Moutinho TJ Jr, Dougherty BV, Papin JA (2020) Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput Biol 16(4):e1007099-e

    Google Scholar 

  • Jensen MK, Keasling JD (2015) Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res 15(1):1–10

    Article  CAS  PubMed  Google Scholar 

  • Jeon WY, Shim WY, Lee SH, Choi JH, Kim JH (2013) Effect of heterologous xylose transporter expression in Candida tropicalis on xylitol production rate. Bioprocess Biosyst Eng 36(6):809–817

    Article  CAS  PubMed  Google Scholar 

  • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 337(6096):816–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson EA (2013) Biotechnology of non-Saccharomyces yeasts-the basidiomycetes. Appl Microbiol Biotechnol 97(17):7563–7577

    Article  CAS  PubMed  Google Scholar 

  • Jones HD (2003) Genetic modification | transformation, general principles. In: Thomas B (ed) Encyclopedia of applied plant sciences. Elsevier, Oxford, pp 377–382

    Chapter  Google Scholar 

  • Ju JH, Oh BR, Heo SY, Lee YU, Shon JH, Kim CH et al (2020) Production of adipic acid by short- and long-chain fatty acid acyl-CoA oxidase engineered in yeast Candida tropicalis. Bioprocess Biosyst Eng 43(1):33–43

    Article  CAS  PubMed  Google Scholar 

  • Juers DH, Matthews BW, Huber RE (2012) LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci 21(12):1792–1807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karkowska-Kuleta J, Kulig K, Karnas E, Zuba-Surma E, Woznicka O, Pyza E et al (2020) Characteristics of extracellular vesicles released by the pathogenic yeast-like fungi Candida glabrata, Candida parapsilosis and Candida tropicalis. Cells 9(7):1722

    Article  CAS  PubMed Central  Google Scholar 

  • Kawaguchi Y, Honda H, Taniguchi-Morimura J, Iwasaki S (1989) The codon CUG is read as serine in an asporogenic yeast Candida cylindracea. Nature 341(6238):164–166

    Article  CAS  PubMed  Google Scholar 

  • Keppler-Ross S, Noffz C, Dean N (2008) A new purple fluorescent color marker for genetic studies in Saccharomyces cerevisiae and Candida albicans. Genetics 179(1):705–710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS et al (2005) Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics 6(2–3):63–70

    Article  CAS  PubMed  Google Scholar 

  • Kim KH, Lee H-Y, Lee CY (2015) Pretreatment of sugarcane molasses and citric acid production by Candida zeylanoides. Microbiol Biotechnol Lett 43(2):164–168

    Article  Google Scholar 

  • Köhler GA, White TC, Agabian N (1997) Overexpression of a cloned IMP dehydrogenase gene of Candida albicans confers resistance to the specific inhibitor mycophenolic acid. J Bacteriol 179(7):2331–2338

    Article  PubMed  PubMed Central  Google Scholar 

  • Kosa P, Gavenciakova B, Nosek J (2007) Development of a set of plasmid vectors for genetic manipulations of the pathogenic yeast Candida parapsilosis. Gene 396(2):338–345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kouzuma A, Kato S, Watanabe K (2015) Microbial interspecies interactions: recent findings in syntrophic consortia. Front Microbiol 6(477)

    Google Scholar 

  • Križanović S, Butorac A, Mrvčić J, Krpan M, Cindrić M, Bačun-Družina V et al (2015) Characterization of a S-adenosyl-l-methionine (SAM)-accumulating strain of Scheffersomyces stipitis. Int Microbiol 18(2):117–125

    PubMed  Google Scholar 

  • Lam CMC, Godinho M, dos Santos VAPM (2010) An introduction to synthetic biology. In: Schmidt M, Kelle A, Ganguli-Mitra A, Vriend H (eds) Synthetic biology: the technoscience and its societal consequences. Springer, Netherlands, Dordrecht, pp 23–48

    Google Scholar 

  • Laplaza JM, Torres BR, Jin Y-S, Jeffries TW (2006) Sh ble and Cre adapted for functional genomics and metabolic engineering of Pichia stipitis. Enzyme Microb Technol 38(6):741–747

    Article  CAS  Google Scholar 

  • Larbi NB, Jefferies C (2009) 2D-DIGE: comparative proteomics of cellular signalling pathways. Methods in Molecular Biology (clifton, NJ) 517:105–132

    Article  Google Scholar 

  • Larsson DGJ (2014) Pollution from drug manufacturing: review and perspectives. Philos Trans R Soc Lond B Biol Sci 369(1656):20130571

    Article  PubMed  PubMed Central  Google Scholar 

  • Ledesma-Amaro R, Santos MA, Jiménez A, Revuelta JL (2013) Microbial production of vitamins (Chap 21). In: McNeil B, Archer D, Giavasis I, Harvey L (eds) Microbial production of food ingredients, enzymes and nutraceuticals. Woodhead Publishing, pp 571–594

    Google Scholar 

  • Leonard E, Nielsen D, Solomon K, Prather KJ (2008) Engineering microbes with synthetic biology frameworks. Trends Biotechnol 26(12):674–681

    Article  CAS  PubMed  Google Scholar 

  • Leuker CE, Hahn AM, Ernst JF (1992) beta-Galactosidase of Kluyveromyces lactis (Lac4p) as reporter of gene expression in Candida albicans and C. tropicalis. Mol Gen Genet 235(2–3):235–241

    Google Scholar 

  • Li Y, Chen Y, Tian X, Chu J (2020) Advances in sophorolipid-producing strain performance improvement and fermentation optimization technology. Appl Microbiol Biotechnol 104:10325–10337

    Article  CAS  PubMed  Google Scholar 

  • Lin C-H, Choi A, Bennett RJ (2011) Defining pheromone-receptor signaling in Candida albicans and related asexual Candida species. Mol Biol Cell 22(24):4918–4930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu S, Hu W, Wang Z, Chen T (2020) Production of riboflavin and related cofactors by biotechnological processes. Microb Cell Fact 19(1):31

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu GL, Fu GY, Chi Z, Chi ZM (2014) Enhanced expression of the codon-optimized exo-inulinase gene from the yeast Meyerozyma guilliermondii in Saccharomyces sp. W0 and bioethanol production from inulin. Appl Microbiol Biotechnol 98(21):9129–9138

    Google Scholar 

  • Löbs AK, Schwartz C, Wheeldon I (2017) Genome and metabolic engineering in non-conventional yeasts: current advances and applications. Synth Syst Biotechnol 2(3):198–207

    Article  PubMed  PubMed Central  Google Scholar 

  • Loeffler J, Hebart H, Magga S, Schmidt D, Klingspor L, Tollemar J et al (2000) Identification of rare Candida species and other yeasts by polymerase chain reaction and slot blot hybridization. Diagn Microbiol Infect Dis 38(4):207–212

    Article  CAS  PubMed  Google Scholar 

  • Lombardi L, Turner SA, Zhao F, Butler G (2017) Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9. Sci Rep 7(1):8051

    Article  PubMed  PubMed Central  Google Scholar 

  • Lombardi L, Oliveira-Pacheco J, Butler G (2019) Plasmid-based CRISPR-Cas9 gene editing in multiple Candida species. mSphere 4(2)

    Google Scholar 

  • Maguire SL, ÓhÉigeartaigh SS, Byrne KP, Schröder MS, O’Gaora P, Wolfe KH et al (2013) Comparative genome analysis and gene finding in Candida Species using CGOB. Mol Biol Evol 30(6):1281–1291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maier T, Güell M, Serrano L (2009) Correlation of mRNA and protein in complex biological samples. FEBS Lett 583(24):3966–3973

    Article  CAS  PubMed  Google Scholar 

  • Maldonado I, Cataldi S, Garbasz C, Relloso S, Striebeck P, Guelfand L et al (2018) Identification of Candida yeasts: conventional methods and MALDI-TOF MS. Rev Iberoam Micol 35(3):151–154

    Article  PubMed  Google Scholar 

  • Mancera E, Frazer C, Porman AM, Ruiz-Castro S, Johnson AD, Bennett RJ (2019) Genetic modification of closely related Candida species. Front Microbiol 10(357)

    Google Scholar 

  • Marian M, Shimizu M (2019) Improving performance of microbial biocontrol agents against plant diseases. J Gen Plant Pathol 85(5):329–336

    Article  Google Scholar 

  • Marton T, Maufrais C, d'Enfert C, Legrand M (2020) Use of CRISPR-Cas9 to target homologous recombination limits transformation-induced genomic changes in Candida albicans. mSphere 5(5)

    Google Scholar 

  • Masuda Y, Park SM, Ohkuma M, Ohta A, Takagi M (1994) Expression of an endogenous and a heterologous gene in Candida maltosa by using a promoter of a newly-isolated phosphoglycerate kinase (PGK) gene. Curr Genet 25(5):412–417

    Article  CAS  PubMed  Google Scholar 

  • McCarty NS, Ledesma-Amaro R (2019) Synthetic biology tools to Engineer microbial communities for biotechnology. Trends Biotechnol 37(2):181–197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McLellan MA, Rosenthal NA, Pinto AR (2017) Cre-loxP-mediated recombination: general principles and experimental considerations. Curr Protoc Mouse Biol 7(1):1–12

    Article  PubMed  Google Scholar 

  • Messing R, Brodeur J (2018) Current challenges to the implementation of classical biological control. Biocontrol 63(1):1–9

    Article  CAS  Google Scholar 

  • Michel S, Ushinsky S, Klebl B, Leberer E, Thomas D, Whiteway M et al (2002) Generation of conditional lethal Candida albicans mutants by inducible deletion of essential genes. Mol Microbiol 46(1):269–280

    Article  CAS  PubMed  Google Scholar 

  • Millerioux Y, Clastre M, Simkin AJ, Courdavault V, Marais E, Sibirny AA et al (2011) Drug-resistant cassettes for the efficient transformation of Candida guilliermondii wild-type strains. FEMS Yeast Res 11(6):457–463

    Article  CAS  PubMed  Google Scholar 

  • Min K, Ichikawa Y, Woolford CA, Mitchell AP (2016) Candida albicans gene deletion with a transient CRISPR-Cas9 system. mSphere 1(3)

    Google Scholar 

  • Min et al (2016) Candida albicans gene deletion with a transient CRISPR-Cas9 system. https://doi.org/10.1128/mSphere.00130-16

  • Mishra P, Park GY, Lakshmanan M, Lee HS, Lee H, Chang MW et al (2016) Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeast Candida tropicalis for dicarboxylic acid production. Biotechnol Bioeng 113(9):1993–2004

    Article  CAS  PubMed  Google Scholar 

  • Möckli N, Auerbach D (2004) Quantitative β-galactosidase assay suitable for high-throughput applications in the yeast two-hybrid system. Biotechniques 36(5):872–876

    Article  PubMed  Google Scholar 

  • Moreno-Ruiz E, Ortu G, de Groot PWJ, Cottier F, Loussert C, Prévost M-C et al (2009) The GPI-modified proteins Pga59 and Pga62 of Candida albicans are required for cell wall integrity. Microbiology 155(6):2004–2020

    Article  CAS  PubMed  Google Scholar 

  • Morschhäuser J, Michel S, Hacker J (1998) Expression of a chromosomally integrated, single-copy GFP gene in Candida albicans, and its use as a reporter of gene regulation. Mol Gen Genet MGG 257(4):412–420

    Article  PubMed  Google Scholar 

  • Morschhäuser J, Michel S, Staib P (1999) Sequential gene disruption in Candida albicans by FLP-mediated site-specific recombination. Mol Microbiol 32(3):547–556

    Article  PubMed  Google Scholar 

  • Mühlhausen S, Kollmar M (2014) Molecular phylogeny of sequenced Saccharomycetes reveals polyphyly of the alternative yeast codon usage. Genome Biol Evol 6(12):3222–3237

    Article  PubMed  PubMed Central  Google Scholar 

  • Nakayama H, Mio T, Nagahashi S, Kokado M, Arisawa M, Aoki Y (2000) Tetracycline-regulatable system to tightly control gene expression in the pathogenic fungus Candida albicans. Infect Immun 68(12):6712–6719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Narad P, Kirthanashri SV (2018) Introduction to omics. In: Arivaradarajan P, Misra G (eds) Omics approaches, technologies and applications: integrative approaches for understanding OMICS data. Springer Singapore, Singapore, pp 1–10

    Google Scholar 

  • Nguyen LN, Trofa D, Nosanchuk JD (2009) Fatty acid synthase impacts the pathobiology of Candida parapsilosis in vitro and during mammalian infection. PLoS One 4(12):e8421

    Google Scholar 

  • Nguyen N, Quail MMF, Hernday AD (2017) An efficient, rapid, and recyclable system for CRISPR-mediated genome editing in Candida albicans. mSphere 2(2)

    Google Scholar 

  • Norton EL, Sherwood RK, Bennett RJ (2017) Development of a CRISPR-Cas9 system for efficient genome editing of Candida lusitaniae. mSphere 2(3)

    Google Scholar 

  • Nosek J, Holesova Z, Kosa P, Gacser A, Tomaska L (2009) Biology and genetics of the pathogenic yeast Candida parapsilosis. Curr Genet 55(5):497–509

    Article  CAS  PubMed  Google Scholar 

  • Nunes-Düby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26(2):391–406

    Article  PubMed  PubMed Central  Google Scholar 

  • Obando Montoya EJ, Mélin C, Blanc N, Lanoue A, Foureau E, Boudesocque L et al (2014) Disrupting the methionine biosynthetic pathway in Candida guilliermondii: characterization of the MET2 gene as counter-selectable marker. Yeast 31(7):243–251

    Article  CAS  PubMed  Google Scholar 

  • Olivares-Hernández R, Usaite R, Nielsen J (2010) Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level. Biotechnol Bioeng 107(5):865–875

    Article  PubMed  Google Scholar 

  • Olivares-Hernández R, Bordel S, Nielsen J (2011) Codon usage variability determines the correlation between proteome and transcriptome fold changes. BMC Syst Biol 5(1):33

    Article  PubMed  PubMed Central  Google Scholar 

  • Orr-Weaver TL, Szostak JW, Rothstein RJ (1981) Yeast transformation: a model system for the study of recombination. Proc Natl Acad Sci U S A 78(10):6354–6358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orth JD, Thiele I, Palsson BØ (2010) What is flux balance analysis? Nat Biotechnol 28(3):245–248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Papon N, Courdavault V, Clastre M, Simkin AJ, Crèche J, Giglioli-Guivarc’h N (2012) Deus ex Candida genetics: overcoming the hurdles for the development of a molecular toolbox in the CTG clade. Microbiology 158(Pt 3):585–600

    Article  CAS  PubMed  Google Scholar 

  • Papon N, Savini V, Lanoue A, Simkin AJ, Crèche J, Giglioli-Guivarc’h N et al (2013) Candida guilliermondii: biotechnological applications, perspectives for biological control, emerging clinical importance and recent advances in genetics. Curr Genet 59(3):73–90

    Article  CAS  PubMed  Google Scholar 

  • Papon N, Courdavault V, Clastre M (2014) Biotechnological potential of the fungal CTG clade species in the synthetic biology era. Trends Biotechnol 32(4):167–168

    Article  CAS  PubMed  Google Scholar 

  • Park Y-N, Morschhäuser J (2005) Tetracycline-inducible gene expression and gene deletion in Candida albicans. Eukaryot Cell 4(8):1328–1342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Passoth V, Cohn M, Schäfer B, Hahn-Hägerdal B, Klinner U (2003) Analysis of the hypoxia-induced ADH2 promoter of the respiratory yeast Pichia stipitis reveals a new mechanism for sensing of oxygen limitation in yeast. Yeast 20(1):39–51

    Article  CAS  PubMed  Google Scholar 

  • Patra P, Das M, Kundu P, Ghosh A (2021) Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 47:107695

    Google Scholar 

  • Pereira SC, Maehara L, Machado CMM, Farinas CS (2015) 2G ethanol from the whole sugarcane lignocellulosic biomass. Biotechnol Biofuels 8(1):44

    Article  PubMed  PubMed Central  Google Scholar 

  • Pharkya P, Maranas C (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8:1–13

    Article  CAS  PubMed  Google Scholar 

  • Pharkya P, Burgard A, Maranas C (2004) OptStrain: A computational framework for redesign of microbial production systems. Genome Res 14:2367–2376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pickford R (2019) Mass spectrometry-based metabolomic analysis. In: Ranganathan S, Gribskov M, Nakai K, Schönbach C (eds) Encyclopedia of bioinformatics and computational biology. Academic Press, Oxford, pp 410–425

    Chapter  Google Scholar 

  • Polen T, Spelberg M, Bott M (2013) Toward biotechnological production of adipic acid and precursors from biorenewables. J Biotechnol 167(2):75–84

    Article  CAS  PubMed  Google Scholar 

  • Price ND, Reed JL, Palsson B (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2(11):886–897

    Article  CAS  PubMed  Google Scholar 

  • Prista C, Michán C, Miranda IM, Ramos J (2016) The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts. Yeast 33(10):523–533

    Article  CAS  PubMed  Google Scholar 

  • Raghavachari N (2011) Overview of omics pp 1–20

    Google Scholar 

  • Ramírez-Ramírez R, Calvo-Méndez C, Avila-Rodriguez M, Lappe-Oliveras P, Ulloa M, Vázques-Juárez R et al (2004) Cr(VI) reduction in chromate-resistant strain of Candida maltosa isolated from the leather industry. Antonie Van Leeuwenhoek 85:63–68

    Article  PubMed  Google Scholar 

  • Ratcliffe RG, Shachar-Hill Y (2005) Revealing metabolic phenotypes in plants: inputs from NMR analysis. Biol Rev Camb Philos Soc 80(1):27–43

    Article  CAS  PubMed  Google Scholar 

  • Reijnst P, Walther A, Wendland J (2011) Dual-colour fluorescence microscopy using yEmCherry-/GFP-tagging of eisosome components Pil1 and Lsp1 in Candida albicans. Yeast 28(4):331–338

    Article  CAS  PubMed  Google Scholar 

  • Ren J, Lee J, Na D (2020) Recent advances in genetic engineering tools based on synthetic biology. Microbiology 58(1):1–10

    CAS  Google Scholar 

  • Reuss O, Vik A, Kolter R, Morschhäuser J (2004) The SAT1 flipper, an optimized tool for gene disruption in Candida albicans. Gene 341:119–127

    Article  CAS  PubMed  Google Scholar 

  • Revuelta JL, Buey RM, Ledesma-Amaro R, Vandamme EJ (2016) Microbial biotechnology for the synthesis of (pro)vitamins, biopigments and antioxidants: challenges and opportunities. Microb Biotechnol 9(5):564–567

    Article  PubMed  PubMed Central  Google Scholar 

  • Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M et al (2016) Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A 113(35):9882–9887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roa Engel CA, Straathof AJJ, Zijlmans TW, van Gulik WM, van der Wielen LAM (2008) Fumaric acid production by fermentation. Appl Microbiol Biotechnol 78(3):379–389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roda A, Pasini P, Mirasoli M, Michelini E, Guardigli M (2004) Biotechnological applications of bioluminescence and chemiluminescence. Trends Biotechnol 22(6):295–303

    Article  CAS  PubMed  Google Scholar 

  • Rodrussamee N, Sattayawat P, Yamada M (2018) Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2. BMC Microbiol 18(1):73

    Article  PubMed  PubMed Central  Google Scholar 

  • Roemer T, Jiang B, Davison J, Ketela T, Veillette K, Breton A et al (2003) Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol 50(1):167–181

    Article  CAS  PubMed  Google Scholar 

  • Røkke G, Korvald E, Pahr J, Øyås O, Lale R (2014) BioBrick assembly standards and techniques and associated software tools. In: Valla S, Lale R (eds) DNA cloning and assembly methods. Humana Press, Totowa, NJ, pp 1–24

    Google Scholar 

  • Roldão A, Kim I-K, Nielsen J (2012) Bridging omics technologies with synthetic biology in yeast industrial biotechnology. In: Wittmann C, Lee SY (eds) Systems metabolic engineering. Springer, Netherlands, Dordrecht, pp 271–327

    Chapter  Google Scholar 

  • Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA (2020) Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 47(1):109–132

    Article  CAS  PubMed  Google Scholar 

  • Samaranayake DP, Hanes SD (2011) Milestones in Candida albicans gene manipulation. Fungal Genet Biol: FG & B 48(9):858–865

    Article  CAS  Google Scholar 

  • Sampaio P, Gusmão L, Correia A, Alves C, Rodrigues AG, Pina-Vaz C et al (2005) New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes. J Clin Microbiol 43(8):3869–3876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sánchez-Martínez C, Pérez-Martín J (2002) Site-specific targeting of exogenous DNA into the genome of Candida albicans using the FLP recombinase. Mol Genet Genomics 268(3):418–424

    Article  PubMed  Google Scholar 

  • Santos MAS, Moura G, Massey SE, Tuite MF (2004) Driving change: the evolution of alternative genetic codes. Trends Genet: TIG 20(2):95–102

    Article  CAS  PubMed  Google Scholar 

  • Santos MA, Gomes AC, Santos MC, Carreto LC, Moura GR (2011) The genetic code of the fungal CTG clade. C R Biol 334(8–9):607–611

    Article  CAS  PubMed  Google Scholar 

  • Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM et al (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6(9):1290–1307

    Google Scholar 

  • Schindler D (2020) Genetic engineering and synthetic genomics in yeast to understand life and boost biotechnology. Bioengineering 7(4)

    Google Scholar 

  • Schulze S, Schleicher J, Guthke R, Linde J (2016) How to predict molecular interactions between species? Front Microbiol 7:442

    Article  PubMed  PubMed Central  Google Scholar 

  • Segal E, Yehuda H, Droby S, Wisniewski M, Goldway M (2002) Cloning and analysis of CoEXG1, a secreted 1,3-β-glucanase of the yeast biocontrol agent Candida oleophila. Yeast 19(13):1171–1182

    Article  CAS  PubMed  Google Scholar 

  • Shahana S, Childers DS, Ballou ER, Bohovych I, Odds FC, Gow NA et al (2014) New clox systems for rapid and efficient gene disruption in Candida albicans. PLoS One 9(6):e100390

    Google Scholar 

  • Shen J, Guo W, Köhler JR (2005) CaNAT1, a heterologous dominant selectable marker for transformation of Candida albicans and other pathogenic Candida species. Infect Immun 73(2):1239–1242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen X-X, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A (2016) Reconstructing the backbone of the saccharomycotina yeast phylogeny using genome-scale data. G3 Genes Genomes Genet 6(12):3927–3939

    Google Scholar 

  • Shi J, Zhang M, Zhang L, Wang P, Jiang L, Deng H (2014) Xylose-fermenting Pichia stipitis by genome shuffling for improved ethanol production. Microb Biotechnol 7(2):90–99

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shin M, Kim JW, Ye S, Kim S, Jeong D, Lee DY et al (2019) Comparative global metabolite profiling of xylose-fermenting Saccharomyces cerevisiae SR8 and Scheffersomyces stipitis. Appl Microbiol Biotechnol 103(13):5435–5446

    Article  CAS  PubMed  Google Scholar 

  • Singh Dhillon G, Kaur Brar S, Verma M, Tyagi RD (2011) Recent advances in citric acid bio-production and recovery. Food Bioprocess Technol 4(4):505–529

    Article  Google Scholar 

  • Smale ST (2010) Beta-galactosidase assay. Cold Spring Harb Protoc 2010(5):pdb.prot5423

    Google Scholar 

  • Spasskaya DS, Kotlov MI, Lekanov DS, Tutyaeva VV, Snezhkina AV, Kudryavtseva AV et al (2021) CRISPR/Cas9-mediated genome engineering reveals the contribution of the 26S proteasome to the extremophilic nature of the yeast Debaryomyces hansenii. ACS Synthetic Biol

    Google Scholar 

  • Sprengel R, Hasan MT (2007) Tetracycline-controlled genetic switches. Handb Exp Pharmacol 178:49–72

    Article  CAS  Google Scholar 

  • Sreenath HK, Jeffries TW (1999) 2-Deoxyglucose as a selective agent for derepressed mutants of Pichia stipitis. Appl Biochem Biotechnol 77(1):211–222

    Article  Google Scholar 

  • Srikantha T, Klapach A, Lorenz WW, Tsai LK, Laughlin LA, Gorman JA et al (1996) The sea pansy Renilla reniformis luciferase serves as a sensitive bioluminescent reporter for differential gene expression in Candida albicans. J Bacteriol 178(1):121–129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stagljar I (2016) The power of OMICs. Biochem Biophys Res Commun 479(4):607–609

    Article  CAS  PubMed  Google Scholar 

  • Staib P, Kretschmar M, Nichterlein T, Köhler G, Michel S, Hof H et al (1999) Host-induced, stage-specific virulence gene activation in Candida albicans during infection. Mol Microbiol 32(3):533–546

    Article  CAS  PubMed  Google Scholar 

  • Staib P, Kretschmar M, Nichterlein T, Hof H, Morschhäuser J (2000a) Differential activation of a Candida albicans virulence gene family during infection. PNAS 97(11):6102–6107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Staib P, Michel S, Köhler G, Morschhäuser J (2000b) A molecular genetic system for the pathogenic yeast Candida dubliniensis. Gene 242(1–2):393–398

    Article  CAS  PubMed  Google Scholar 

  • Stenuit B, Agathos SN (2015) Deciphering microbial community robustness through synthetic ecology and molecular systems synecology. Curr Opin Biotechnol 33:305–317

    Article  CAS  PubMed  Google Scholar 

  • Sternberg N, Hamilton D (1981) Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J Mol Biol 150(4):467–486

    Google Scholar 

  • Stoneman HR, Wrobel RL, Place M, Graham M, Krause DJ, De Chiara M et al (2020) CRISpy-pop: a web tool for designing CRISPR/Cas9-driven genetic modifications in diverse populations. G3 Genes Genomes Genet

    Google Scholar 

  • Sun C, Huang Y, Lian S, Saleem M, Li B, Wang C (2021) Improving the biocontrol efficacy of Meyerozyma guilliermondii Y-1 with melatonin against postharvest gray mold in apple fruit. Postharvest Biol Technol 171:111351

    Google Scholar 

  • Tang S-J, Sun K-H, Sun G-H, Chang T-Y, Wu W-L, Lee G-C (2003) A transformation system for the nonuniversal CUGSer codon usage species Candida rugosa. J Microbiol Methods 52(2):231–238

    Article  CAS  PubMed  Google Scholar 

  • Tanner FW Jr, Vojnovich C, Van Lanen JM (1945) Riboflavin production by Candida species. Science 101(2616):180–1

    Google Scholar 

  • Treu R, Falandysz J (2017) Mycoremediation of hydrocarbons with basidiomycetes—a review. J Environ Sci Health B 52(3):148–155

    Article  CAS  PubMed  Google Scholar 

  • Tsoi R, Wu F, Zhang C, Bewick S, Karig D, You L (2018) Metabolic division of labor in microbial systems. PNAS 115(10):2526–2531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsui CKM, Daniel H-M, Robert V, Meyer W (2008) Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. FEMS Yeast Res 8(4):651–659

    Article  CAS  PubMed  Google Scholar 

  • Turner SA, Butler G (2014) The Candida pathogenic species complex. Cold Spring Harb Perspect Med 4(9):a019778

    Google Scholar 

  • Uhl MA, Johnson AD (2001) Development of Streptococcus thermophilus lacZ as a reporter gene for Candida albicans. Microbiology 147(Pt 5):1189–1195

    Article  CAS  PubMed  Google Scholar 

  • Unrean P, Jeennor S, Laoteng K (2016) Systematic development of biomass overproducing Scheffersomyces stipitis for high-cell-density fermentations. Synth Syst Biotechnol 1(1):47–55

    Article  PubMed  PubMed Central  Google Scholar 

  • Ur-Rehman S, Mushtaq Z, Zahoor T, Jamil A, Murtaza MA (2015) Xylitol: a review on bioproduction, application, health benefits, and related safety issues. Crit Rev Food Sci Nutr 55(11):1514–1528

    Article  CAS  PubMed  Google Scholar 

  • Varga E, Maraz A (2002) Yeast cells as sources of essential microelements and vitamins B1 and B2. Acta Alimentaria 31:393–405

    Google Scholar 

  • Van Vleet JH, Jeffries TW (2009) Yeast metabolic engineering for hemicellulosic ethanol production. Curr Opin Biotechnol 20(3):300–306

    Article  PubMed  Google Scholar 

  • Veras HCT, Campos CG, Nascimento IF, Abdelnur PV, Almeida JRM, Parachin NS (2019) Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts. BMC Biotechnol 19(1):58

    Article  PubMed  PubMed Central  Google Scholar 

  • Vyas VK, Barrasa MI, Fink GR (2015) A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci Adv 1(3):e1500248

    Google Scholar 

  • Wang X, Li G, Deng Y, Yu X, Chen F (2006) A site-directed integration system for the nonuniversal CUG(Ser) codon usage species Pichia farinosa by electroporation. Arch Microbiol 184(6):419–424

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Chu J, Zhuang Y, Wang Y, Xia J, Zhang S (2009) Industrial bioprocess control and optimization in the context of systems biotechnology. Biotechnol Adv 27(6):989–995

    Article  CAS  PubMed  Google Scholar 

  • Wang H, La Russa M, Qi LS (2016a) CRISPR/Cas9 in genome editing and beyond. Annu Rev Biochem 85:227–264

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Cheng G, Joshua C, He Z, Sun X, Li R et al (2016b) Furfural tolerance and detoxification mechanism in Candida tropicalis. Biotechnol Biofuels 9:250

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang J, Peng J, Fan H, Xiu X, Xue L, Wang L et al (2018) Development of mazF-based markerless genome editing system and metabolic pathway engineering in Candida tropicalis for producing long-chain dicarboxylic acids. J Ind Microbiol Biotechnol 45(11):971–981

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Roelants SL, To MH, Patria RD, Kaur G, Lau NS et al (2019) Starmerella bombicola: recent advances on sophorolipid production and prospects of waste stream utilization. J Chem Technol Biotechnol 94(4):999–1007

    Article  CAS  Google Scholar 

  • Wang J, Liu Y, Zhao G, Gao J, Liu J, Wu X et al (2020) Integrated proteomic and metabolomic analysis to study the effects of spaceflight on Candida albicans. BMC Genomics 21(1):57

    Article  PubMed  PubMed Central  Google Scholar 

  • Wei L, Liu J, Qi H, Wen J (2015) Engineering Scheffersomyces stipitis for fumaric acid production from xylose. Biores Technol 187:246–254

    Article  CAS  Google Scholar 

  • Werner N, Dreyer M, Wagner W, Papon N, Rupp S, Zibek S (2017) Candida guilliermondii as a potential biocatalyst for the production of long-chain α,ω-dicarboxylic acids. Biotechnol Lett 39

    Google Scholar 

  • Wirsching S, Moran GP, Sullivan DJ, Coleman DC, Morschhäuser J (2001) MDR1-mediated drug resistance in Candida dubliniensis. Antimicrob Agents Chemother 45(12):3416–3421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM et al (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. PNAS 108(32):13212–13217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiang Z, Chen X, Zhang L, Shen W, Fan Y, Lu M (2014) Development of a genetic transformation system for Candida tropicalis based on a reusable selection marker of URA3 gene. Hereditas (beijing) 36:1053–1061

    CAS  Google Scholar 

  • Yan W, Qian X, Zhang W, Zhou J, Weiliang D, Xu B et al (2020) Enhanced 2-phenylethanol production by newly isolated Meyerozyma sp. strain YLG18 and characterization of its synthetic pathways 140:109629

    Google Scholar 

  • Yan W, Gao H, Qian X, Jiang Y, Zhou J, Dong W et al (2021) Biotechnological applications of the non-conventional yeast Meyerozyma guilliermondii. Biotechnol Adv 46:107674

    Google Scholar 

  • Yan et al (2021) Biotechnological applications of the non-conventional yeast Meyerozyma guilliermondii. https://doi.org/10.1016/j.biotechadv.2020.107674

  • Yehuda H, Droby S, Wisniewski M, Goldway M (2002) A transformation system for the biocontrol yeast, Candida oleophila, based on hygromycin B resistance. Curr Genet 40:282–287

    Article  Google Scholar 

  • Yoon G-S, Tae-Sik L, Chul K, Jin-Ho S, Yeon-Woo R (1996) Characterization of alcohol fermentation and segregation of protoplast fusant of Saccharomyces cerevisiae and Pichia stipitis. J Microbiol Biotechnol 6(4):286–291

    CAS  Google Scholar 

  • Younes S, Bracharz F, Awad D, Qoura F, Mehlmer N, Brueck T (2020) Microbial lipid production by oleaginous yeasts grown on Scenedesmus obtusiusculus microalgae biomass hydrolysate. Bioprocess Biosyst Eng 43(9):1629–1638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu KO, Jung J, Kim SW, Park CH, Han SO (2012) Synthesis of FAEEs from glycerol in engineered Saccharomyces cerevisiae using endogenously produced ethanol by heterologous expression of an unspecific bacterial acyltransferase. Biotechnol Bioeng 109(1):110–115

    Article  CAS  PubMed  Google Scholar 

  • Zhang C, Konopka JB (2010) A photostable green fluorescent protein variant for analysis of protein localization in Candida albicans. Eukaryot Cell 9(1):224–226

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Jia D, Sun W, Yang X, Zhang C, Zhao F et al (2018) Semicontinuous sophorolipid fermentation using a novel bioreactor with dual ventilation pipes and dual sieve-plates coupled with a novel separation system. Microb Biotechnol 11(3):455–464

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Li B, Zhang Z, Chen Y, Tian S (2020) Antagonistic yeasts: a promising alternative to chemical fungicides for controlling postharvest decay of fruit. J Fungi 6(3):158

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon

    Dalal Kasir, Monzer Hamze & Marwan Osman

  2. Université de Tours, BBV EA 2106, 31 avenue Monge, 37200, Tours, France

    Sébastien Besseau, Marc Clastre, Audrey Oudin & Vincent Courdavault

  3. Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA

    Marwan Osman

  4. Université d’Angers, GEIHP, E3142, SFR 4208 ICAT, Angers, France

    Nicolas Papon

Authors
  1. Dalal Kasir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sébastien Besseau
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marc Clastre
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Audrey Oudin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Monzer Hamze
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vincent Courdavault
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Marwan Osman
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nicolas Papon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Vincent Courdavault or Nicolas Papon .

Editor information

Editors and Affiliations

  1. Department of Microbiology, Alzahra University, Tehran, Iran

    Farshad Darvishi Harzevili

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kasir, D. et al. (2022). Synthetic Biology in the Candida (CTG) Clade. In: Darvishi Harzevili, F. (eds) Synthetic Biology of Yeasts. Springer, Cham. https://doi.org/10.1007/978-3-030-89680-5_12

Download citation

Publish with us

Policies and ethics

Search

Navigation