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Bassett S, Da Silva NA. Engineering a carbon source-responsive promoter for improved biosynthesis in the non-conventional yeast Kluyveromyces marxianus. Metab Eng Commun 2024; 18:e00238. [PMID: 38845682 PMCID: PMC11153928 DOI: 10.1016/j.mec.2024.e00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Many desired biobased chemicals exhibit a range of toxicity to microbial cell factories, making industry-level biomanufacturing more challenging. Separating microbial growth and production phases is known to be beneficial for improving production of toxic products. Here, we developed a novel synthetic carbon-responsive promoter for use in the rapidly growing, stress-tolerant yeast Kluyveromyces marxianus, by fusing carbon-source responsive elements of the native ICL1 promoter to the strong S. cerevisiae TDH3 or native NC1 promoter cores. Two hybrids, P IT350 and P IN450 , were validated via EGFP fluorescence and demonstrated exceptional strength, partial repression during growth, and late phase activation in glucose- and lactose-based medium, respectively. Expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for synthesis of the polyketide triacetic acid lactone (TAL) under the control of P IN450 increased TAL more than 50% relative to the native NC1 promoter, and additional promoter engineering further increased TAL titer to 1.39 g/L in tube culture. Expression of the Penicillium griseofulvum 6-methylsalicylic acid synthase (6-MSAS) under the control of P IN450 resulted in a 6.6-fold increase in 6-MSA titer to 1.09 g/L and a simultaneous 1.5-fold increase in cell growth. Finally, we used P IN450 to express the Pseudomonas savastanoi IaaM and IaaH proteins and the Salvia pomifera sabinene synthase protein to improve production of the auxin hormone indole-3-acetic acid and the monoterpene sabinene, respectively, both extremely toxic to yeast. The development of carbon-responsive promoters adds to the synthetic biology toolbox and available metabolic engineering strategies for K. marxianus, allowing greater control over heterologous protein expression and improved production of toxic metabolites.
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Affiliation(s)
- Shane Bassett
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
| | - Nancy A. Da Silva
- Department of Chemical & Biomolecular Engineering, University of California, Irvine, CA, 92697-2580, USA
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Gutiérrez-Corona JF, González-Hernández GA, Padilla-Guerrero IE, Olmedo-Monfil V, Martínez-Rocha AL, Patiño-Medina JA, Meza-Carmen V, Torres-Guzmán JC. Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential. Cells 2023; 12:2239. [PMID: 37759461 PMCID: PMC10526403 DOI: 10.3390/cells12182239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Fungal alcohol dehydrogenases (ADHs) participate in growth under aerobic or anaerobic conditions, morphogenetic processes, and pathogenesis of diverse fungal genera. These processes are associated with metabolic operation routes related to alcohol, aldehyde, and acid production. The number of ADH enzymes, their metabolic roles, and their functions vary within fungal species. The most studied ADHs are associated with ethanol metabolism, either as fermentative enzymes involved in the production of this alcohol or as oxidative enzymes necessary for the use of ethanol as a carbon source; other enzymes participate in survival under microaerobic conditions. The fast generation of data using genome sequencing provides an excellent opportunity to determine a correlation between the number of ADHs and fungal lifestyle. Therefore, this review aims to summarize the latest knowledge about the importance of ADH enzymes in the physiology and metabolism of fungal cells, as well as their structure, regulation, evolutionary relationships, and biotechnological potential.
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Affiliation(s)
- J. Félix Gutiérrez-Corona
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Gloria Angélica González-Hernández
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Israel Enrique Padilla-Guerrero
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Ana Lilia Martínez-Rocha
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - J. Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Víctor Meza-Carmen
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Juan Carlos Torres-Guzmán
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
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Past, Present, and Future Perspectives on Whey as a Promising Feedstock for Bioethanol Production by Yeast. J Fungi (Basel) 2022; 8:jof8040395. [PMID: 35448626 PMCID: PMC9031875 DOI: 10.3390/jof8040395] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 12/10/2022] Open
Abstract
Concerns about fossil fuel depletion and the environmental effects of greenhouse gas emissions have led to widespread fermentation-based production of bioethanol from corn starch or sugarcane. However, competition for arable land with food production has led to the extensive investigation of lignocellulosic sources and waste products of the food industry as alternative sources of fermentable sugars. In particular, whey, a lactose-rich, inexpensive byproduct of dairy production, is available in stable, high quantities worldwide. This review summarizes strategies and specific factors essential for efficient lactose/whey fermentation to ethanol. In particular, we cover the most commonly used strains and approaches for developing high-performance strains that tolerate fermentation conditions. The relevant genes and regulatory systems controlling lactose utilization and sources of new genes are also discussed in detail. Moreover, this review covers the optimal conditions, various feedstocks that can be coupled with whey substrates, and enzyme supplements for increasing efficiency and yield. In addition to the historical advances in bioethanol production from whey, this review explores the future of yeast-based fermentation of lactose or whey products for beverage or fuel ethanol as a fertile research area for advanced, environmentally friendly uses of industrial waste products.
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Betinova V, Toth Hervay N, Elias D, Horvathova A, Gbelska Y. The UPC2 gene in Kluyveromyces lactis stress adaptation. Folia Microbiol (Praha) 2022; 67:641-647. [PMID: 35352326 DOI: 10.1007/s12223-022-00968-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
KlUpc2p, a transcription factor belonging to the fungal binuclear cluster family, is an important regulator of ergosterol biosynthesis and azole drug resistance in Kluyveromyces lactis. In this work, we show that the absence of KlUpc2p generates Rag- phenotype and modulates the K. lactis susceptibility to oxidants and calcofuor white. The KlUPC2 deletion leads to increased expression of KlMGA2 gene, encoding an important regulator of hypoxic and lipid biosynthetic genes in K. lactis and also KlHOG1 gene. The absence of KlUpc2p does not lead to statistically significant changes in glycerol, corroborating the expression of KlGPD1 gene, encoding NAD+-dependent glycerol-3-phosphate dehydrogenase, that is similar in both the deletion mutant and the parental wild-type strain. Increased sensitivity of Klupc2 mutant cells to brefeldin A accompanied with significant increase in KlARF2 gene expression point to the involvement of KlUpc2p in intracellular signaling. Our observations highlight the connections between ergosterol and fatty acid metabolism to modulate membrane properties and point to the possible involvement of KlUpc2p in K. lactis oxidative stress response.
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Affiliation(s)
- Veronika Betinova
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Nora Toth Hervay
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Daniel Elias
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Agnes Horvathova
- Centre for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovak Republic
| | - Yvetta Gbelska
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15, Bratislava, Slovak Republic.
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Genetic and Physiological Characterization of Fructose-1,6-Bisphosphate Aldolase and Glyceraldehyde-3-Phosphate Dehydrogenase in the Crabtree-Negative Yeast Kluyveromyces lactis. Int J Mol Sci 2022; 23:ijms23020772. [PMID: 35054955 PMCID: PMC8776025 DOI: 10.3390/ijms23020772] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 02/01/2023] Open
Abstract
The milk yeast Kluyveromyces lactis degrades glucose through glycolysis and the pentose phosphate pathway and follows a mainly respiratory metabolism. Here, we investigated the role of two reactions which are required for the final steps of glucose degradation from both pathways, as well as for gluconeogenesis, namely fructose-1,6-bisphosphate aldolase (FBA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In silico analyses identified one gene encoding the former (KlFBA1), and three genes encoding isoforms of the latter (KlTDH1, KlTDH2, KlGDP1). Phenotypic analyses were performed by deleting the genes from the haploid K. lactis genome. While Klfba1 deletions lacked detectable FBA activity, they still grew poorly on glucose. To investigate the in vivo importance of the GAPDH isoforms, different mutant combinations were analyzed for their growth behavior and enzymatic activity. KlTdh2 represented the major glycolytic GAPDH isoform, as its lack caused a slower growth on glucose. Cells lacking both KlTdh1 and KlTdh2 failed to grow on glucose but were still able to use ethanol as sole carbon sources, indicating that KlGdp1 is sufficient to promote gluconeogenesis. Life-cell fluorescence microscopy revealed that KlTdh2 accumulated in the nucleus upon exposure to oxidative stress, suggesting a moonlighting function of this isoform in the regulation of gene expression. Heterologous complementation of the Klfba1 deletion by the human ALDOA gene renders K. lactis a promising host for heterologous expression of human disease alleles and/or a screening system for specific drugs.
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Rico-Díaz A, Barreiro-Alonso A, Rey-Souto C, Becerra M, Lamas-Maceiras M, Cerdán ME, Vizoso-Vázquez Á. The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis. Biomolecules 2021; 11:biom11091392. [PMID: 34572607 PMCID: PMC8465852 DOI: 10.3390/biom11091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
In the traditional fermentative model yeast Saccharomyces cerevisiae, ScIxr1 is an HMGB (High Mobility Group box B) protein that has been considered as an important regulator of gene transcription in response to external changes like oxygen, carbon source, or nutrient availability. Kluyveromyces lactis is also a useful eukaryotic model, more similar to many human cells due to its respiratory metabolism. We cloned and functionally characterized by different methodologies KlIXR1, which encodes a protein with only 34.4% amino acid sequence similarity to ScIxr1. Our data indicate that both proteins share common functions, including their involvement in the response to hypoxia or oxidative stress induced by hydrogen peroxide or metal treatments, as well as in the control of key regulators for maintenance of the dNTP (deoxyribonucleotide triphosphate) pool and ribosome synthesis. KlIxr1 is able to bind specific regulatory DNA sequences in the promoter of its target genes, which are well conserved between S. cerevisiae and K. lactis. Oppositely, we found important differences between ScIrx1 and KlIxr1 affecting cellular responses to cisplatin or cycloheximide in these yeasts, which could be dependent on specific and non-conserved domains present in these two proteins.
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Lyutova LV, Naumov GI, Shnyreva AV, Naumova ES. Molecular Polymorphism of β-Galactosidase LAC4 Genes in Dairy and Natural Strains of Kluyveromyces Yeasts. Mol Biol 2021. [DOI: 10.1134/s0026893321010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Burghardt JP, Fan R, Baas M, Eckhardt D, Gerlach D, Czermak P. Enhancing the Heterologous Fructosyltransferase Activity of Kluyveromyces lactis: Developing a Scaled-Up Process and Abolishing Invertase by CRISPR/Cas9 Genome Editing. Front Bioeng Biotechnol 2020; 8:607507. [PMID: 33324627 PMCID: PMC7724039 DOI: 10.3389/fbioe.2020.607507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
The enzymatic production of prebiotic fructo-oligosaccharides (FOS) from sucrose involves fructosyltransferases (FFTs) and invertases, both of which catalyze forward (transferase) and reverse (hydrolysis) reactions. FOS yields can therefore be increased by favoring the forward reaction. We investigated process conditions that favored transferase activity in the yeast strain Kluyveromyces lactis GG799, which expresses a native invertase and a heterologous FFT from Aspergillus terreus. To maximize transferase activity while minimizing native invertase activity in a scaled-up process, we evaluated two reactor systems in terms of oxygen input capacity in relation to the cell dry weight. In the 0.5-L reactor, we found that galactose was superior to lactose for the induction of the LAC4 promoter, and we optimized the induction time and induction to carbon source ratio using a response surface model. Based on the critical parameter of oxygen supply, we scaled up the process to 7 L using geometric similarity and a higher oxygen transport rate, which boosted the transferase activity by 159%. To favor the forward reaction even more, we deleted the native invertase gene by CRISPR/Cas9 genome editing and compared the ΔInv mutant to the original production strain in batch and fed-batch reactions. In fed-batch mode, we found that the ΔInv mutant increased the transferase activity by a further 66.9%. The enhanced mutant strain therefore provides the basis for a highly efficient and scalable fed-batch process for the production of FOS.
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Affiliation(s)
- Jan Philipp Burghardt
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
| | - Rong Fan
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Markus Baas
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Dustin Eckhardt
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
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Santomartino R, Ottaviano D, Camponeschi I, Landicho TAA, Falato L, Visca A, Soulard A, Lemaire M, Bianchi MM. The hypoxic expression of the glucose transporter RAG1 reveals the role of the bHLH transcription factor Sck1 as a novel hypoxic modulator in Kluyveromyces lactis. FEMS Yeast Res 2020; 19:5519861. [PMID: 31210264 DOI: 10.1093/femsyr/foz041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/16/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is the preferred nutrient for most living cells and is also a signaling molecule that modulates several cellular processes. Glucose regulates the expression of glucose permease genes in yeasts through signaling pathways dependent on plasma membrane glucose sensors. In the yeast Kluyveromyces lactis, sufficient levels of glucose induction of the low-affinity glucose transporter RAG1 gene also depends on a functional glycolysis, suggesting additional intracellular signaling. We have found that the expression of RAG1 gene is also induced by hypoxia in the presence of glucose, indicating that glucose and oxygen signaling pathways are interconnected. In this study we investigated the molecular mechanisms underlying this crosstalk. By analyzing RAG1 expression in various K. lactis mutants, we found that the bHLH transcriptional activator Sck1 is required for the hypoxic induction of RAG1 gene. The RAG1 promoter region essential for its hypoxic induction was identified by promoter deletion experiments. Taken together, these results show that the RAG1 glucose permease gene is synergistically induced by hypoxia and glucose and highlighted a novel role for the transcriptional activator Sck1 as a key mediator in this mechanism.
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Affiliation(s)
- Rosa Santomartino
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Ottaviano
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Ilaria Camponeschi
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | | | - Luca Falato
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Visca
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
| | - Alexandre Soulard
- Université Lyon 1, CNRS, INSA de Lyon, UMR5240 Microbiologie, Adaptation et Pathogénie, Génétique Moléculaire des Levures, Villeurbanne F69622, France
| | - Marc Lemaire
- Université Lyon 1, CNRS, INSA de Lyon, UMR5240 Microbiologie, Adaptation et Pathogénie, Génétique Moléculaire des Levures, Villeurbanne F69622, France
| | - Michele Maria Bianchi
- Sapienza Università di Roma, Dept. Biologia e Biotecnologie C. Darwin, p.le Aldo Moro 5, 00185 Rome, Italy
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Gebauer M, Hürlimann HC, Behrens M, Wolff T, Behrens SE. Subunit vaccines based on recombinant yeast protect against influenza A virus in a one-shot vaccination scheme. Vaccine 2019; 37:5578-5587. [PMID: 31399274 DOI: 10.1016/j.vaccine.2019.07.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/22/2019] [Accepted: 07/27/2019] [Indexed: 01/03/2023]
Abstract
Here we report on new subunit vaccines based on recombinant yeast of the type Kluyveromyces lactis (K. lactis), which protect mice from a lethal influenza A virus infection. Applying a genetic system that enables the rapid generation of transgenic yeast, we have developed K. lactis strains that express the influenza A virus hemagglutinin, HA, either individually or in combination with the viral M1 matrix protein. Subcutaneous application of the inactivated, but otherwise non-processed yeast material shows a complete protection of BALB/c mice in prime/boost and even one-shot/single dose vaccination schemes against a subsequent, lethal challenge with the cognate influenza virus. The yeast vaccines induce titers of neutralizing antibodies that are readily comparable to those induced by an inactivated virus vaccine. These data suggest that HA and M1 are produced with a high antigenicity in the yeast cells. Based on these findings, multivalent, DIVA-capable, yeast-based subunit vaccines may be developed as promising alternatives to conventional virus-based anti-flu vaccines for veterinary applications.
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Affiliation(s)
- Mandy Gebauer
- Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Institute of Biochemistry and Biotechnology, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Hans C Hürlimann
- Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Institute of Biology, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Martina Behrens
- Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Institute of Biochemistry and Biotechnology, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Thorsten Wolff
- Robert Koch Institute, Unit 17 "Influenza and Other Respiratory Viruses", Seestr. 10, 13353 Berlin, Germany
| | - Sven-Erik Behrens
- Martin Luther University Halle-Wittenberg, Faculty of Life Sciences (NFI), Institute of Biochemistry and Biotechnology, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany.
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Stb5p is involved in Kluyveromyces lactis response to 4-nitroquinoline-N-oxide stress. Folia Microbiol (Praha) 2019; 64:579-586. [PMID: 30706300 DOI: 10.1007/s12223-019-00682-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
Abstract
In yeast, the STB5 gene encodes a transcriptional factor belonging to binuclear cluster class (Zn2Cys6) of transcriptional regulators specific to ascomycetes. In this study, we prepared the Kluyveromyces lactis stb5Δ strain and assessed its responses to different stresses. We showed that KlSTB5 gene is able to complement the deficiencies of Saccharomyces cerevisiae stb5Δ mutant. The results of phenotypic analysis suggested that KlSTB5 gene deletion did not sensitize K. lactis cells to oxidative stress inducing compounds but led to Klstb5Δ resistance to 4-nitroquinoline-N-oxide and hygromycin B. Expression analysis indicated that the loss of KlSTB5 gene function induced the transcription of drug efflux pump encoding genes that might contribute to increased 4-nitroquinoline-N-oxide and hygromycin B tolerance. Our results show that KlStb5p functions as negative regulator of some ABC transporter genes in K. lactis.
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Varela JA, Puricelli M, Montini N, Morrissey JP. Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus. Front Microbiol 2019; 9:3330. [PMID: 30687296 PMCID: PMC6335341 DOI: 10.3389/fmicb.2018.03330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 11/24/2022] Open
Abstract
In yeasts, proteins of the Major Superfamily Transporter selectively bind and allow the uptake of sugars to permit growth on varied substrates. The genome of brewer’s yeast, Saccharomyces cerevisiae, encodes multiple hexose transporters (Hxt) to transport glucose and other MFS proteins for maltose, galactose, and other monomers. For sugar uptake, the dairy yeast, Kluyveromyces lactis, uses Rag1p for glucose, Hgt1 for glucose and galactose, and Lac12 for lactose. In the related industrial species Kluyveromyces marxianus, there are four genes encoding Lac12-like proteins but only one of them, Lac12, can transport lactose. In this study, which initiated with efforts to investigate possible functions encoded by the additional LAC12 genes in K. marxianus, a genome-wide survey of putative MFS sugar transporters was performed. Unexpectedly, it was found that the KHT and the HGT genes are present as tandem arrays of five to six copies, with the precise number varying between isolates. Heterologous expression of individual genes in S. cerevisiae and mutagenesis of single and multiple genes in K. marxianus was performed to establish possible substrates for these transporters. The focus was on the sugar galactose since it was already reported in K. lactis that this hexose was a substrate for both Lac12 and Hgt1. It emerged that three of the four copies of Lac12, four Hgt-like proteins and one Kht-like protein have some capacity to transport galactose when expressed in S. cerevisiae and inactivation of all eight genes was required to completely abolish galactose uptake in K. marxianus. Analysis of the amino acid sequence of all known yeast galactose transporters failed to identify common residues that explain the selectivity for galactose. Instead, the capacity to transport galactose has arisen three different times in K. marxianus via polymorphisms in proteins that are probably ancestral glucose transporters. Although, this is analogous to S. cerevisiae, in which Gal2 is related to glucose transporters, there are not conserved amino acid changes, either with Gal2, or among the K. marxianus galactose transporters. The data highlight how gene duplication and functional diversification has provided K. marxianus with versatile capacity to utilise sugars for growth.
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Affiliation(s)
- Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Martina Puricelli
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Noemi Montini
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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Mojardín L, Vega M, Moreno F, Schmitz HP, Heinisch JJ, Rodicio R. Lack of the NAD+-dependent glycerol 3-phosphate dehydrogenase impairs the function of transcription factors Sip4 and Cat8 required for ethanol utilization in Kluyveromyces lactis. Fungal Genet Biol 2018; 111:16-29. [DOI: 10.1016/j.fgb.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 11/25/2022]
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Dias O, Basso TO, Rocha I, Ferreira EC, Gombert AK. Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates. Antonie van Leeuwenhoek 2017; 111:183-195. [PMID: 28900755 DOI: 10.1007/s10482-017-0940-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The yeast Kluyveromyces lactis has received attention both from academia and industry due to some important features, such as its capacity to grow in lactose-based media, its safe status, its suitability for large-scale cultivation and for heterologous protein synthesis. It has also been considered as a model organism for genomics and metabolic regulation. Despite this, very few studies were carried out hitherto under strictly controlled conditions, such as those found in a chemostat. Here we report a set of quantitative physiological data generated during chemostat cultivations with the K. lactis CBS 2359 strain, obtained under glucose-limiting and fully aerobic conditions. This dataset serves [corrected] as a basis for the comparison of K. lactis with the model yeast Saccharomyces cerevisiae in terms of their elemental compositions, as well as for future metabolic flux analysis and metabolic modelling studies with K. lactis.
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Affiliation(s)
- Oscar Dias
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil
| | - Thiago O Basso
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil.
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Eugénio C Ferreira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreas K Gombert
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, Av. Prof. Luciano Gualberto 380, São Paulo, SP, 05508-010, Brazil.,School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
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15
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Escalera-Fanjul X, Campero-Basaldua C, Colón M, González J, Márquez D, González A. Evolutionary Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy. Front Microbiol 2017; 8:1150. [PMID: 28694796 PMCID: PMC5483587 DOI: 10.3389/fmicb.2017.01150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1, alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display LkAlt1 and KlAlt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s). Furthermore, phenotypic analysis of null mutants uncovered the fact that KlAlt1 and LkAlt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that ScAlt2 conserves 64% identity with LkAlt1 and 66% with KlAlt1, suggests that ScAlt2 diversified after the ancestral hybrid was formed. ScALT2 functional diversification resulted in loss of both alanine transaminase activity and the additional alanine-independent LkAlt1 function, since ScALT2 did not complement the Lkalt1Δ phenotype. It can be concluded that LkALT1 and KlLALT1 functional role as alanine transaminases was delegated to ScALT1, while ScALT2 lost this role during diversification.
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Affiliation(s)
| | | | | | | | | | - Alicia González
- Instituto de Fisiología Celular, Departamento de Bioquímica y Biología Estructural, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
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16
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Campero‐Basaldua C, Quezada H, Riego‐Ruíz L, Márquez D, Rojas E, González J, El‐Hafidi M, González A. Diversification of the kinetic properties of yeast NADP-glutamate-dehydrogenase isozymes proceeds independently of their evolutionary origin. Microbiologyopen 2017; 6:e00419. [PMID: 27864882 PMCID: PMC5387307 DOI: 10.1002/mbo3.419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 02/02/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, the ScGDH1 and ScGDH3 encoded glutamate dehydrogenases (NADP-GDHs) catalyze the synthesis of glutamate from ammonium and α-ketoglutarate (α-KG). Previous kinetic characterization showed that these enzymes displayed different allosteric properties and respectively high or low rate of α-KG utilization. Accordingly, the coordinated action of ScGdh1 and ScGdh3, regulated balanced α-KG utilization for glutamate biosynthesis under either fermentative or respiratory conditions, safeguarding energy provision. Here, we have addressed the question of whether there is a correlation between the regulation and kinetic properties of the NADP-GDH isozymes present in S. cerevisiae (ScGdh1 and ScGdh3), Kluyveromyces lactis (KlGdh1), and Lachancea kluyveri (LkGdh1) and their evolutionary history. Our results show that the kinetic properties of K. lactis and L. kluyveri single NADP-GDHs are respectively similar to either ScGDH3 or ScGDH1, which arose from the whole genome duplication event of the S. cerevisiae lineage, although, KlGDH1 and LkGDH1 originated from a GDH clade, through an ancient interspecies hybridization event that preceded the divergence between the Saccharomyces clade and the one containing the genera Kluyveromyces, Lachancea, and Eremothecium. Thus, the kinetic properties which determine the NADP-GDHs capacity to utilize α-KG and synthesize glutamate do not correlate with their evolutionary origin.
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Affiliation(s)
- Carlos Campero‐Basaldua
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Héctor Quezada
- Laboratorio de Inmunología y ProteómicaHospital Infantil de México Federico GómezMexico CityMéxico
| | | | - Dariel Márquez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Erendira Rojas
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - James González
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
| | - Mohammed El‐Hafidi
- Departamento de Biomedicina CardiovascularInstituto Nacional de Cardiología Ignacio ChávezMexico CityMéxico
| | - Alicia González
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMéxico
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17
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Díaz-Vergara L, Pereyra CM, Montenegro M, Pena GA, Aminahuel CA, Cavaglieri LR. Encapsulated whey-native yeast Kluyveromyces marxianus as a feed additive for animal production. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2017; 34:750-759. [PMID: 28277172 DOI: 10.1080/19440049.2017.1290830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Whey is the main byproduct of the cheese industry. While the composition is variable, it retains up to 55% of milk nutrients. The beneficial features of whey indicates a promising source of new potentially probiotic strains for the development of food additives destined for animal production. The aim of this study was to identify Kluyveromyces spp. isolated from whey, to study some probiotic properties and to select the best strain to be encapsulated using derivatised chitosan. Kluyveromyces marxianus strains (VM003, VM004 and VM005) were isolated from whey and identified by phenotypic and molecular techniques. These three yeast strains were able to survive under gastrointestinal conditions. Moreover, they exhibited weak auto-aggregation and co-aggregation with pathogenic bacteria (Salmonella sp., Serratia sp., Escherichia coli and Salmonella typhimurium). In general the K. marxianus strains had a strong antimicrobial activity against pathogenic bacteria. The potential probiotic K. marxianus VM004 strain was selected for derivatised-chitosan encapsulation. Material treated with native chitosan exhibited a strong antimicrobial activity of K. marxianus, showing a total growth inhibition at 10 min exposure. However, derivatised-chitosan encapsulation showed a reduced antimicrobial activity. This is the first study to show some probiotic properties of whey-native K. marxianus, in vitro. An encapsulation strategy was applied using derivatised chitosan.
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Affiliation(s)
- Ladislao Díaz-Vergara
- a Centro de Investigaciones y Transferencia Villa María, Instituto de Ciencias Básicas y Aplicadas , Universidad Nacional de Villa María , Villa María , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
| | - Carina Maricel Pereyra
- a Centro de Investigaciones y Transferencia Villa María, Instituto de Ciencias Básicas y Aplicadas , Universidad Nacional de Villa María , Villa María , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
| | - Mariana Montenegro
- a Centro de Investigaciones y Transferencia Villa María, Instituto de Ciencias Básicas y Aplicadas , Universidad Nacional de Villa María , Villa María , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
| | - Gabriela Alejandra Pena
- b Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
| | - Carla Ayelen Aminahuel
- a Centro de Investigaciones y Transferencia Villa María, Instituto de Ciencias Básicas y Aplicadas , Universidad Nacional de Villa María , Villa María , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
| | - Lilia R Cavaglieri
- b Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Argentina
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18
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Wellenbeck W, Mampel J, Naumer C, Knepper A, Neubauer P. Fast-track development of a lactase production process with Kluyveromyces lactis by a progressive parameter-control workflow. Eng Life Sci 2016; 17:1185-1194. [PMID: 32624746 DOI: 10.1002/elsc.201600031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/12/2016] [Accepted: 09/07/2016] [Indexed: 11/12/2022] Open
Abstract
The time-to-market challenge is key to success for consumer goods affiliated industries. In recent years, the dairy industry faces a fast and constantly growing demand for enzymatically produced lactose-free milk products, mainly driven by emerging markets in South America and Asia. In order to take advantage of this opportunity, we developed a fermentation process for lactase (β-galactosidase) from Kluyveromyces lactis within short time. Here, we describe the process of stepwise increasing the level of control over relevant process parameters during scale-up that established a highly efficient and stable production system. Process development started with evolutionary engineering to generate catabolite-derepressed variants of the K. lactis wild-type strain. A high-throughput screening mimicking fed-batch cultivation identified a constitutive lactase overproducer with 260-fold improved activity of 4.4 U per milligram dry cell weight when cultivated in glucose minimal medium. During scale-up, process control was progressively increased up to the level of conventional, fully controlled fed-batch cultivations by simulating glucose feed, applying pH- and dissolved oxygen tension (DOT)-sensor technology to small scale, and by the use of a milliliter stirred tank bioreactor. Additionally, process development was assisted by design-of-experiments optimization of the growth medium employing the response surface methodology.
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Affiliation(s)
- Wenzel Wellenbeck
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Christian Naumer
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Andreas Knepper
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
| | - Peter Neubauer
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
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19
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Growth kinetics and physiological behavior of co-cultures of Saccharomyces cerevisiae and Kluyveromyces lactis , fermenting carob sugars extracted with whey. Enzyme Microb Technol 2016; 92:41-8. [DOI: 10.1016/j.enzmictec.2016.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/10/2016] [Accepted: 06/18/2016] [Indexed: 11/20/2022]
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20
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Madhavan A, Sukumaran RK. Secreted expression of an active human interferon‐beta (HuIFNβ) in
Kluyveromyces lactis. Eng Life Sci 2016. [DOI: 10.1002/elsc.201500120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Aravind Madhavan
- Centre for Biofuels, Biotechnology Division CSIR‐National Institute for Interdisciplinary Science and Technology Trivandrum India
| | - Rajeev Kumar Sukumaran
- Centre for Biofuels, Biotechnology Division CSIR‐National Institute for Interdisciplinary Science and Technology Trivandrum India
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21
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Legrand J, Bolotin-Fukuhara M, Bourgais A, Fairhead C, Sicard D. Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Res 2015; 16:fov112. [PMID: 26684721 DOI: 10.1093/femsyr/fov112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 12/14/2022] Open
Abstract
The Nakaseomyces clade consists of a group of six hemiascomyceteous yeasts (Candida glabrata, Nakaseomyces delphensis, C. nivarensis, C. bracarensis, C. castelli, N. bacillisporus), phylogenetically close to the yeast Saccharomyces cerevisiae, their representative being the well-known pathogenic yeast C. glabrata. Four species had been previously examined for their carbon assimilation properties and found to have similar properties to S. cerevisiae (repression of respiration in high glucose-i.e. Crabtree positivity-and being a facultative anaerobe). We examined here the complete set of the six species for their carbon metabolic gene content. We also measured different metabolic and life-history traits (glucose consumption rate, population growth rate, carrying capacity, cell size, cell and biomass yield). We observed deviations from the glycolytic gene redundancy observed in S. cerevisiae presumed to be an important property for the Crabtree positivity, especially for the two species C. castelli and N. bacillisporus which frequently have only one gene copy, but different life strategies. Therefore, we show that the decrease in carbon metabolic gene copy cannot be simply associated with a reduction of glucose consumption rate and can be counterbalanced by other beneficial genetic variations.
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Affiliation(s)
- Judith Legrand
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Monique Bolotin-Fukuhara
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Aurélie Bourgais
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Cécile Fairhead
- CNRS UMR 8621 Institut de Génétique et Microbiologie, Univ Paris Sud F-91140 Orsay Cedex CNRS, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Delphine Sicard
- Univ Paris-Sud, UMR 0320/UMR8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France INRA, UMR 1083 Sciences pour l'oenologie, 34060 Montpellier Cedex 2, France
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22
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Mehlgarten C, Krijger JJ, Lemnian I, Gohr A, Kasper L, Diesing AK, Grosse I, Breunig KD. Divergent Evolution of the Transcriptional Network Controlled by Snf1-Interacting Protein Sip4 in Budding Yeasts. PLoS One 2015; 10:e0139464. [PMID: 26440109 PMCID: PMC4634231 DOI: 10.1371/journal.pone.0139464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022] Open
Abstract
Cellular responses to starvation are of ancient origin since nutrient limitation has always been a common challenge to the stability of living systems. Hence, signaling molecules involved in sensing or transducing information about limiting metabolites are highly conserved, whereas transcription factors and the genes they regulate have diverged. In eukaryotes the AMP-activated protein kinase (AMPK) functions as a central regulator of cellular energy homeostasis. The yeast AMPK ortholog SNF1 controls the transcriptional network that counteracts carbon starvation conditions by regulating a set of transcription factors. Among those Cat8 and Sip4 have overlapping DNA-binding specificity for so-called carbon source responsive elements and induce target genes upon SNF1 activation. To analyze the evolution of the Cat8-Sip4 controlled transcriptional network we have compared the response to carbon limitation of Saccharomyces cerevisiae to that of Kluyveromyces lactis. In high glucose, S. cerevisiae displays tumor cell-like aerobic fermentation and repression of respiration (Crabtree-positive) while K. lactis has a respiratory-fermentative life-style, respiration being regulated by oxygen availability (Crabtree-negative), which is typical for many yeasts and for differentiated higher cells. We demonstrate divergent evolution of the Cat8-Sip4 network and present evidence that a role of Sip4 in controlling anabolic metabolism has been lost in the Saccharomyces lineage. We find that in K. lactis, but not in S. cerevisiae, the Sip4 protein plays an essential role in C2 carbon assimilation including induction of the glyoxylate cycle and the carnitine shuttle genes. Induction of KlSIP4 gene expression by KlCat8 is essential under these growth conditions and a primary function of KlCat8. Both KlCat8 and KlSip4 are involved in the regulation of lactose metabolism in K. lactis. In chromatin-immunoprecipitation experiments we demonstrate binding of both, KlSip4 and KlCat8, to selected CSREs and provide evidence that KlSip4 counteracts KlCat8-mediated transcription activation by competing for binding to some but not all CSREs. The finding that the hierarchical relationship of these transcription factors differs between K. lactis and S. cerevisiae and that the sets of target genes have diverged contributes to explaining the phenotypic differences in metabolic life-style.
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Affiliation(s)
| | - Jorrit-Jan Krijger
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ioana Lemnian
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - André Gohr
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Lydia Kasper
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | | | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Karin D. Breunig
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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23
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Callejas-Negrete OA, Torres-Guzmán JC, Padilla-Guerrero IE, Esquivel-Naranjo U, Padilla-Ballesteros MF, García-Tapia A, Schrank A, Salazar-Solís E, Gutiérrez-Corona F, González-Hernández GA. The Adh1 gene of the fungus Metarhizium anisopliae is expressed during insect colonization and required for full virulence. Microbiol Res 2015; 172:57-67. [DOI: 10.1016/j.micres.2014.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/18/2014] [Accepted: 11/25/2014] [Indexed: 12/22/2022]
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Yamaoka C, Kurita O, Kubo T. Improved ethanol tolerance of Saccharomyces cerevisiae in mixed cultures with Kluyveromyces lactis on high-sugar fermentation. Microbiol Res 2014; 169:907-14. [DOI: 10.1016/j.micres.2014.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/29/2014] [Accepted: 04/14/2014] [Indexed: 10/25/2022]
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25
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Lu M, Wang X, Sun G, Qin B, Xiao J, Yan S, Pan Y, Wang Y. Fine structure of Tibetan kefir grains and their yeast distribution, diversity, and shift. PLoS One 2014; 9:e101387. [PMID: 24977409 PMCID: PMC4076316 DOI: 10.1371/journal.pone.0101387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/06/2014] [Indexed: 02/03/2023] Open
Abstract
Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species – Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S. cerevisiae and Lactobacillus bacteria in TKGs.
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Affiliation(s)
- Man Lu
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Xingxing Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Guowei Sun
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Bing Qin
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jinzhou Xiao
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shuling Yan
- Institute of Biochemistry and Molecular Cell Biology, University of Goettingen, Goettingen, Germany
| | - Yingjie Pan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongjie Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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26
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Hesham AEL, Wambui V, Ogola J.O. H, Maina JM. Phylogenetic analysis of isolated biofuel yeasts based on 5.8S-ITS rDNA and D1/D2 26S rDNA sequences. J Genet Eng Biotechnol 2014. [DOI: 10.1016/j.jgeb.2014.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Koleva DI, Petrova VY, Nedeva TS, Kujumdzieva AV. Sugar Utilization Influences Yeast Glutathione Synthetases and Transferases:in SilicoAnalysis. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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28
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Fuzi SFZM, Razali F, Jahim JM, Rahman RA, Illias RM. Simplified feeding strategies for the fed-batch cultivation of Kluyveromyces lactis GG799 for enhanced recombinant xylanase production. Bioprocess Biosyst Eng 2014; 37:1887-98. [DOI: 10.1007/s00449-014-1163-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/26/2014] [Indexed: 12/19/2022]
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Santos AM, Silveira WB, Fietto LG, Brandão RL, Castro IM. Kinetics and regulation of lactose transport and metabolism in Kluyveromyces lactis JA6. World J Microbiol Biotechnol 2014; 30:1977-83. [DOI: 10.1007/s11274-014-1620-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 01/31/2014] [Indexed: 11/29/2022]
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Mates N, Kettner K, Heidenreich F, Pursche T, Migotti R, Kahlert G, Kuhlisch E, Breunig KD, Schellenberger W, Dittmar G, Hoflack B, Kriegel TM. Proteomic and functional consequences of hexokinase deficiency in glucose-repressible Kluyveromyces lactis. Mol Cell Proteomics 2014; 13:860-75. [PMID: 24434903 DOI: 10.1074/mcp.m113.032714] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The analysis of glucose signaling in the Crabtree-positive eukaryotic model organism Saccharomyces cerevisiae has disclosed a dual role of its hexokinase ScHxk2, which acts as a glycolytic enzyme and key signal transducer adapting central metabolism to glucose availability. In order to identify evolutionarily conserved characteristics of hexokinase structure and function, the cellular response of the Crabtree-negative yeast Kluyveromyces lactis to rag5 null mutation and concomitant deficiency of its unique hexokinase KlHxk1 was analyzed by means of difference gel electrophoresis. In total, 2,851 fluorescent spots containing different protein species were detected in the master gel representing all of the K. lactis proteins that were solubilized from glucose-grown KlHxk1 wild-type and mutant cells. Mass spectrometric peptide analysis identified 45 individual hexokinase-dependent proteins related to carbohydrate, short-chain fatty acid and tricarboxylic acid metabolism as well as to amino acid and protein turnover, but also to general stress response and chromatin remodeling, which occurred as a consequence of KlHxk1 deficiency at a minimum 3-fold enhanced or reduced level in the mutant proteome. In addition, three proteins exhibiting homology to 2-methylcitrate cycle enzymes of S. cerevisiae were detected at increased concentrations, suggesting a stimulation of pyruvate formation from amino acids and/or fatty acids. Experimental validation of the difference gel electrophoresis approach by post-lysis dimethyl labeling largely confirmed the abundance changes detected in the mutant proteome via the former method. Taking into consideration the high proportion of identified hexokinase-dependent proteins exhibiting increased proteomic levels, KlHxk1 is likely to have a repressive function in a multitude of metabolic pathways. The proteomic alterations detected in the mutant classify KlHxk1 as a multifunctional enzyme and support the view of evolutionary conservation of dual-role hexokinases even in organisms that are less specialized than S. cerevisiae in terms of glucose utilization.
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Affiliation(s)
- Nadia Mates
- Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Institute of Physiological Chemistry, D-01307 Dresden, Germany
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Rodicio R, Heinisch JJ. Yeast on the milky way: genetics, physiology and biotechnology of Kluyveromyces lactis. Yeast 2013; 30:165-77. [PMID: 23576126 DOI: 10.1002/yea.2954] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 11/08/2022] Open
Abstract
The milk yeast Kluyveromyces lactis has a life cycle similar to that of Saccharomyces cerevisiae and can be employed as a model eukaryote using classical genetics, such as the combination of desired traits, by crossing and tetrad analysis. Likewise, a growing set of vectors, marker cassettes and tags for fluorescence microscopy are available for manipulation by genetic engineering and investigating its basic cell biology. We here summarize these applications, as well as the current knowledge regarding its central metabolism, glucose and extracellular stress signalling pathways. A short overview on the biotechnological potential of K. lactis concludes this review.
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Affiliation(s)
- Rosaura Rodicio
- Departamento de Bioquímica y Biología Molecular and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, Spain
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Regulations of sugar transporters: insights from yeast. Curr Genet 2013; 59:1-31. [PMID: 23455612 DOI: 10.1007/s00294-013-0388-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 02/02/2013] [Indexed: 12/24/2022]
Abstract
Transport across the plasma membrane is the first step at which nutrient supply is tightly regulated in response to intracellular needs and often also rapidly changing external environment. In this review, I describe primarily our current understanding of multiple interconnected glucose-sensing systems and signal-transduction pathways that ensure fast and optimum expression of genes encoding hexose transporters in three yeast species, Saccharomyces cerevisiae, Kluyveromyces lactis and Candida albicans. In addition, an overview of GAL- and MAL-specific regulatory networks, controlling galactose and maltose utilization, is provided. Finally, pathways generating signals inducing posttranslational degradation of sugar transporters will be highlighted.
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Agarwal PK, Uppada V, Noronha SB. Comparison of pyruvate decarboxylases from Saccharomyces cerevisiae and Komagataella pastoris (Pichia pastoris). Appl Microbiol Biotechnol 2013; 97:9439-49. [DOI: 10.1007/s00253-013-4758-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/03/2013] [Accepted: 02/05/2013] [Indexed: 11/30/2022]
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Protective vaccination against infectious bursal disease virus with whole recombinant Kluyveromyces lactis yeast expressing the viral VP2 subunit. PLoS One 2012; 7:e42870. [PMID: 23024743 PMCID: PMC3443089 DOI: 10.1371/journal.pone.0042870] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/12/2012] [Indexed: 01/09/2023] Open
Abstract
Here we report on vaccination approaches against infectious bursal disease (IBD) of poultry that were performed with complete yeast of the species Kluyveromyces lactis (K. lactis). Employing a genetic system that enables the rapid production of stably transfected recombinant K. lactis, we generated yeast strains that expressed defined quantities of the virus capsid forming protein VP2 of infectious bursal disease virus (IBDV). Both, subcutaneous as well as oral vaccination regiments with the heat-inactivated but otherwise untreated yeast induced IBDV-neutralizing antibodies in mice and chickens. A full protection against a subsequent IBDV infection was achieved by subcutaneous inoculation of only milligram amounts of yeast per chicken. Oral vaccination also generated protection: while mortality was observed in control animals after virus challenge, none of the vaccinees died and ca. one-tenth were protected as indicated by the absence of lesions in the bursa of Fabricius. Recombinant K. lactis was thus indicated as a potent tool for the induction of a protective immune response by different applications. Subcutaneously applied K. lactis that expresses the IBDV VP2 was shown to function as an efficacious anti-IBD subunit vaccine.
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Genetic structure of a novel biofuel-producing microorganism community. J Genet 2012; 91:183-91. [PMID: 22942088 DOI: 10.1007/s12041-012-0173-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Biofuels are an important alternative, renewable source of energy in the face of the ongoing depletion of fossil fuels. Cheese whey is a dairy industry waste characterized by high lactose concentration, which represents a significant environmental problem. Bio-ethanol production by cheese whey could be an effective nonvegetable source for renewable energy production. Here, we report the isolation of a mixed microbial population, able to produce ethanol as main fermentation product from fermenting whey. The microbial consortium has been used to perform a batch fermentation of crude whey in both anoxic and hypoxic conditions. Maximum ethanol concentrations achieved in this study was obtained using the mixed culture in hypoxic conditions, grown at pH 4 and 30 °C, with ethanol production yield of 60 g/L. Our research has pointed out an alternative way to both dispose and valorize cheese whey, a dairy by-product that could cause water pollution and harm to the environment if not properly treated.
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Hodurova Z, Ferreira L, Sánchez-Juanes F, Dominguez A, Gbelska Y. Cytosolic proteome of Kluyveromyces lactis affected by the multidrug resistance regulating transcription factor KlPdr1p. J Proteomics 2012; 75:5316-26. [DOI: 10.1016/j.jprot.2012.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/25/2012] [Accepted: 06/13/2012] [Indexed: 01/25/2023]
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Krijger JJ, Baumann J, Wagner M, Schulze K, Reinsch C, Klose T, Onuma OF, Simon C, Behrens SE, Breunig KD. A novel, lactase-based selection and strain improvement strategy for recombinant protein expression in Kluyveromyces lactis. Microb Cell Fact 2012; 11:112. [PMID: 22905717 PMCID: PMC3520740 DOI: 10.1186/1475-2859-11-112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Crabtree-negative yeast species Kluyveromyces lactis has been established as an attractive microbial expression system for recombinant proteins at industrial scale. Its LAC genes allow for utilization of the inexpensive sugar lactose as a sole source of carbon and energy. Lactose efficiently induces the LAC4 promoter, which can be used to drive regulated expression of heterologous genes. So far, strain manipulation of K. lactis by homologous recombination was hampered by the high rate of non-homologous end-joining. RESULTS Selection for growth on lactose was applied to target the insertion of heterologous genes downstream of the LAC4 promoter into the K. lactis genome and found to yield high numbers of positive transformants. Concurrent reconstitution of the β-galactosidase gene indicated the desired integration event of the expression cassette, and β-galactosidase activity measurements were used to monitor gene expression for strain improvement and fermentation optimization. The system was particularly improved by usage of a cell lysis resistant strain, VAK367-D4, which allowed for protein accumulation in long-term fermentation. Further optimization was achieved by increased gene dosage of KlGAL4 encoding the activator of lactose and galactose metabolic genes that led to elevated transcription rates. Pilot experiments were performed with strains expressing a single-chain antibody fragment (scFvox) and a viral envelope protein (BVDV-E2), respectively. scFvox was shown to be secreted into the culture medium in an active, epitope-binding form indicating correct processing and protein folding; the E2 protein could be expressed intracellularly. Further data on the influence of protein toxicity on batch fermentation and potential post-transcriptional bottlenecks in protein accumulation were obtained. CONCLUSIONS A novel Kluyveromyces lactis host-vector system was developed that places heterologous genes under the control of the chromosomal LAC4 promoter and that allows monitoring of its transcription rates by β-galactosidase measurement. The procedure is rapid and efficient, and the resulting recombinant strains contain no foreign genes other than the gene of interest. The recombinant strains can be grown non-selectively in rich medium and stably maintained even when the gene product exerts protein toxicity.
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Affiliation(s)
- Jorrit-Jan Krijger
- Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
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Kluyveromyces lactis: a suitable yeast model to study cellular defense mechanisms against hypoxia-induced oxidative stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:634674. [PMID: 22928082 PMCID: PMC3425888 DOI: 10.1155/2012/634674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/22/2012] [Indexed: 11/17/2022]
Abstract
Studies about hypoxia-induced oxidative stress in human health disorders take advantage from the use of unicellular eukaryote models. A widely extended model is the fermentative yeast Saccharomyces cerevisiae. In this paper, we describe an overview of the molecular mechanisms induced by a decrease in oxygen availability and their interrelationship with the oxidative stress response in yeast. We focus on the differential characteristics between S. cerevisiae and the respiratory yeast Kluyveromyces lactis, a complementary emerging model, in reference to multicellular eukaryotes.
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Milk and sugar: Regulation of cell wall synthesis in the milk yeast Kluyveromyces lactis. Eur J Cell Biol 2011; 90:745-50. [DOI: 10.1016/j.ejcb.2011.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Cialfi S, Uccelletti D, Carducci A, Wésolowski-Louvel M, Mancini P, Heipieper HJ, Saliola M. KlHsl1 is a component of glycerol response pathways in the milk yeast Kluyveromyces lactis. MICROBIOLOGY-SGM 2011; 157:1509-1518. [PMID: 21310785 DOI: 10.1099/mic.0.044040-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In Saccharomyces cerevisiae, HSL1 (NIK1) encodes a serine-threonine protein kinase involved in cell cycle control and morphogenesis. Deletion of its putative orthologue in Kluyveromyces lactis, KlHSL1, gives rise to sensitivity to the respiratory inhibitor antimycin A (AA). Resistance to AA on glucose (Rag+ phenotype) is associated with genes (RAG) required for glucose metabolism/glycolysis. To understand the relationship between RAG and KlHSL1, rag and Klhsl1Δ mutant strains were investigated. The analysis showed that all the mutants contained a phosphorylated form of Hog1 and displayed an inability to synthesize/accumulate glycerol as a compatible solute. In addition, rag mutants also showed alterations in both cell wall and membrane fatty acids. The pleiotropic defects of these strains indicate that a common pathway regulates glucose utilization and stress response mechanisms, suggesting impaired adaptation of the plasma membrane/cell wall during the respiratory-fermentative transition. KlHsl1 could be the link between these adaptive pathways and the morphogenetic checkpoint.
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Affiliation(s)
- Samantha Cialfi
- Department of Biology and Biotechnology 'C. Darwin', University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Uccelletti
- Department of Biology and Biotechnology 'C. Darwin', University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Augusto Carducci
- Department of Biology and Biotechnology 'C. Darwin', University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Micheline Wésolowski-Louvel
- UMR, Microbiologie, Adaptation et Pathogénie, Université de Lyon, Lyon, F-69003, France; Université Lyon 1, Lyon, F-69003, France; CNRS, Villeurbanne, F-69622, France; and INSA de Lyon, Villeurbanne, F-69621, France
| | - Patrizia Mancini
- Department of Experimental Medicine, University of Rome 'La Sapienza', Viale Regina Elena 324, 00161 Rome, Italy
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Michele Saliola
- Department of Biology and Biotechnology 'C. Darwin', University of Rome 'La Sapienza', Piazzale Aldo Moro 5, 00185 Rome, Italy
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41
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Rigamonte TA, Silveira WB, Fietto LG, Castro IM, Breunig KD, Passos FM. Restricted sugar uptake by sugar-induced internalization of the yeast lactose/galactose permease Lac12. FEMS Yeast Res 2011; 11:243-51. [DOI: 10.1111/j.1567-1364.2010.00709.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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42
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Colón M, Hernández F, López K, Quezada H, González J, López G, Aranda C, González A. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme. PLoS One 2011; 6:e16099. [PMID: 21267457 PMCID: PMC3022659 DOI: 10.1371/journal.pone.0016099] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 12/06/2010] [Indexed: 11/19/2022] Open
Abstract
Background Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. Principal Findings Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs). This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1), while catabolic substrates are accumulated in the cytosol (Bat2). Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. Conclusions Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the biosynthetic and catabolic roles of the ancestral BCAT in two isozymes improving BCAAs metabolism and constituting an adaptation to facultative metabolism.
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Affiliation(s)
- Maritrini Colón
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Fabiola Hernández
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Karla López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Héctor Quezada
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México City, México
| | - James González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Geovani López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Cristina Aranda
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
- * E-mail:
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Anders A, Breunig KD. Evolutionary aspects of a genetic network: studying the lactose/galactose regulon of Kluyveromyces lactis. Methods Mol Biol 2011; 734:259-277. [PMID: 21468994 DOI: 10.1007/978-1-61779-086-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The budding yeast Kluyveromyces lactis has diverged from the Saccharomyces lineage before the whole-genome duplication and its genome sequence reveals lower redundancy of many genes. Moreover, it shows lower preference for fermentative carbon metabolism and a broader substrate spectrum making it a particularly rewarding system for comparative and evolutionary studies of carbon-regulated genetic networks. The lactose/galactose regulon of K. lactis, which is regulated by the prototypic transcription activator Gal4 exemplifies important aspects of network evolution when compared with the model GAL regulon of Saccharomyces cerevisiae. Differences in physiology relate to different subcellular compartmentation of regulatory components and, importantly, to quantitative differences in protein-protein interactions rather than major differences in network architecture. Here, we introduce genetic and biochemical tools to study K. lactis in general and the lactose/galactose regulon in particular. We present methods to quantify relevant protein-protein interactions in that network and to visualize such differences in simple plate assays allowing for genetic approaches in further studies.
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Affiliation(s)
- Alexander Anders
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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44
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Kuettner EB, Kettner K, Keim A, Svergun DI, Volke D, Singer D, Hoffmann R, Müller EC, Otto A, Kriegel TM, Sträter N. Crystal structure of hexokinase KlHxk1 of Kluyveromyces lactis: a molecular basis for understanding the control of yeast hexokinase functions via covalent modification and oligomerization. J Biol Chem 2010; 285:41019-33. [PMID: 20943665 PMCID: PMC3003401 DOI: 10.1074/jbc.m110.185850] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of the unique hexokinase KlHxk1 of the yeast Kluyveromyces lactis were determined using eight independent crystal forms. In five crystal forms, a symmetrical ring-shaped homodimer was observed, corresponding to the physiological dimer existing in solution as shown by small-angle x-ray scattering. The dimer has a head-to-tail arrangement such that the small domain of one subunit interacts with the large domain of the other subunit. Dimer formation requires favorable interactions of the 15 N-terminal amino acids that are part of the large domain with amino acids of the small domain of the opposite subunit, respectively. The head-to-tail arrangement involving both domains of the two KlHxk1 subunits is appropriate to explain the reduced activity of the homodimer as compared with the monomeric enzyme and the influence of substrates and products on dimer formation and dissociation. In particular, the structure of the symmetrical KlHxk1 dimer serves to explain why phosphorylation of conserved residue Ser-15 may cause electrostatic repulsions with nearby negatively charged residues of the adjacent subunit, thereby inducing a dissociation of the homologous dimeric hexokinases KlHxk1 and ScHxk2. Two complex structures of KlHxk1 with bound glucose provide a molecular model of substrate binding to the open conformation and the subsequent classical domain closure motion of yeast hexokinases. The entirety of the novel data extends the current concept of glucose signaling in yeast and complements the induced-fit model by integrating the events of N-terminal phosphorylation and dissociation of homodimeric yeast hexokinases.
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Affiliation(s)
- E. Bartholomeus Kuettner
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Karina Kettner
- the Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Dresden University of Technology, D-01307 Dresden, Germany
| | - Antje Keim
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Dmitri I. Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, Deutsches Elektronen-Synchrotron, D-22603 Hamburg, Germany, and
| | - Daniela Volke
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - David Singer
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Ralf Hoffmann
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | | | - Albrecht Otto
- the Max Delbrück Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Thomas M. Kriegel
- the Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Dresden University of Technology, D-01307 Dresden, Germany
| | - Norbert Sträter
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
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45
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Backhaus K, Heilmann CJ, Sorgo AG, Purschke G, de Koster CG, Klis FM, Heinisch JJ. A systematic study of the cell wall composition of Kluyveromyces lactis. Yeast 2010; 27:647-60. [PMID: 20641021 DOI: 10.1002/yea.1781] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In many ascomycetous yeasts, the cell wall is composed of two main types of macromolecules: (a) polysaccharides, with a high content of beta-1,6- and beta-1,3-linked glucan chains and minor amounts of chitin; and (b) cell wall proteins of different types. Synthesis and maintenance of these macromolecules respond to environmental changes, which are sensed by the cell wall integrity (CWI) signal transduction pathway. We here present a first systematic analysis of the cell wall composition of the milk yeast, Kluyveromyces lactis. Electron microscopic analyses revealed that exponentially growing cells of K. lactis supplied with glucose as a carbon source have a wall thickness of 64 nm, as compared to 105 nm when growing on 3% ethanol. Despite their increased wall thickness, ethanol-grown cells were more sensitive to the presence of zymolyase in the growth medium. Mass spectrometric analysis identified 22 covalently linked cell wall proteins, including 19 GPI-modified proteins and two Pir wall proteins. Importantly, the composition of the cell wall glycoproteome depended on carbon source and growth phase. Our results clearly illustrate the dynamic nature of the cell wall of K. lactis and provide a firm base for studying its regulation.
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Affiliation(s)
- Katja Backhaus
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Osnabrück, Germany
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Fermentation of lactose to bio-ethanol by yeasts as part of integrated solutions for the valorisation of cheese whey. Biotechnol Adv 2010; 28:375-84. [DOI: 10.1016/j.biotechadv.2010.02.002] [Citation(s) in RCA: 278] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 02/03/2010] [Accepted: 02/04/2010] [Indexed: 11/18/2022]
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47
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Saliola M, D'Amici S, Sponziello M, Mancini P, Tassone P, Falcone C. The transdehydrogenase genes KlNDE1 and KlNDI1 regulate the expression of KlGUT2 in the yeast Kluyveromyces lactis. FEMS Yeast Res 2010; 10:518-26. [PMID: 20491935 DOI: 10.1111/j.1567-1364.2010.00631.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
KlNDE1 and KlNDI1 code for two inner mitochondrial membrane transdehydrogenases involved in the maintenance of the intracellular NAD(P)H redox balance. The function of these genes during the utilization of fermentative and respiratory carbon sources was studied. During growth in glucose, deletion of KlNDE1 and KlNDI1 led to an altered kinetic of ethanol and glycerol accumulation compared with the wild type; in addition, KlndiDelta was unable to grow in respiratory substrates. Northern analysis and GFP-fusion experiments showed that KlNDE1 and KlNDI1 regulate the expression of KlGUT2, a component of the glycerol-3-phosphate shuttle. Moreover, both genes seem to be involved in the biogenesis of the mitochondrial tubular network.
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Affiliation(s)
- Michele Saliola
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy.
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Domingues L, Guimarães PMR, Oliveira C. Metabolic engineering of Saccharomyces cerevisiae for lactose/whey fermentation. Bioeng Bugs 2009; 1:164-71. [PMID: 21326922 DOI: 10.4161/bbug.1.3.10619] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 11/19/2022] Open
Abstract
Lactose is an interesting carbon source for the production of several bio-products by fermentation, primarily because it is the major component of cheese whey, the main by-product of dairy activities. However, the microorganism more widely used in industrial fermentation processes, the yeast Saccharomyces cerevisiae, does not have a lactose metabolization system. Therefore, several metabolic engineering approaches have been used to construct lactose-consuming S. cerevisiae strains, particularly involving the expression of the lactose genes of the phylogenetically related yeast Kluyveromyces lactis, but also the lactose genes from Escherichia coli and Aspergillus niger, as reviewed here. Due to the existing large amounts of whey, the production of bio-ethanol from lactose by engineered S. cerevisiae has been considered as a possible route for whey surplus. Emphasis is given in the present review on strain improvement for lactose-to-ethanol bioprocesses, namely flocculent yeast strains for continuous high-cell-density systems with enhanced ethanol productivity.
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Affiliation(s)
- Lucília Domingues
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal.
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Roux AE, Chartrand P, Ferbeyre G, Rokeach LA. Fission yeast and other yeasts as emergent models to unravel cellular aging in eukaryotes. J Gerontol A Biol Sci Med Sci 2009; 65:1-8. [PMID: 19875745 DOI: 10.1093/gerona/glp152] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the past years, simple organisms such as yeasts and worms have contributed a great deal to aging research. Studies pioneered in Saccharomyces cerevisiae were useful to elucidate a significant number of molecular mechanisms underlying cellular aging and to discover novel longevity genes. Importantly, these genes proved many times to be conserved in multicellular eukaryotes. Consequently, such discovery approaches are being extended to other yeast models, such as Schizosaccharomyces pombe, Candida albicans, Kluyveromyces lactis, and Cryptococcus neoformans. In fission yeast, researchers have found links between asymmetrical cell division and nutrient signaling pathways with aging. In this review, we discuss the state of knowledge on the mechanisms controlling both replicative and chronological aging in S pombe and the other emergent yeast models.
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Affiliation(s)
- Antoine E Roux
- Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada.
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Oxygen-dependent transcriptional regulator Hap1p limits glucose uptake by repressing the expression of the major glucose transporter gene RAG1 in Kluyveromyces lactis. EUKARYOTIC CELL 2008; 7:1895-905. [PMID: 18806211 DOI: 10.1128/ec.00018-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The HAP1 (CYP1) gene product of Saccharomyces cerevisiae is known to regulate the transcription of many genes in response to oxygen availability. This response varies according to yeast species, probably reflecting the specific nature of their oxidative metabolism. It is suspected that a difference in the interaction of Hap1p with its target genes may explain some of the species-related variation in oxygen responses. As opposed to the fermentative S. cerevisiae, Kluyveromyces lactis is an aerobic yeast species which shows different oxygen responses. We examined the role of the HAP1-equivalent gene (KlHAP1) in K. lactis. KlHap1p showed a number of sequence features and some gene targets (such as KlCYC1) in common with its S. cerevisiae counterpart, and KlHAP1 was capable of complementing the hap1 mutation. However, the KlHAP1 disruptant showed temperature-sensitive growth on glucose, especially at low glucose concentrations. At normal temperature, 28 degrees C, the mutant grew well, the colony size being even greater than that of the wild type. The most striking observation was that KlHap1p repressed the expression of the major glucose transporter gene RAG1 and reduced the glucose uptake rate. This suggested an involvement of KlHap1p in the regulation of glycolytic flux through the glucose transport system. The DeltaKlhap1 mutant showed an increased ability to produce ethanol during aerobic growth, indicating a possible transformation of its physiological property to Crabtree positivity or partial Crabtree positivity. Dual roles of KlHap1p in activating respiration and repressing fermentation may be seen as a basis of the Crabtree-negative physiology of K. lactis.
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