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Roldán-López D, Groenewald M, Pérez-Torrado R. Fermentative and metabolic screening of candidate yeast strains hybridisable with Saccharomyces cerevisiae for beer production optimisation. Int J Food Microbiol 2025; 426:110899. [PMID: 39244812 DOI: 10.1016/j.ijfoodmicro.2024.110899] [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: 06/19/2024] [Revised: 08/20/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
Yeast optimisation has been crucial in improving the quality and efficiency of beer production, one of the world's most widely consumed beverages. In this context, rare mating hybridisation is a promising technique for yeast optimization to generate novel and improved non-GMO strains. The limitation of this technique is the lack of knowledge and comparable data on yeast strains hybridisable to Saccharomyces cerevisiae, probably the most important yeast species in beer production. Yeast from the genera Saccharomyces, Naumovozyma, Nakaseomyces and Kazachstania have been described to be able to form hybrids with S. cerevisiae. In the present study, 242 yeast strains were analysed under brewing conditions, including Saccharomyces species (S. cerevisiae, S. kudriavzevii, S. uvarum, S. eubayanus, S. paradoxus, S. mikatae, S. jurei and S. arboricola) and non-Saccharomyces species (Naumovozyma, Nakaseomyces and Kazaschtania), representing the full genetic variability (species and subpopulations) described up to the start of the study. The fermentation profile was analysed by monitoring weight loss during fermentation to determine kinetic parameters and CO2 production. Metabolic analysis was performed to determine the concentration of sugars (maltotriose, maltose and glucose), alcohols (ethanol, glycerol and 2,3-butanediol) and organic acids (malic acid, succinic acid and acetic acid). Maltose and maltotriose are the predominant sugars in beer wort. The ability to consume these sugars determines the characteristics of the final product. Dataset comparisons were then made at species, subpopulation and isolation source level. The results obtained in this study demonstrate the great phenotypic variability that exists within the genus Saccharomyces and within each species of this genus, which could be useful in the generation of optimised brewing hybrids. Yeasts with different fermentative capacities and fermentative behaviours can be found under brewing conditions. S. cerevisiae, S. uvarum and S. eubayanus are the species that contain strains with similar fermentation performance to commercial strains.
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Affiliation(s)
- David Roldán-López
- Instituto de Agroquímica y Tecnología de Alimentos, IATA-CSIC, Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | | | - Roberto Pérez-Torrado
- Instituto de Agroquímica y Tecnología de Alimentos, IATA-CSIC, Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain.
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Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters. Mol Biol Evol 2024; 41:msae228. [PMID: 39492761 PMCID: PMC11571961 DOI: 10.1093/molbev/msae228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/22/2024] [Accepted: 10/25/2024] [Indexed: 11/05/2024] Open
Abstract
Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ∼400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
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Affiliation(s)
- Johnathan G Crandall
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
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3
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Hernández-Vásquez CI, García-García JH, Pérez-Ortega ER, Martínez-Segundo AG, Damas-Buenrostro LC, Pereyra-Alférez B. Expression patterns of Mal genes and association with differential maltose and maltotriose transport rate of two Saccharomyces pastorianus yeasts. Appl Environ Microbiol 2024; 90:e0039724. [PMID: 38975758 PMCID: PMC11267901 DOI: 10.1128/aem.00397-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 07/09/2024] Open
Abstract
Beer brewing is a well-known process that still faces great challenges, such as the total consumption of sugars present in the fermentation media. Lager-style beer, a major worldwide beer type, is elaborated by Saccharomyces pastorianus (Sp) yeast, which must ferment high maltotriose content worts, but its consumption represents a notable problem, especially among Sp strains belonging to group I. Factors, such as fermentation conditions, presence of maltotriose transporters, transporter copy number variation, and genetic regulation variations contribute to this issue. We assess the factors affecting fermentation in two Sp yeast strains: SpIB1, with limited maltotriose uptake, and SpIB2, known for efficient maltotriose transport. Here, SpIB2 transported significantly more maltose (28%) and maltotriose (32%) compared with SpIB1. Furthermore, SpIB2 expressed all MAL transporters (ScMALx1, SeMALx1, ScAGT1, SeAGT1, MTT1, and MPHx) on the first day of fermentation, whereas SpIB1 only exhibited ScMalx1, ScAGT1, and MPH2/3 genes. Some SpIB2 transporters had polymorphic transmembrane domains (TMD) resembling MTT1, accompanied by higher expression of these transporters and its positive regulator genes, such as MAL63. These findings suggest that, in addition to the factors mentioned above, positive regulators of Mal transporters contribute significantly to phenotypic diversity in maltose and maltotriose consumption among the studied lager yeast strains.IMPORTANCEBeer, the third most popular beverage globally with a 90% market share in the alcoholic beverage industry, relies on Saccharomyces pastorianus (Sp) strains for lager beer production. These strains exhibit phenotypic diversity in maltotriose consumption, a crucial process for the acceptable organoleptic profile in lager beer. This diversity ranges from Sp group II strains with a notable maltotriose-consuming ability to Sp group I strains with limited capacity. Our study highlights that differential gene expression of maltose and maltotriose transporters and its upstream trans-elements, such as MAL gene-positive regulators, adds complexity to this variation. This insight can contribute to a more comprehensive analysis needed to the development of controlled and efficient biotechnological processes in the beer brewing industry.
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Affiliation(s)
- César I. Hernández-Vásquez
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
| | - Jorge H. García-García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
| | | | | | | | - Benito Pereyra-Alférez
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Instituto de Biotecnología, Nuevo León, Mexico
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Obsilova V, Obsil T. The yeast 14-3-3 proteins Bmh1 and Bmh2 regulate key signaling pathways. Front Mol Biosci 2024; 11:1327014. [PMID: 38328397 PMCID: PMC10847541 DOI: 10.3389/fmolb.2024.1327014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Cell signaling regulates several physiological processes by receiving, processing, and transmitting signals between the extracellular and intracellular environments. In signal transduction, phosphorylation is a crucial effector as the most common posttranslational modification. Selectively recognizing specific phosphorylated motifs of target proteins and modulating their functions through binding interactions, the yeast 14-3-3 proteins Bmh1 and Bmh2 are involved in catabolite repression, carbon metabolism, endocytosis, and mitochondrial retrograde signaling, among other key cellular processes. These conserved scaffolding molecules also mediate crosstalk between ubiquitination and phosphorylation, the spatiotemporal control of meiosis, and the activity of ion transporters Trk1 and Nha1. In humans, deregulation of analogous processes triggers the development of serious diseases, such as diabetes, cancer, viral infections, microbial conditions and neuronal and age-related diseases. Accordingly, the aim of this review article is to provide a brief overview of the latest findings on the functions of yeast 14-3-3 proteins, focusing on their role in modulating the aforementioned processes.
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Affiliation(s)
- Veronika Obsilova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Structural Biology of Signaling Proteins, Division, BIOCEV, Vestec, Czechia
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia
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Navale AM. Glucose Transporter and Sensor Mechanisms in Fungal Pathogens as Potential Drug Targets. Curr Rev Clin Exp Pharmacol 2024; 19:250-258. [PMID: 37861001 DOI: 10.2174/0127724328263050230923154326] [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: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023]
Abstract
Fungal infections are emerging as major health challenges in recent years. The development of resistance against existing antifungal agents needs urgent attention and action. The limited classes of antifungal drugs available, their tendency to cause adverse effects, lack of effectiveness, etc., are the major limitations of current therapy. Thus, there is a pressing demand for new antifungal drug classes to cope with the present circumstances. Glucose is the key source of energy for all organisms, including fungi. Glucose plays a crucial role as a source of carbon and energy for processes like virulence, growth, invasion, biofilm formation, and resistance development. The glucose transport and sensing mechanisms are well developed in these organisms as an important strategy to sustain survival. Modulating these transport or sensor mechanisms may serve as an important strategy to inhibit fungal growth. Moreover, the structural difference between human and fungal glucose transporters makes them more appealing as drug targets. Limited literature is available for fungal glucose entry mechanisms. This review provides a comprehensive account of sugar transport mechanisms in common fungal pathogens.
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Affiliation(s)
- Archana Mohit Navale
- Department of Pharmacology, Parul Institute of Pharmacy, Parul University, Limda, India
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Besada-Lombana PB, Chen W, Da Silva NA. An extracellular glucose sensor for substrate-dependent secretion and display of cellulose-degrading enzymes. Biotechnol Bioeng 2024; 121:403-408. [PMID: 37749915 DOI: 10.1002/bit.28549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
The efficient hydrolysis of lignocellulosic biomass into fermentable sugars is key for viable economic production of biofuels and biorenewable chemicals from second-generation feedstocks. Consolidated bioprocessing (CBP) combines lignocellulose saccharification and chemical production in a single step. To avoid wasting valuable resources during CBP, the selective secretion of enzymes (independent or attached to the surface) based on the carbon source available is advantageous. To enable enzyme expression and secretion based on extracellular glucose levels, we implemented a G-protein-coupled receptor (GPCR)-based extracellular glucose sensor; this allows the secretion and display of cellulases in the presence of the cellulosic fraction of lignocellulose by leveraging cellobiose-dependent signal amplification. We focused on the glucose-responsiveness of the HXT1 promoter and engineered PHXT1 by changing its core to that of the strong promoter PTHD3 , increasing extracellular enzyme activity by 81%. We then demonstrated glucose-mediated expression and cell-surface display of the β-glucosidase BglI on the surface of Saccharomyces cerevisiae. The display system was further optimized by re-directing fatty acid pools from lipid droplet synthesis toward formation of membrane precursors via knock-out of PAH1. This resulted in an up to 4.2-fold improvement with respect to the baseline strain. Finally, we observed cellobiose-dependent signal amplification of the system with an increase in enzymatic activity of up to 3.1-fold when cellobiose was added.
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Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
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Xiao C, Pan Y, Huang M. Advances in the dynamic control of metabolic pathways in Saccharomyces cerevisiae. ENGINEERING MICROBIOLOGY 2023; 3:100103. [PMID: 39628908 PMCID: PMC11610979 DOI: 10.1016/j.engmic.2023.100103] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 12/06/2024]
Abstract
The metabolic engineering of Saccharomyces cerevisiae has great potential for enhancing the production of high-value chemicals and recombinant proteins. Recent studies have demonstrated the effectiveness of dynamic regulation as a strategy for optimizing metabolic flux and improving production efficiency. In this review, we provide an overview of recent advancements in the dynamic regulation of S. cerevisiae metabolism. Here, we focused on the successful utilization of transcription factor (TF)-based biosensors within the dynamic regulatory network of S. cerevisiae. These biosensors are responsive to a wide range of endogenous and exogenous signals, including chemical inducers, light, temperature, cell density, intracellular metabolites, and stress. Additionally, we explored the potential of omics tools for the discovery of novel responsive promoters and their roles in fine-tuning metabolic networks. We also provide an outlook on the development trends in this field.
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Affiliation(s)
- Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
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8
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Crandall JG, Fisher KJ, Sato TK, Hittinger CT. Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism. PLoS Biol 2023; 21:e3001909. [PMID: 37943740 PMCID: PMC10635434 DOI: 10.1371/journal.pbio.3001909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kaitlin J. Fisher
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Donzella L, Sousa MJ, Morrissey JP. Evolution and functional diversification of yeast sugar transporters. Essays Biochem 2023; 67:811-827. [PMID: 36928992 PMCID: PMC10500205 DOI: 10.1042/ebc20220233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
While simple sugars such as monosaccharides and disaccharide are the typical carbon source for most yeasts, whether a species can grow on a particular sugar is generally a consequence of presence or absence of a suitable transporter to enable its uptake. The most common transporters that mediate sugar import in yeasts belong to the major facilitator superfamily (MFS). Some of these, for example the Saccharomyces cerevisiae Hxt proteins have been extensively studied, but detailed information on many others is sparce. In part, this is because there are many lineages of MFS transporters that are either absent from, or poorly represented in, the model S. cerevisiae, which actually has quite a restricted substrate range. It is important to address this knowledge gap to gain better understanding of the evolution of yeasts and to take advantage of sugar transporters to exploit or engineer yeasts for biotechnological applications. This article examines the full repertoire of MFS proteins in representative budding yeasts (Saccharomycotina). A comprehensive analysis of 139 putative sugar transporters retrieved from 10 complete genomes sheds new light on the diversity and evolution of this family. Using the phylogenetic lens, it is apparent that proteins have often been misassigned putative functions and this can now be corrected. It is also often seen that patterns of expansion of particular genes reflects the differential importance of transport of specific sugars (and related molecules) in different yeasts, and this knowledge also provides an improved resource for the selection or design of tailored transporters.
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Affiliation(s)
- Lorena Donzella
- School of Microbiology, Environmental Research Institute, APC Microbiome Ireland, SUSFERM Research Centre, University College Cork, T12 K8AF, Cork, Ireland
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria João Sousa
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Ireland, SUSFERM Research Centre, University College Cork, T12 K8AF, Cork, Ireland
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Chen L, Chen B, Zhu QH, Zhang X, Sun T, Liu F, Yang Y, Sun J, Li Y. Identification of sugar transporter genes and their roles in the pathogenicity of Verticillium dahliae on cotton. FRONTIERS IN PLANT SCIENCE 2023; 14:1123523. [PMID: 36778686 PMCID: PMC9910176 DOI: 10.3389/fpls.2023.1123523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Verticillium wilt (VW) caused by Verticillium dahliae is a soil-borne vascular fungal disease that severely affects cotton yield and fiber quality. Sugar metabolism plays an important role in the growth and pathogenicity of V. dahliae. However, limited information is known about the sugar transporter genes and their roles in the growth and pathogenicity of V. dahliae. METHOD In this study, genome-wide identification of sugar transporter genes in V. dahliae was conducted and the expression profiles of these genes in response to root exudates from cotton varieties susceptible or resistant to V. dahliae were investigated based on RNA-seq data. Tobacco Rattle Virus-based host-induced gene silencing (TRV-based HIGS) and artificial small interfering RNAs (asiRNAs) were applied to investigate the function of candidate genes involved in the growth and pathogenic process of V. dahliae. RESULTS A total of 65 putative sugar transporter genes were identified and clustered into 8 Clades. Of the 65 sugar transporter genes, 9 were found to be induced only by root exudates from the susceptible variety, including VdST3 and VdST12 that were selected for further functional study. Silencing of VdST3 or VdST12 in host plants by TRV-based HIGS reduced fungal biomass and enhanced cotton resistance against V. dahliae. Additionally, silencing of VdST12 and VdST3 by feeding asiRNAs targeting VdST12 (asiR815 or asiR1436) and VdST3 (asiR201 or asiR1238) inhibited fungal growth, exhibiting significant reduction in hyphae and colony diameter, with a more significant effect observed for the asiRNAs targeting VdST12. The inhibitory effect of asiRNAs on the growth of V. dahliae was enhanced with the increasing concentration of asiRNAs. Silencing of VdST12 by feeding asiR815+asiR1436 significantly decreased the pathogenicity of V. dahliae. DISCUSSION The results suggest that VdST3 and VdST12 are sugar transporter genes required for growth and pathogenicity of V. dahliae and that asiRNA is a valuable tool for functional characterization of V. dahliae genes.
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Affiliation(s)
- Lihua Chen
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | - Bin Chen
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | | | - Xinyu Zhang
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | - Tiange Sun
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | - Feng Liu
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Jie Sun
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
| | - Yanjun Li
- The Key Laboratory of Oasis Eco-agriculture, Agriculture College, Shihezi University, Shihezi, Xinjiang, China
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Natural Variation in Diauxic Shift between Patagonian Saccharomyces eubayanus Strains. mSystems 2022; 7:e0064022. [PMID: 36468850 PMCID: PMC9765239 DOI: 10.1128/msystems.00640-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The study of natural variation can untap novel alleles with immense value for biotechnological applications. Saccharomyces eubayanus Patagonian isolates exhibit differences in the diauxic shift between glucose and maltose, representing a suitable model to study their natural genetic variation for novel strains for brewing. However, little is known about the genetic variants and chromatin regulators responsible for these differences. Here, we show how genome-wide chromatin accessibility and gene expression differences underlie distinct diauxic shift profiles in S. eubayanus. We identified two strains with a rapid diauxic shift between glucose and maltose (CL467.1 and CBS12357) and one strain with a remarkably low fermentation efficiency and longer lag phase during diauxic shift (QC18). This is associated in the QC18 strain with lower transcriptional activity and chromatin accessibility of specific genes of maltose metabolism and higher expression levels of glucose transporters. These differences are governed by the HAP complex, which differentially regulates gene expression depending on the genetic background. We found in the QC18 strain a contrasting phenotype to those phenotypes described in S. cerevisiae, where hap4Δ, hap5Δ, and cin5Δ knockouts significantly improved the QC18 growth rate in the glucose-maltose shift. The most profound effects were found between CIN5 allelic variants, suggesting that Cin5p could strongly activate a repressor of the diauxic shift in the QC18 strain but not necessarily in the other strains. The differences between strains could originate from the tree host from which the strains were obtained, which might determine the sugar source preference and the brewing potential of the strain. IMPORTANCE The diauxic shift has been studied in budding yeast under laboratory conditions; however, few studies have addressed the diauxic shift between carbon sources under fermentative conditions. Here, we study the transcriptional and chromatin structure differences that explain the natural variation in fermentative capacity and efficiency during diauxic shift of natural isolates of S. eubayanus. Our results show how natural genetic variants in transcription factors impact sugar consumption preferences between strains. These variants have different effects depending on the genetic background, with a contrasting phenotype to those phenotypes previously described in S. cerevisiae. Our study shows how relatively simple genetic/molecular modifications/editing in the lab can facilitate the study of natural variations of microorganisms for the brewing industry.
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Abstract
Although beer is a widely used beverage in many cultures, there is a need for a new drinking alternative in the face of rising issues such as health concerns or weight problems. However, non-alcoholic and low-alcoholic beers (NABLAB) still have some sensory problems that have not been fully remedied today, such as “wort-like”/”potato-like” flavours or a lack of aroma. These defects are due to the lack of alcohol (and the lack of the aldehyde-reducing effect of alcohol fermentation), as well as production techniques. The use of new yeast strains that cannot ferment maltose—the foremost sugar in the wort—is highly promising to produce a more palatable and sustainable NABLAB product because production with these yeast strains can be performed with standard brewery equipment. In the scientific literature, it is clear that interest in the production of NABLAB has increased recently, and experiments have been carried out with maltose-negative yeast strains isolated from many different environments. This study describes maltose-negative yeasts and their aromatic potential for the production of NABLAB by comprehensively examining recent academic studies.
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Lorca Mandujano GP, Alves HC, Prado CD, Martins JG, Novaes HR, Maia de Oliveira da Silva JP, Teixeira GS, Ohara A, Alves MH, Pedrino IC, Malavazi I, Paiva de Sousa C, da Cunha AF. Identification and selection of a new Saccharomyces cerevisiae strain isolated from Brazilian ethanol fermentation process for application in beer production. Food Microbiol 2022; 103:103958. [DOI: 10.1016/j.fm.2021.103958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 11/26/2022]
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Snf1p/Hxk2p/Mig1p pathway regulates hexose transporters transcript levels, affecting the exponential growth and mitochondrial respiration of Saccharomyces cerevisiae. Fungal Genet Biol 2022; 161:103701. [DOI: 10.1016/j.fgb.2022.103701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/12/2022] [Accepted: 04/30/2022] [Indexed: 11/19/2022]
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15
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Hanumantha Rao K, Roy K, Paul S, Ghosh S. N-acetylglucosamine transporter, Ngt1, undergoes sugar-responsive endosomal trafficking in Candida albicans. Mol Microbiol 2021; 117:429-449. [PMID: 34877729 DOI: 10.1111/mmi.14857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022]
Abstract
N-acetylglucosamine (GlcNAc), an important amino sugar at the infection sites of the fungal pathogen Candida albicans, triggers multiple cellular processes. GlcNAc import at the cell surface is mediated by GlcNAc transporter, Ngt1 which seems to play a critical role during GlcNAc signaling. We have investigated the Ngt1 dynamics that provide a platform for further studies aimed at understanding the mechanistic insights of regulating process(es) in C. albicans. The expression of this transporter is prolific and highly sensitive to even very low levels (˂2 µM) of GlcNAc. Under these conditions, Ngt1 undergoes phosphorylation-associated ubiquitylation as a code for internalization. This ubiquitylation process involves the triggering proteins like protein kinase Snf1, arrestin-related trafficking adaptors (ART) protein Rod1, and yeast ubiquitin ligase Rsp5. Interestingly, analysis of ∆snf1 and ∆rsp5 mutants revealed that while Rsp5 is promoting the endosomal trafficking of Ngt1-GFPɤ, Snf1 hinders the process. Furthermore, colocalization experiments of Ngt1 with Vps17 (an endosomal marker), Sec7 (a trans-Golgi marker), and a vacuolar marker revealed the fate of Ngt1 during sugar-responsive endosomal trafficking. ∆ras1 and ∆ubi4 mutants showed decreased ubiquitylation and delayed endocytosis of Ngt1. According to our knowledge, this is the first report which illustrates the mechanistic insights that are responsible for endosomal trafficking of a GlcNAc transporter in an eukaryotic organism.
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Affiliation(s)
- Kongara Hanumantha Rao
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India.,Central Instrumentation Facility, Division of Research and Development, Lovely Professional University, Phagwara, India
| | - Kasturi Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India
| | - Soumita Paul
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India
| | - Swagata Ghosh
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India
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16
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Shayevitz A, Abbott E, Van Zandycke S, Fischborn T. The Impact of Lactic and Acetic Acid on Primary Beer Fermentation Performance and Secondary Re-Fermentation during Bottle-Conditioning with Active Dry Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1952508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Avi Shayevitz
- Research & Development, Lallemand Inc., Montreal, Quebec, Canada
| | - Eric Abbott
- Research & Development, Lallemand Inc., Montreal, Quebec, Canada
| | | | - Tobias Fischborn
- Research & Development, Lallemand Inc., Montreal, Quebec, Canada
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17
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Chen X, Wang Y, He CY, Wang GL, Zhang GC, Wang CL, Wang DH, Zou X, Wei GY. Improved production of β-glucan by a T-DNA-based mutant of Aureobasidium pullulans. Appl Microbiol Biotechnol 2021; 105:6887-6898. [PMID: 34448899 DOI: 10.1007/s00253-021-11538-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/26/2022]
Abstract
To improve β-1,3-1,6-D-glucan (β-glucan) production by Aureobasidium pullulans, an Agrobacterium tumefaciens-mediated transformation method was developed to screen a mutant A. pullulans CGMCC 19650. Based on thermal asymmetric-interlaced PCR detection, DNA sequencing, BLAST analysis, and quantitative real-time PCR assay, the T-DNA was identified to be inserted in the coding region of mal31 gene, which encodes a sugar transporter involved in pullulan biosynthesis in the mutant. The maximal biomass and β-glucan production under batch fermentation were significantly increased by 47.6% and 78.6%, respectively, while pullulan production was decreased by 41.7% in the mutant, as compared to the parental strain A. pullulans CCTCC M 2012259. Analysis of the physiological mechanism of these changes revealed that mal31 gene disruption increased the transcriptional levels of pgm2, ugp, fks1, and kre6 genes; increased the amounts of key enzymes associated with UDPG and β-glucan biosynthesis; and improved intracellular UDPG contents and energy supply, all of which favored β-glucan production. However, the T-DNA insertion decreased the transcriptional levels of ags2 genes, and reduced the biosynthetic capability to form pullulan, resulting in the decrease in pullulan production. This study not only provides an effective approach for improved β-glucan production by A. pullulans, but also presents an accurate and useful gene for metabolic engineering of the producer for efficient polysaccharide production. KEY POINTS: • A mutant A. pullulans CGMCC 19650 was screened by using the ATMT method. • The mal31 gene encoding a sugar transporter was disrupted in the mutant. • β-Glucan produced by the mutant was significantly improved.
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Affiliation(s)
- Xing Chen
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Ying Wang
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Chao-Yong He
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Guo-Liang Wang
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Gao-Chuan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Chong-Long Wang
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Da-Hui Wang
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China
| | - Xiang Zou
- College of Pharmaceutical Sciences, Southwest University, 2# TianSheng Road, Beibei, Chongqing, 400715, People's Republic of China.
| | - Gong-Yuan Wei
- School of Biology and Basic Medical Sciences, Soochow University, 199# Ren'ai Road, Suzhou, 215123, People's Republic of China.
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18
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Different Gene Expression Patterns of Hexose Transporter Genes Modulate Fermentation Performance of Four Saccharomyces cerevisiae Strains. FERMENTATION 2021. [DOI: 10.3390/fermentation7030164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In Saccharomyces cerevisiae, the fermentation rate and the ability to complete the sugar transformation process depend on the glucose and fructose transporter set-up. Hexose transport mainly occurs via facilitated diffusion carriers and these are encoded by the HXT gene family and GAL2. In addition, FSY1, coding a fructose/H+ symporter, was identified in some wine strains. This little-known transporter could be relevant in the last part of the fermentation process when fructose is the most abundant sugar. In this work, we investigated the gene expression of the hexose transporters during late fermentation phase, by means of qPCR. Four S. cerevisiae strains (P301.9, R31.3, R008, isolated from vineyard, and the commercial EC1118) were considered and the transporter gene expression levels were determined to evaluate how the strain gene expression pattern modulated the late fermentation process. The very low global gene expression and the poor fermentation performance of R008 suggested that the overall expression level is a determinant to obtain the total sugar consumption. Each strain showed a specific gene expression profile that was strongly variable. This led to rethinking the importance of the HXT3 gene that was previously considered to play a major role in sugar transport. In vineyard strains, other transporter genes, such as HXT6/7, HXT8, and FSY1, showed higher expression levels, and the resulting gene expression patterns properly supported the late fermentation process.
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19
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Tamayo Rojas SA, Schmidl S, Boles E, Oreb M. Glucose-induced internalization of the S. cerevisiae galactose permease Gal2 is dependent on phosphorylation and ubiquitination of its aminoterminal cytoplasmic tail. FEMS Yeast Res 2021; 21:6206829. [PMID: 33791789 DOI: 10.1093/femsyr/foab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
The hexose permease Gal2 of Saccharomyces cerevisiae is expressed only in the presence of its physiological substrate galactose. Glucose tightly represses the GAL2 gene and also induces the clearance of the transporter from the plasma membrane by ubiquitination and subsequent degradation in the vacuole. Although many factors involved in this process, especially those responsible for the upstream signaling, have been elucidated, the mechanisms by which Gal2 is specifically targeted by the ubiquitination machinery have remained elusive. Here, we show that ubiquitination occurs within the N-terminal cytoplasmic tail and that the arrestin-like proteins Bul1 and Rod1 are likely acting as adaptors for docking of the ubiquitin E3-ligase Rsp5. We further demonstrate that phosphorylation on multiple residues within the tail is indispensable for the internalization and possibly represents a primary signal that might trigger the recruitment of arrestins to the transporter. In addition to these new fundamental insights, we describe Gal2 mutants with improved stability in the presence of glucose, which should prove valuable for engineering yeast strains utilizing complex carbohydrate mixtures present in hydrolysates of lignocellulosic or pectin-rich biomass.
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Affiliation(s)
- Sebastian A Tamayo Rojas
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Sina Schmidl
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
| | - Mislav Oreb
- Faculty of Biological Sciences, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, Frankfurt am Main 60438, Germany
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20
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Li J, Liu Q, Li J, Lin L, Li X, Zhang Y, Tian C. RCO-3 and COL-26 form an external-to-internal module that regulates the dual-affinity glucose transport system in Neurospora crassa. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:33. [PMID: 33509260 PMCID: PMC7841889 DOI: 10.1186/s13068-021-01877-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/07/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Low- and high-affinity glucose transport system is a conserved strategy of microorganism to cope with environmental glucose fluctuation for their growth and competitiveness. In Neurospora crassa, the dual-affinity glucose transport system consists of a low-affinity glucose transporter GLT-1 and two high-affinity glucose transporters HGT-1/HGT-2, which play diverse roles in glucose transport, carbon metabolism, and cellulase expression regulation. However, the regulation of this dual-transporter system in response to environmental glucose fluctuation is not yet clear. RESULTS In this study, we report that a regulation module consisting of a downstream transcription factor COL-26 and an upstream non-transporting glucose sensor RCO-3 regulates the dual-affinity glucose transport system in N. crassa. COL-26 directly binds to the promoter regions of glt-1, hgt-1, and hgt-2, whereas RCO-3 is an upstream factor of the module whose deletion mutant resembles the Δcol-26 mutant phenotypically. Transcriptional profiling analysis revealed that Δcol-26 and Δrco-3 mutants had similar transcriptional profiles, and both mutants had impaired response to a glucose gradient. We also showed that the AMP-activated protein kinase (AMPK) complex is involved in regulation of the glucose transporters. AMPK is required for repression of glt-1 expression in starvation conditions by inhibiting the activity of RCO-3. CONCLUSIONS RCO-3 and COL-26 form an external-to-internal module that regulates the glucose dual-affinity transport system. Transcription factor COL-26 was identified as the key regulator. AMPK was also involved in the regulation of the dual-transporter system. Our findings provide novel insight into the molecular basis of glucose uptake and signaling in filamentous fungi, which may aid in the rational design of fungal strains for industrial purposes.
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Affiliation(s)
- Jinyang Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Xiaolin Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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21
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Datamining and functional environmental genomics reassess the phylogenetics and functional diversity of fungal monosaccharide transporters. Appl Microbiol Biotechnol 2021; 105:647-660. [PMID: 33394157 DOI: 10.1007/s00253-020-11076-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Sugar transporters are essential components of carbon metabolism and have been extensively studied to control sugar uptake by yeasts and filamentous fungi used in fermentation processes. Based on published information on characterized fungal sugar porters, we show that this protein family encompasses phylogenetically distinct clades. While several clades encompass transporters that seemingly specialized on specific "sugar-related" molecules (e.g., myo-inositol, charged sugar analogs), others include mostly either mono- or di/oligosaccharide low-specificity transporters. To address the issue of substrate specificity of sugar transporters, that protein primary sequences do not fully reveal, we screened "multi-species" soil eukaryotic cDNA libraries for mannose transporters, a sugar that had never been used to select transporters. We obtained 19 environmental transporters, mostly from Basidiomycota and Ascomycota. Among them, one belonged to the unusual "Fucose H+ Symporter" family, which is only known in Fungi for a rhamnose transporter in Aspergillus niger. Functional analysis of the 19 transporters by expression in yeast and for two of them in Xenopus laevis oocytes for electrophysiological measurements indicated that most of them showed a preference for D-mannose over other tested D-C6 (glucose, fructose, galactose) or D-C5 (xylose) sugars. For the several glucose and fructose-negative transporters, growth of the corresponding recombinant yeast strains was prevented on mannose in the presence of one of these sugars that may act by competition for the binding site. Our results highlight the potential of environmental genomics to figure out the functional diversity of key fungal protein families and that can be explored in a context of biotechnology. KEY POINTS: • Most fungal sugar transporters accept several sugars as substrates. • Transporters, belonging to 2 protein families, were isolated from soil cDNA libraries. • Environmental transporters featured novel substrate specificities.
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22
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Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast. Metab Eng 2020; 65:243-254. [PMID: 33279674 DOI: 10.1016/j.ymben.2020.11.014] [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: 07/11/2020] [Revised: 11/04/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022]
Abstract
Proton coupled transport of α-glucosides via Mal11 into Saccharomyces cerevisiae costs one ATP per imported molecule. Targeted mutation of all three acidic residues in the active site resulted in sugar uniport, but expression of these mutant transporters in yeast did not enable growth on sucrose. We then isolated six unique transporter variants of these mutants by directed evolution of yeast for growth on sucrose. In three variants, new acidic residues emerged near the active site that restored proton-coupled sucrose transport, whereas the other evolved transporters still catalysed sucrose uniport. The localization of mutations and transport properties of the mutants enabled us to propose a mechanistic model of proton-coupled sugar transport by Mal11. Cultivation of yeast strains expressing one of the sucrose uniporters in anaerobic, sucrose-limited chemostat cultures indicated an increase in the efficiency of sucrose dissimilation by 21% when additional changes in strain physiology were taken into account. We thus show that a combination of directed and evolutionary engineering results in more energy efficient sucrose transport, as a starting point to engineer yeast strains with increased yields for industrially relevant products.
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23
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Bueno JGR, Borelli G, Corrêa TLR, Fiamenghi MB, José J, de Carvalho M, de Oliveira LC, Pereira GAG, dos Santos LV. Novel xylose transporter Cs4130 expands the sugar uptake repertoire in recombinant Saccharomyces cerevisiae strains at high xylose concentrations. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:145. [PMID: 32818042 PMCID: PMC7427733 DOI: 10.1186/s13068-020-01782-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/04/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND The need to restructure the world's energy matrix based on fossil fuels and mitigate greenhouse gas emissions stimulated the development of new biobased technologies for renewable energy. One promising and cleaner alternative is the use of second-generation (2G) fuels, produced from lignocellulosic biomass sugars. A major challenge on 2G technologies establishment is the inefficient assimilation of the five-carbon sugar xylose by engineered Saccharomyces cerevisiae strains, increasing fermentation time. The uptake of xylose across the plasma membrane is a critical limiting step and the budding yeast S. cerevisiae is not designed with a broad transport system and regulatory mechanisms to assimilate xylose in a wide range of concentrations present in 2G processes. RESULTS Assessing diverse microbiomes such as the digestive tract of plague insects and several decayed lignocellulosic biomasses, we isolated several yeast species capable of using xylose. Comparative fermentations selected the yeast Candida sojae as a potential source of high-affinity transporters. Comparative genomic analysis elects four potential xylose transporters whose properties were evaluated in the transporter null EBY.VW4000 strain carrying the xylose-utilizing pathway integrated into the genome. While the traditional xylose transporter Gxf1 allows an improved growth at lower concentrations (10 g/L), strains containing Cs3894 and Cs4130 show opposite responses with superior xylose uptake at higher concentrations (up to 50 g/L). Docking and normal mode analysis of Cs4130 and Gxf1 variants pointed out important residues related to xylose transport, identifying key differences regarding substrate translocation comparing both transporters. CONCLUSIONS Considering that xylose concentrations in second-generation hydrolysates can reach high values in several designed processes, Cs4130 is a promising novel candidate for xylose uptake. Here, we demonstrate a novel eukaryotic molecular transporter protein that improves growth at high xylose concentrations and can be used as a promising target towards engineering efficient pentose utilization in yeast.
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Affiliation(s)
- João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Guilherme Borelli
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
| | - Mateus Bernabe Fiamenghi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Juliana José
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Murilo de Carvalho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics-Institute of Biosciences, Humanities and Exact Sciences, UNESP, São Paulo State University, São José do Rio Preto, São Paulo 15054-000 Brazil
| | - Gonçalo A. G. Pereira
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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24
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Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P. Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device. Bio Protoc 2020; 10:e3668. [PMID: 33659338 DOI: 10.21769/bioprotoc.3668] [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: 11/25/2019] [Revised: 03/26/2020] [Accepted: 05/18/2020] [Indexed: 11/02/2022] Open
Abstract
The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of research is performed in simple homogeneous environments (e.g., bulk liquid cultures), which cannot capture full spatiotemporal community dynamics, studying biofilms or colonies is complex and usually does not give access to the spatiotemporal dynamics at single cell level. Here, we detail a protocol for generation of a microfluidic device, the "yeast machine", with arrays of long monolayers of yeast colonies to advance the global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined and customizable spatial dimensions. With Saccharomyces cerevisiae as a model yeast system we used the "yeast machine" to demonstrate the emergence of glucose gradients by following expression of fluorescently labelled hexose transporters. We further quantified the expression spatial patterns with intra-colony growth rates and expression of other genes regulated by glucose availability. In addition to this, we showed that gradients of amino acids also form within a colony, potentially opening similar approaches to study spatiotemporal formation of gradients of many other nutrients and metabolic waste products. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development, and morphogenesis in other same species or more complex multi-species systems at single-cell resolution and timescales relevant to ecology and evolution.
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Affiliation(s)
- Zoran S Marinkovic
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Clément Vulin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - Mislav Acman
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Xiaohu Song
- U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Jean Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France
| | - Ariel B Lindner
- U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,Institut Curie, PSL Research University, CNRS, Physico Chimie Curie, UMR 168, 75005, Paris, France.,Sorbonne Université, CNRS, Physico Chimie Curie, UMR 168, 75005, Paris, France
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25
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Kavatalkar V, Saini S, Bhat PJ. Role of Noise-Induced Cellular Variability in Saccharomyces cerevisiae During Metabolic Adaptation: Causes, Consequences and Ramifications. J Indian Inst Sci 2020. [DOI: 10.1007/s41745-020-00180-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Bellut K, Krogerus K, Arendt EK. Lachancea fermentati Strains Isolated From Kombucha: Fundamental Insights, and Practical Application in Low Alcohol Beer Brewing. Front Microbiol 2020; 11:764. [PMID: 32390994 PMCID: PMC7191199 DOI: 10.3389/fmicb.2020.00764] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023] Open
Abstract
With a growing interest in non-alcoholic and low alcohol beer (NABLAB), researchers are looking into non-conventional yeasts to harness their special metabolic traits for their production. One of the investigated species is Lachancea fermentati, which possesses the uncommon ability to produce significant amounts of lactic acid during alcoholic fermentation, resulting in the accumulation of lactic acid while exhibiting reduced ethanol production. In this study, four Lachancea fermentati strains isolated from individual kombucha cultures were investigated. Whole genome sequencing was performed, and the strains were characterized for important brewing characteristics (e.g., sugar utilization) and sensitivities toward stress factors. A screening in wort extract was performed to elucidate strain-dependent differences, followed by fermentation optimization to enhance lactic acid production. Finally, a low alcohol beer was produced at 60 L pilot-scale. The genomes of the kombucha isolates were diverse and could be separated into two phylogenetic groups, which were related to their geographical origin. Compared to a Saccharomyces cerevisiae brewers' yeast, the strains' sensitivities to alcohol and acidic conditions were low, while their sensitivities toward osmotic stress were higher. In the screening, lactic acid production showed significant, strain-dependent differences. Fermentation optimization by means of response surface methodology (RSM) revealed an increased lactic acid production at a low pitching rate, high fermentation temperature, and high extract content. It was shown that a high initial glucose concentration led to the highest lactic acid production (max. 18.0 mM). The data indicated that simultaneous lactic acid production and ethanol production occurred as long as glucose was present. When glucose was depleted and/or lactic acid concentrations were high, the production shifted toward the ethanol pathway as the sole pathway. A low alcohol beer (<1.3% ABV) was produced at 60 L pilot-scale by means of stopped fermentation. The beer exhibited a balanced ratio of sweetness from residual sugars and acidity from the lactic acid produced (13.6 mM). However, due to the stopped fermentation, high levels of diacetyl were present, which could necessitate further process intervention to reduce concentrations to acceptable levels.
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Affiliation(s)
- Konstantin Bellut
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | | | - Elke K. Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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27
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Colomer MS, Chailyan A, Fennessy RT, Olsson KF, Johnsen L, Solodovnikova N, Forster J. Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications. Front Microbiol 2020; 11:637. [PMID: 32373090 PMCID: PMC7177047 DOI: 10.3389/fmicb.2020.00637] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Brettanomyces yeasts have gained popularity in many sectors of the biotechnological industry, specifically in the field of beer production, but also in wine and ethanol production. Their unique properties enable Brettanomyces to outcompete conventional brewer’s yeast in industrially relevant traits such as production of ethanol and pleasant flavors. Recent advances in next-generation sequencing (NGS) and high-throughput screening techniques have facilitated large population studies allowing the selection of appropriate yeast strains with improved traits. In order to get a better understanding of Brettanomyces species and its potential for beer production, we sequenced the whole genome of 84 strains, which we make available to the scientific community and carried out several in vitro assays for brewing-relevant properties. The collection includes isolates from different substrates and geographical origin. Additionally, we have included two of the oldest Carlsberg Research Laboratory isolates. In this study, we reveal the phylogenetic pattern of Brettanomyces species by comparing the predicted proteomes of each strain. Furthermore, we show that the Brettanomyces collection is well described using similarity in genomic organization, and that there is a direct correlation between genomic background and phenotypic characteristics. Particularly, genomic patterns affecting flavor production, maltose assimilation, beta-glucosidase activity, and phenolic off-flavor (POF) production are reported. This knowledge yields new insights into Brettanomyces population survival strategies, artificial selection pressure, and loss of carbon assimilation traits. On a species-specific level, we have identified for the first time a POF negative Brettanomyces anomalus strain, without the main spoilage character of Brettanomyces species. This strain (CRL-90) has lost DaPAD1, making it incapable of converting ferulic acid to 4-ethylguaiacol (4-EG) and 4-ethylphenol (4-EP). This loss of function makes CRL-90 a good candidate for the production of characteristic Brettanomyces flavors in beverages, without the contaminant increase in POF. Overall, this study displays the potential of exploring Brettanomyces yeast species biodiversity to find strains with relevant properties applicable to the brewing industry.
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Affiliation(s)
- Marc Serra Colomer
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark.,National Institute for Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Chailyan
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Ross T Fennessy
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Kim Friis Olsson
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | | | | | - Jochen Forster
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
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28
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Designing New Yeasts for Craft Brewing: When Natural Biodiversity Meets Biotechnology. BEVERAGES 2020. [DOI: 10.3390/beverages6010003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Beer is a fermented beverage with a history as old as human civilization. Ales and lagers are by far the most common beers; however, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the range of products, especially in the craft brewery sector. Fermentation is one of the widest spaces for innovation in the brewing process. Besides Saccharomyces cerevisiae ale and Saccharomyces pastorianus lager strains conventionally used in macro-breweries, there is an increasing demand for novel yeast starter cultures tailored for producing beer styles with diversified aroma profiles. Recently, four genetic engineering-free approaches expanded the genetic background and the phenotypic biodiversity of brewing yeasts and allowed novel costumed-designed starter cultures to be developed: (1) the research for new performant S. cerevisiae yeasts from fermented foods alternative to beer; (2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts; (3) the exploitation of evolutionary engineering approaches; (4) the usage of non-Saccharomyces yeasts. Here, we summarized the pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. The resulting correlation maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts, enhancing the portfolio of diversified products offered to the final customer.
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29
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Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol 2019; 3:1576-1586. [PMID: 31636426 DOI: 10.1038/s41559-019-0998-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022]
Abstract
The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.
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Affiliation(s)
- Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - EmilyClare P Baker
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ursula Bond
- Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. .,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. .,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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30
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Zhang P, Chen Q, Fu G, Xia L, Hu X. Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae. World J Microbiol Biotechnol 2019; 35:112. [PMID: 31286266 DOI: 10.1007/s11274-019-2684-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 06/26/2019] [Indexed: 12/19/2022]
Abstract
Microorganisms have evolved permeases to incorporate various essential nutrients and exclude harmful products, which assists in adaptation to different environmental conditions for survival. As permeases are directly involved in the utilization of and regulatory response to nutrient sources, metabolic engineering of microbial permeases can predictably influence nutrient metabolism and regulation. In this mini-review, we have summarized the mechanisms underlying the general regulation of permeases, and the current advancements and future prospects of metabolic engineering strategies targeting the permeases in Saccharomyces cerevisiae. The different types of permeases and their regulatory mechanisms have been discussed. Furthermore, methods for metabolic engineering of permeases have been highlighted. Understanding the mechanisms via which permeases are meticulously regulated and engineered will not only facilitate research on regulation of global nutrition and yeast metabolic engineering, but can also provide important insights for future studies on the synthesis of valuable products and elimination of harmful substances in S. cerevisiae.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China.,School of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang, 330047, Jiangxi, China
| | - Qian Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China.,School of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang, 330047, Jiangxi, China
| | - Guiming Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China.,School of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang, 330047, Jiangxi, China
| | - Linglin Xia
- Department of Software, Nanchang University, Nanchang, 330047, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, China. .,School of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang, 330047, Jiangxi, China.
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31
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Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P. A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies. eLife 2019; 8:e47951. [PMID: 31259688 PMCID: PMC6624017 DOI: 10.7554/elife.47951] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023] Open
Abstract
Microbial colonies are fascinating structures in which growth and internal organization reflect complex morphogenetic processes. Here, we generated a microfluidics device with arrays of long monolayer yeast colonies to further global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined boundary conditions. We observed the emergence of stable glucose gradients using fluorescently labeled hexose transporters and quantified the spatial correlations with intra-colony growth rates and expression of other genes regulated by glucose availability. These landscapes depended on the external glucose concentration as well as secondary gradients, for example amino acid availability. This work demonstrates the regulatory genetic networks governing cellular physiological adaptation are the key to internal structuration of cellular assemblies. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development and morphogenesis in more complex systems.
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Affiliation(s)
- Zoran S Marinkovic
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- U1001 INSERMParisFrance
- CRIUniversité de ParisParisFrance
| | - Clément Vulin
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- Institute of Biogeochemistry and Pollutant DynamicsETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyEawagDübendorfSwitzerland
| | - Mislav Acman
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- CRIUniversité de ParisParisFrance
| | | | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
| | | | - Pascal Hersen
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
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32
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Vakirlis N, Monerawela C, McManus G, Ribeiro O, McLysaght A, James T, Bond U. Evolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae. Yeast 2019; 36:425-437. [PMID: 30963617 DOI: 10.1002/yea.3391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/19/2022] Open
Abstract
The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a subset of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as "pan-genes," being part of the pangenome but not the core genome. Here, we describe the evolutionary journey and characterisation of a novel pan-gene, originally named hypothetical (HYPO) open-reading frame. Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to Saccharomyces paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and Saccharomyces pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The overexpression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium-containing glucose, maltose, maltotriose, or wort at different concentrations.
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Affiliation(s)
- Nikolaos Vakirlis
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Chandre Monerawela
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Gavin McManus
- School of Biochemistry and Immunology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Orquidea Ribeiro
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Aoife McLysaght
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Tharappel James
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Ursula Bond
- School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin 2, Ireland
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33
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Todd RT, Wikoff TD, Forche A, Selmecki A. Genome plasticity in Candida albicans is driven by long repeat sequences. eLife 2019; 8:45954. [PMID: 31172944 PMCID: PMC6591007 DOI: 10.7554/elife.45954] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to novel environments. In the human fungal pathogen Candida albicans, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65-6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
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Affiliation(s)
- Robert T Todd
- Creighton University Medical School, Omaha, United States
| | - Tyler D Wikoff
- Creighton University Medical School, Omaha, United States
| | | | - Anna Selmecki
- Creighton University Medical School, Omaha, United States
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34
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Baker EP, Hittinger CT. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genet 2019; 15:e1007786. [PMID: 30946740 PMCID: PMC6448821 DOI: 10.1371/journal.pgen.1007786] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022] Open
Abstract
At the molecular level, the evolution of new traits can be broadly divided between changes in gene expression and changes in protein-coding sequence. For proteins, the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units. In Saccharomyces, the uptake of the sugar maltotriose into the cell is the primary limiting factor in its utilization, but maltotriose transporters are relatively rare, except in brewing strains. No known wild strains of Saccharomyces eubayanus, the cold-tolerant parent of hybrid lager-brewing yeasts (Saccharomyces cerevisiae x S. eubayanus), are able to consume maltotriose, which limits their ability to fully ferment malt extract. In one strain of S. eubayanus, we found a gene closely related to a known maltotriose transporter and were able to confer maltotriose consumption by overexpressing this gene or by passaging the strain on maltose. Even so, most wild strains of S. eubayanus lack native maltotriose transporters. To determine how this rare trait could evolve in naive genetic backgrounds, we performed an adaptive evolution experiment for maltotriose consumption, which yielded a single strain of S. eubayanus able to grow on maltotriose. We mapped the causative locus to a gene encoding a novel chimeric transporter that was formed by an ectopic recombination event between two genes encoding transporters that are unable to import maltotriose. In contrast to classic models of the evolution of novel protein functions, the recombination breakpoints occurred within a single functional domain. Thus, the ability of the new protein to carry maltotriose was likely acquired through epistatic interactions between independently evolved substitutions. By acquiring multiple mutations at once, the transporter rapidly gained a novel function, while bypassing potentially deleterious intermediate steps. This study provides an illuminating example of how recombination between paralogs can establish novel interactions among substitutions to create adaptive functions. Hybrids of the yeasts Saccharomyces cerevisiae and Saccharomyces eubayanus (lager-brewing yeasts) dominate the modern brewing industry. S. cerevisiae, also known as baker’s yeast, is well-known for its role in industry and scientific research. Less well recognized is S. eubayanus, which was only discovered as a pure species in 2011. While most lager-brewing yeasts rapidly and completely utilize the important brewing sugar maltotriose, no strain of S. eubayanus isolated to date is known to do so. Despite being unable to consume maltotriose, we identified one strain of S. eubayanus carrying a gene for a functional maltotriose transporter, although most strains lack this gene. During an adaptive evolution experiment, a strain of S. eubayanus without native maltotriose transporters evolved the ability to grow on maltotriose. Maltotriose consumption in the evolved strain resulted from a chimeric transporter that arose by shuffling genes encoding parent proteins that were unable to transport maltotriose. Traditionally, functional chimeric proteins are thought to evolve by shuffling discrete functional domains or modules, but the breakpoints in the chimera studied here occurred within the single functional module of the protein. These results support the less well-recognized role of shuffling duplicate gene sequences to generate novel proteins with adaptive functions.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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35
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Duan SF, Shi JY, Yin Q, Zhang RP, Han PJ, Wang QM, Bai FY. Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage. Curr Biol 2019; 29:1126-1136.e5. [PMID: 30905601 DOI: 10.1016/j.cub.2019.02.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/04/2019] [Accepted: 02/15/2019] [Indexed: 11/26/2022]
Abstract
Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.
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Affiliation(s)
- Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Qi Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China.
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36
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Welkenhuysen N, Schnitzer B, Österberg L, Cvijovic M. Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways. Front Physiol 2019; 9:1964. [PMID: 30719010 PMCID: PMC6348271 DOI: 10.3389/fphys.2018.01964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/31/2018] [Indexed: 12/16/2022] Open
Abstract
Systems biology approaches provide means to study the interplay between biological processes leading to the mechanistic understanding of the properties of complex biological systems. Here, we developed a vector format rule-based Boolean logic model of the yeast S. cerevisiae cAMP-PKA, Snf1, and the Snf3-Rgt2 pathway to better understand the role of crosstalk on network robustness and function. We identified that phosphatases are the common unknown components of the network and that crosstalk from the cAMP-PKA pathway to other pathways plays a critical role in nutrient sensing events. The model was simulated with known crosstalk combinations and subsequent analysis led to the identification of characteristics and impact of pathway interconnections. Our results revealed that the interconnections between the Snf1 and Snf3-Rgt2 pathway led to increased robustness in these signaling pathways. Overall, our approach contributes to the understanding of the function and importance of crosstalk in nutrient signaling.
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Affiliation(s)
- Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Barbara Schnitzer
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Linnea Österberg
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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37
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Henderson RK, Fendler K, Poolman B. Coupling efficiency of secondary active transporters. Curr Opin Biotechnol 2018; 58:62-71. [PMID: 30502621 DOI: 10.1016/j.copbio.2018.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Secondary active transporters are fundamental to a myriad of biological processes. They use the electrochemical gradient of one solute to drive transport of another solute against its concentration gradient. Central to this mechanism is that the transport of one does not occur in the absence of the other. However, like in most of biology, imperfections in the coupling mechanism exist and we argue that these are innocuous and may even be beneficial for the cell. We discuss the energetics and kinetics of alternating-access in secondary transport and focus on the mechanistic aspects of imperfect coupling that give rise to leak pathways. Additionally, inspection of available transporter structures gives valuable insight into coupling mechanics, and we review literature where proteins have been altered to change their coupling efficiency.
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Affiliation(s)
- Ryan K Henderson
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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38
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Regulation of Aspergillus nidulans CreA-Mediated Catabolite Repression by the F-Box Proteins Fbx23 and Fbx47. mBio 2018; 9:mBio.00840-18. [PMID: 29921666 PMCID: PMC6016232 DOI: 10.1128/mbio.00840-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The attachment of one or more ubiquitin molecules by SCF (Skp-Cullin-F-box) complexes to protein substrates targets them for subsequent degradation by the 26S proteasome, allowing the control of numerous cellular processes. Glucose-mediated signaling and subsequent carbon catabolite repression (CCR) are processes relying on the functional regulation of target proteins, ultimately controlling the utilization of this carbon source. In the filamentous fungus Aspergillus nidulans, CCR is mediated by the transcription factor CreA, which modulates the expression of genes encoding biotechnologically relevant enzymes. Although CreA-mediated repression of target genes has been extensively studied, less is known about the regulatory pathways governing CCR and this work aimed at further unravelling these events. The Fbx23 F-box protein was identified as being involved in CCR and the Δfbx23 mutant presented impaired xylanase production under repressing (glucose) and derepressing (xylan) conditions. Mass spectrometry showed that Fbx23 is part of an SCF ubiquitin ligase complex that is bridged via the GskA protein kinase to the CreA-SsnF-RcoA repressor complex, resulting in the degradation of the latter under derepressing conditions. Upon the addition of glucose, CreA dissociates from the ubiquitin ligase complex and is transported into the nucleus. Furthermore, casein kinase is important for CreA function during glucose signaling, although the exact role of phosphorylation in CCR remains to be determined. In summary, this study unraveled novel mechanistic details underlying CreA-mediated CCR and provided a solid basis for studying additional factors involved in carbon source utilization which could prove useful for biotechnological applications.IMPORTANCE The production of biofuels from plant biomass has gained interest in recent years as an environmentally friendly alternative to production from petroleum-based energy sources. Filamentous fungi, which naturally thrive on decaying plant matter, are of particular interest for this process due to their ability to secrete enzymes required for the deconstruction of lignocellulosic material. A major drawback in fungal hydrolytic enzyme production is the repression of the corresponding genes in the presence of glucose, a process known as carbon catabolite repression (CCR). This report provides previously unknown mechanistic insights into CCR through elucidating part of the protein-protein interaction regulatory system that governs the CreA transcriptional regulator in the reference organism Aspergillus nidulans in the presence of glucose and the biotechnologically relevant plant polysaccharide xylan.
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Peng M, Aguilar-Pontes MV, de Vries RP, Mäkelä MR. In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics. Front Microbiol 2018; 9:1045. [PMID: 29867914 PMCID: PMC5968117 DOI: 10.3389/fmicb.2018.01045] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Maria V Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
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Monoterpenoid perillyl alcohol impairs metabolic flexibility of Candida albicans by inhibiting glyoxylate cycle. Biochem Biophys Res Commun 2018; 495:560-566. [DOI: 10.1016/j.bbrc.2017.11.064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 01/27/2023]
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Henderson R, Poolman B. Proton-solute coupling mechanism of the maltose transporter from Saccharomyces cerevisiae. Sci Rep 2017; 7:14375. [PMID: 29084970 PMCID: PMC5662749 DOI: 10.1038/s41598-017-14438-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022] Open
Abstract
Mal11 catalyzes proton-coupled maltose transport across the plasma membrane of Saccharomyces cerevisiae. We used structure-based design of mutants and a kinetic analysis of maltose transport to determine the energy coupling mechanism of transport. We find that wildtype Mal11 is extremely well coupled and allows yeast to rapidly accumulate maltose to dangerous levels, resulting under some conditions in self-lysis. Three protonatable residues lining the central membrane-embedded cavity of Mal11 were identified as having potential roles in proton translocation. We probed the mechanistic basis for proton coupling with uphill and downhill transport assays and found that single mutants can still accumulate maltose but with a lower coupling efficiency than the wildtype. Next, we combined the individual mutations and created double and triple mutants. We found some redundancy in the functions of the acidic residues in proton coupling and that no single residue is most critical for proton coupling to maltose uptake, unlike what is usually observed in related transporters. Importantly, the triple mutants were completely uncoupled but still fully active in downhill efflux and equilibrium exchange. Together, these results depict a concerted mechanism of proton transport in Mal11 involving multiple charged residues.
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Affiliation(s)
- Ryan Henderson
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Adamczyk M, Szatkowska R. Low RNA Polymerase III activity results in up regulation of HXT2 glucose transporter independently of glucose signaling and despite changing environment. PLoS One 2017; 12:e0185516. [PMID: 28961268 PMCID: PMC5621690 DOI: 10.1371/journal.pone.0185516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/14/2017] [Indexed: 01/13/2023] Open
Abstract
Background Saccharomyces cerevisiae responds to glucose availability in the environment, inducing the expression of the low-affinity transporters and high-affinity transporters in a concentration dependent manner. This cellular decision making is controlled through finely tuned communication between multiple glucose sensing pathways including the Snf1-Mig1, Snf3/Rgt2-Rgt1 (SRR) and cAMP-PKA pathways. Results We demonstrate the first evidence that RNA Polymerase III (RNAP III) activity affects the expression of the glucose transporter HXT2 (RNA Polymerase II dependent—RNAP II) at the level of transcription. Down-regulation of RNAP III activity in an rpc128-1007 mutant results in a significant increase in HXT2 mRNA, which is considered to respond only to low extracellular glucose concentrations. HXT2 expression is induced in the mutant regardless of the growth conditions either at high glucose concentration or in the presence of a non-fermentable carbon source such as glycerol. Using chromatin immunoprecipitation (ChIP), we found an increased association of Rgt1 and Tup1 transcription factors with the highly activated HXT2 promoter in the rpc128-1007 strain. Furthermore, by measuring cellular abundance of Mth1 corepressor, we found that in rpc128-1007, HXT2 gene expression was independent from Snf3/Rgt2-Rgt1 (SRR) signaling. The Snf1 protein kinase complex, which needs to be active for the release from glucose repression, also did not appear perturbed in the mutated strain. Conclusions/Significance These findings suggest that the general activity of RNAP III can indirectly affect the RNAP II transcriptional machinery on the HXT2 promoter when cellular perception transduced via the major signaling pathways, broadly recognized as on/off switch essential to either positive or negative HXT gene regulation, remain entirely intact. Further, Rgt1/Ssn6-Tup1 complex, which has a dual function in gene transcription as a repressor-activator complex, contributes to HXT2 transcriptional activation.
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Affiliation(s)
- Malgorzata Adamczyk
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
- * E-mail:
| | - Roza Szatkowska
- Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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Marques WL, Mans R, Marella ER, Cordeiro RL, van den Broek M, Daran JMG, Pronk JT, Gombert AK, van Maris AJA. Elimination of sucrose transport and hydrolysis in Saccharomyces cerevisiae: a platform strain for engineering sucrose metabolism. FEMS Yeast Res 2017; 17:fox006. [PMID: 28087672 PMCID: PMC5424818 DOI: 10.1093/femsyr/fox006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2017] [Indexed: 12/17/2022] Open
Abstract
Many relevant options to improve efficacy and kinetics of sucrose metabolism in Saccharomyces cerevisiae and, thereby, the economics of sucrose-based processes remain to be investigated. An essential first step is to identify all native sucrose-hydrolysing enzymes and sucrose transporters in this yeast, including those that can be activated by suppressor mutations in sucrose-negative strains. A strain in which all known sucrose-transporter genes (MAL11, MAL21, MAL31, MPH2, MPH3) were deleted did not grow on sucrose after 2 months of incubation. In contrast, a strain with deletions in genes encoding sucrose-hydrolysing enzymes (SUC2, MAL12, MAL22, MAL32) still grew on sucrose. Its specific growth rate increased from 0.08 to 0.25 h−1 after sequential batch cultivation. This increase was accompanied by a 3-fold increase of in vitro sucrose-hydrolysis and isomaltase activities, as well as by a 3- to 5-fold upregulation of the isomaltase-encoding genes IMA1 and IMA5. One-step Cas9-mediated deletion of all isomaltase-encoding genes (IMA1-5) completely abolished sucrose hydrolysis. Even after 2 months of incubation, the resulting strain did not grow on sucrose. This sucrose-negative strain can be used as a platform to test metabolic engineering strategies and for fundamental studies into sucrose hydrolysis or transport.
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Affiliation(s)
- Wesley Leoricy Marques
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.,School of Food Engineering, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Eko Roy Marella
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | | | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 321] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
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Mahazar NH, Zakuan Z, Norhayati H, MeorHussin AS, Rukayadi Y. Optimization of Culture Medium for the Growth of Candida sp. and Blastobotrys sp. as Starter Culture in Fermentation of Cocoa Beans (Theobroma cacao) Using Response Surface Methodology (RSM). Pak J Biol Sci 2017; 20:154-159. [PMID: 29023007 DOI: 10.3923/pjbs.2017.154.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVE Inoculation of starter culture in cocoa bean fermentation produces consistent, predictable and high quality of fermented cocoa beans. It is important to produce healthy inoculum in cocoa bean fermentation for better fermented products. Inoculum could minimize the length of the lag phase in fermentation. The purpose of this study was to optimize the component of culture medium for the maximum cultivation of Candida sp. and Blastobotrys sp. MATERIALS AND METHODS Molasses and yeast extract were chosen as medium composition and Response Surface Methodology (RSM) was then employed to optimize the molasses and yeast extract. RESULTS Maximum growth of Candida sp. (7.63 log CFU mL-1) and Blastobotrys sp. (8.30 log CFU mL-1) were obtained from the fermentation. Optimum culture media for the growth of Candida sp., consist of 10% (w/v) molasses and 2% (w/v) yeast extract, while for Blastobotrys sp., were 1.94% (w/v) molasses and 2% (w/v) yeast extract. CONCLUSION This study shows that culture medium consists of molasses and yeast extract were able to produce maximum growth of Candida sp. and Blastobotrys sp., as a starter culture for cocoa bean fermentation.
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Affiliation(s)
- N H Mahazar
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Z Zakuan
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - H Norhayati
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - A S MeorHussin
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Y Rukayadi
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Wang B, Li J, Gao J, Cai P, Han X, Tian C. Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:17. [PMID: 28115989 PMCID: PMC5244594 DOI: 10.1186/s13068-017-0705-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/07/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND The glucose dual-affinity transport system (low- and high-affinity) is a conserved strategy used by microorganisms to cope with natural fluctuations in nutrient availability in the environment. The glucose-sensing and uptake processes are believed to be tightly associated with cellulase expression regulation in cellulolytic fungi. However, both the identities and functions of the major molecular components of this evolutionarily conserved system in filamentous fungi remain elusive. Here, we systematically identified and characterized the components of the glucose dual-affinity transport system in the model fungus Neurospora crassa. RESULTS Using RNA sequencing coupled with functional transport analyses, we assigned GLT-1 (Km = 18.42 ± 3.38 mM) and HGT-1/-2 (Km = 16.13 ± 0.95 and 98.97 ± 22.02 µM) to the low- and high-affinity glucose transport systems, respectively. The high-affinity transporters hgt-1/-2 complemented a moderate growth defect under high glucose when glt-1 was deleted. Simultaneous deletion of hgt-1/-2 led to extensive derepression of genes for plant cell wall deconstruction in cells grown on cellulose. The suppression by HGT-1/-2 was connected to both carbon catabolite repression (CCR) and the cyclic adenosine monophosphate-protein kinase A pathway. Alteration of a residue conserved across taxa in hexose transporters resulted in a loss of glucose-transporting function, whereas CCR signal transduction was retained, indicating dual functions for HGT-1/-2 as "transceptors." CONCLUSIONS In this study, GLT-1 and HGT-1/-2 were identified as the key components of the glucose dual-affinity transport system, which plays diverse roles in glucose transport and carbon metabolism. Given the wide conservation of the glucose dual-affinity transport system across fungal species, the identification of its components and their pleiotropic roles in this study shed important new light on the molecular basis of nutrient transport, signaling, and plant cell wall degradation in fungi.
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Affiliation(s)
- Bang Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingfang Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- School of Life Sciences, Heilongjiang University, Harbin, 150080 Heilongjiang China
| | - Pengli Cai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Xiaoyun Han
- School of Life Sciences, Heilongjiang University, Harbin, 150080 Heilongjiang China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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47
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Meister C, Gulko MK, Köhler AM, Braus GH. The devil is in the details: comparison between COP9 signalosome (CSN) and the LID of the 26S proteasome. Curr Genet 2016; 62:129-36. [PMID: 26497135 DOI: 10.1007/s00294-015-0525-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 01/29/2023]
Abstract
The COP9 signalosome (CSN) and the proteasomal LID are conserved macromolecular complexes composed of at least eight subunits with molecular weights of approximately 350 kDa. CSN and LID are part of the ubiquitin–proteasome pathway and cleave isopeptide linkages of lysine side chains on target proteins. CSN cleaves the isopeptide bond of ubiquitin-like protein Nedd8 from cullins, whereas the LID cleaves ubiquitin from target proteins sentenced for degradation. CSN and LID are structurally and functionally similar but the order of the assembly pathway seems to be different. The assembly differs in at least the last subunit joining the pre-assembled subcomplex. This review addresses the similarities and differences in structure, function and assembly of CSN and LID.
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48
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Protein abundance changes of Zygosaccharomyces rouxii in different sugar concentrations. Int J Food Microbiol 2016; 233:44-51. [PMID: 27322723 DOI: 10.1016/j.ijfoodmicro.2016.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/14/2016] [Accepted: 05/04/2016] [Indexed: 11/24/2022]
Abstract
Zygosaccharomyces rouxii is a yeast which can cause spoilage in the concentrated juice industries. It exhibits resistance to high sugar concentrations but genome- and proteome-wide studies on Z. rouxii in response to high sugar concentrations have been poorly investigated. Herein, by using a 2-D electrophoresis based workflow, the proteome of a wild strain of Z. rouxii under different sugar concentrations has been analyzed. Proteins were extracted, quantified, and subjected to 2-DE analysis in the pH range 4-7. Differences in growth (lag phase), protein content (13.97-19.23mg/g cell dry weight) and number of resolved spots (196-296) were found between sugar concentrations. ANOVA test showed that 168 spots were different, and 47 spots, corresponding to 40 unique gene products have been identified. These protein species are involved in carbohydrate and energy metabolism, amino acid metabolism, response to stimulus, protein transport and vesicle organization, cell morphogenesis regulation, transcription and translation, nucleotide metabolism, amino-sugar nucleotide-sugar pathways, oxidoreductases balancing, and ribosome biogenesis. The present study provides important information about how Z. rouxii acts to cope with high sugar concentration at molecular levels, which might enhance our global understanding of Z. rouxii's high sugar-tolerance trait.
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49
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Spiesser T, Kühn C, Krantz M, Klipp E. The MYpop toolbox: Putting yeast stress responses in cellular context on single cell and population scales. Biotechnol J 2016; 11:1158-68. [PMID: 26952199 DOI: 10.1002/biot.201500344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/15/2015] [Accepted: 03/07/2016] [Indexed: 11/05/2022]
Abstract
Systems biology holds the promise to integrate multiple sources of information in order to build ever more complete models of cellular function. To do this, the field must overcome two significant challenges. First, the current strategy to model average cells must be replaced with population based models accounting for cell-to-cell variability. Second, models must be integrated with each other and with basic cellular function. This requires a core model of cellular physiology as well as a multiscale simulation platform to support large-scale simulation of culture or tissues from single cells. Here, we present such a simulation platform with a core model of yeast physiology as scaffold to integrate and simulate SBML models. The software automates this integration helping users simulate their model of choice in context of the cell division cycle. We benchmark model merging, simulation and analysis by integrating a minimal model of osmotic stress into the core model and analyzing it. We characterize the effect of single cell differences on the dynamics of osmoadaptation, estimating when normal cell growth is resumed and obtaining an explanation for experimentally observed glycerol dynamics based on population dynamics. Hence, the platform can be used to reconcile single cell and population level data.
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Affiliation(s)
- Thomas Spiesser
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Clemens Kühn
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany.
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50
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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