1
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Wang D, Zeng N, Li C, Li Z, Zhang N, Li B. Fungal biofilm formation and its regulatory mechanism. Heliyon 2024; 10:e32766. [PMID: 38988529 PMCID: PMC11233959 DOI: 10.1016/j.heliyon.2024.e32766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/12/2024] Open
Abstract
Fungal biofilm is a microbial community composed of fungal cells and extracellular polymeric substances (EPS). In recent years, fungal biofilms have played an increasingly important role in many fields. However, there are few studies on fungal biofilms and their related applications and development are still far from enough. Therefore, this review summarizes the composition and function of EPS in fungal biofilms, and improves and refines the formation process of fungal biofilms according to the latest viewpoints. Moreover, based on the study of Saccharomyces cerevisiae and Candida albicans, this review summarizes the gene regulation network of fungal biofilm synthesis, which is crucial for systematically understanding the molecular mechanism of fungal biofilm formation. It is of great significance to further develop effective methods at the molecular level to control harmful biofilms or enhance and regulate the formation of beneficial biofilms. Finally, the quorum sensing factors and mixed biofilms formed by fungi in the current research of fungal biofilms are summarized. These results will help to deepen the understanding of the formation process and internal regulation mechanism of fungal biofilm, provide reference for the study of EPS composition and structure, formation, regulation, group behavior and mixed biofilm formation of other fungal biofilms, and provide strategies and theoretical basis for the control, development and utilization of fungal biofilms.
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Affiliation(s)
- Dandan Wang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, PR China
| | - Nan Zeng
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, PR China
| | - Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, PR China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, 510225, PR China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, PR China
| | - Zijing Li
- College of Food Science, Shenyang Agricultural University, Shenyang, 110866, PR China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, PR China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, PR China
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2
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Malavia-Jones D, Farrer RA, Stappers MH, Edmondson MB, Borman AM, Johnson EM, Lipke PN, Gow NA. Strain and temperature dependent aggregation of Candida auris is attenuated by inhibition of surface amyloid proteins. Cell Surf 2023; 10:100110. [PMID: 37559873 PMCID: PMC10407437 DOI: 10.1016/j.tcsw.2023.100110] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Candida auris is a multi-drug resistant human fungal pathogen that has become a global threat to human health due to its drug resistant phenotype, persistence in the hospital environment and propensity for patient to patient spread. Isolates display variable aggregation that may affect the relative virulence of strains. Therefore, dissection of this phenotype has gained substantial interest in recent years. We studied eight clinical isolates from four different clades (I-IV); four of which had a strongly aggregating phenotype and four of which did not. Genome analysis identified polymorphisms associated with loss of cell surface proteins were enriched in weakly-aggregating strains. Additionally, we identified down-regulation of chitin synthase genes involved in the synthesis of the chitinous septum. Characterisation of the cells revealed no ultrastructural defects in cytokinesis or cell separation in aggregating isolates. Strongly and weakly aggregating strains did not differ in net surface charge or in cell surface hydrophobicity. The capacity for aggregation and for adhesion to polystyrene microspheres were also not correlated. However, aggregation and extracellular matrix formation were all increased at higher growth temperatures, and treatment with the amyloid protein inhibitor Thioflavin-T markedly attenuated aggregation. Genome analysis further indicated strain specific differences in the genome content of GPI-anchored proteins including those encoding genes with the potential to form amyloid proteins. Collectively our data suggests that aggregation is a complex strain and temperature dependent phenomenon that may be linked in part to the ability to form extracellular matrix and cell surface amyloids.
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Affiliation(s)
- Dhara Malavia-Jones
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rhys A. Farrer
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mark H.T. Stappers
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Matt B. Edmondson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew M. Borman
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Elizabeth M. Johnson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Peter N. Lipke
- Biology Department, Brooklyn College of City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Neil A.R. Gow
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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3
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Heterologous Expression of CFL1 Confers Flocculating Ability to Cutaneotrichosporon oleaginosus Lipid-Rich Cells. J Fungi (Basel) 2022; 8:jof8121293. [PMID: 36547626 PMCID: PMC9786196 DOI: 10.3390/jof8121293] [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: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Lipid extraction from microbial and microalgae biomass requires the separation of oil-rich cells from the production media. This downstream procedure represents a major bottleneck in biodiesel production, increasing the cost of the final product. Flocculation is a rapid and cheap system for removing solid particles from a suspension. This natural characteristic is displayed by some microorganisms due to the presence of lectin-like proteins (called flocculins/adhesins) in the cell wall. In this work, we showed, for the first time, that the heterologous expression of the adhesin Cfl1p endows the oleaginous species Cutaneotrichosporon oleaginosus with the capacity of cell flocculation. We used Helm's test to demonstrate that the acquisition of this trait allows for reducing the time required for the separation of lipid-rich cells from liquid culture by centrifugation without altering the productivity. This improves the lipid production process remarkably by providing a more efficient downstream.
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4
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Shoket H, Parvez S, Sharma M, Pandita M, Sharma V, Kumar P, Bairwa NK. Deletion of autophagy related, ATG1 and F-box motif encoding YDR131C, together, lead to synthetic growth defects and flocculation behavior in Saccharomyces cerevisiae. J Biochem Mol Toxicol 2022; 36:e23064. [PMID: 35385166 DOI: 10.1002/jbt.23064] [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: 03/16/2021] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/09/2022]
Abstract
Ubiquitin proteasome system (UPS) and autophagy both pathways are involved in clearing the nonessential cellular components and also crosstalk during cellular response to normal and stress conditions. The F-box motif proteins constitute the SCF-E3 ligase complex of the UPS pathway in Saccharomyces cerevisiae and are involved in the substrate recruitment for ubiquitination. The ATG1 encoded Atg1p, a conserved serine-threonine kinase is crucial for the autophagy process. Here in this study, we report that loss of F-box motif encoding YDR131C and ATG1 together results in growth defects, floc formation, sensitivity to hydroxyurea, methyl methanesulfonate, and hydrogen peroxide. Both the genes also interact with the flocculation-related genes (FLO) and associate with gene ontology terms "ubiquitin-protein transferase activity" and "cellular catabolic process." Based on in silico analysis and experimental evidence we conclude that YDR131C and ATG1 function in parallel pathways to regulate the growth, flocculation, and stress response.
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Affiliation(s)
- Heena Shoket
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Sadia Parvez
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Meenu Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Monika Pandita
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Vishali Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Prabhat Kumar
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
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Drug-dependent growth curve reshaping reveals mechanisms of antifungal resistance in Saccharomyces cerevisiae. Commun Biol 2022; 5:292. [PMID: 35361876 PMCID: PMC8971432 DOI: 10.1038/s42003-022-03228-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 03/07/2022] [Indexed: 11/15/2022] Open
Abstract
Microbial drug resistance is an emerging global challenge. Current drug resistance assays tend to be simplistic, ignoring complexities of resistance manifestations and mechanisms, such as multicellularity. Here, we characterize multicellular and molecular sources of drug resistance upon deleting the AMN1 gene responsible for clumping multicellularity in a budding yeast strain, causing it to become unicellular. Computational analysis of growth curve changes upon drug treatment indicates that the unicellular strain is more sensitive to four common antifungals. Quantitative models uncover entwined multicellular and molecular processes underlying these differences in sensitivity and suggest AMN1 as an antifungal target in clumping pathogenic yeasts. Similar experimental and mathematical modeling pipelines could reveal multicellular and molecular drug resistance mechanisms, leading to more effective treatments against various microbial infections and possibly even cancers. Combined growth curve experiments and quantitative modeling reveal antifungal responses of planktonic yeast, providing a future framework to examine antimicrobial drug resistance.
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Kahar P, Itomi A, Tsuboi H, Ishizaki M, Yasuda M, Kihira C, Otsuka H, Azmi NB, Matsumoto H, Ogino C, Kondo A. The flocculant Saccharomyces cerevisiae strain gains robustness via alteration of the cell wall hydrophobicity. Metab Eng 2022; 72:82-96. [DOI: 10.1016/j.ymben.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
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7
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Huang Z, Dai H, Zhang X, Wang Q, Sun J, Deng Y, Shi P. BSC2 induces multidrug resistance via contributing to the formation of biofilm in Saccharomyces cerevisiae. Cell Microbiol 2021; 23:e13391. [PMID: 34482605 DOI: 10.1111/cmi.13391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023]
Abstract
Biofilm plays an important role in fungal multidrug resistance (MDR). Our previous studies showed that BSC2 is involved in resistance to amphotericin B (AMB) through antioxidation in Saccharomyces cerevisiae. In this study, the overexpression of BSC2 and IRC23 induced strong MDR in S. cerevisiae. BSC2-overexpression affected cellular flocculation, cell surface hydrophobicity, biofilm formation and invasive growth. However, it failed to induce caspofungin (CAS) resistance and affect the invasive growth in FLO mutant strains (FLO11Δ, FLO1Δ, FLO8Δ and TUP1Δ). Furthermore, the overexpression of BSC2 compensated for chitin synthesis defects to maintain the cell wall integrity and significantly reduced the cell morphology abnormality induced by CAS. However, it could not repair the cell wall damage caused by CAS in the FLO mutant strains. Although BSC2 overexpression increased the level of mannose in the cell wall, DPM1 overexpression in both BY4741 and bsc2∆ could confer resistance to CAS and AMB. In addition, BSC2 overexpression significantly increased the mRNA expression of FLO11, FLO1, FLO8 and TUP1. BSC2 may function as a regulator of FLO genes and be involved in cell wall integrity in yeast. Taken together, our data demonstrate that BSC2 induces MDR in a FLO pathway-dependent manner via contributing to the formation of biofilms in S. cerevisiae. TAKE AWAYS: Overexpression of BSC2 induced strong MDR in S. cerevisiae. BSC2 affected cellular flocculation, CSH, biofilm formation and invasive growth. BSC2 could not repair the cell wall damage caused by CAS in the FLO mutants. BSC2 may function as a regulator of FLO genes to maintain cell wall integrity. BSC2 promotes biofilm formation in a FLO pathway-dependent manner to induce MDR.
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Affiliation(s)
- Zhiwei Huang
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Hongsheng Dai
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Xiaoyu Zhang
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Qiao Wang
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xining, China
| | - Yunxia Deng
- Key Lab of Science & Technology of Eco-textile, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, China
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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8
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Zhong W, Liu S, Yang H, Li E. Effect of selected yeast on physicochemical and oenological properties of blueberry wine fermented with citrate-degrading Pichia fermentans. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Pentz JT, Márquez-Zacarías P, Bozdag GO, Burnetti A, Yunker PJ, Libby E, Ratcliff WC. Ecological Advantages and Evolutionary Limitations of Aggregative Multicellular Development. Curr Biol 2020; 30:4155-4164.e6. [PMID: 32888478 DOI: 10.1016/j.cub.2020.08.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 01/24/2023]
Abstract
All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. Although evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically identical organisms. We engineered unicellular baker's yeast (Saccharomyces cerevisiae) to develop either clonally ("snowflake"; Δace2) or aggregatively ("floc"; GAL1p::FLO1) and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical "choosy floc" that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage-the ability to quickly form groups-but this very feature leads to its exploitation.
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Affiliation(s)
- Jennifer T Pentz
- Department of Molecular Biology, Umeå University, Umeå 90187, Sweden; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pedro Márquez-Zacarías
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eric Libby
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå 90187, Sweden
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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10
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Mehta DV, Curtis SJ, Rudolph AB, Mary CS, Goodrich R, Schneider KR, MacIntosh AJ. A Mini Review: The History of Yeast Flocculation with an Emphasis on Measurement Techniques. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1806006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Devanshu V. Mehta
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, U.S.A
| | - Savanna J. Curtis
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, U.S.A
| | - Arthur B. Rudolph
- Chemistry Research Unit, Center for Medical, Agricultural, and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL, U.S.A
| | - Colette St. Mary
- Department of Biology, University of Florida, Gainesville, FL, U.S.A
| | - Renee Goodrich
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, U.S.A
| | - Keith R. Schneider
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, U.S.A
| | - Andrew J. MacIntosh
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, U.S.A
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11
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Qin L, Dong S, Yu J, Ning X, Xu K, Zhang SJ, Xu L, Li BZ, Li J, Yuan YJ, Li C. Stress-driven dynamic regulation of multiple tolerance genes improves robustness and productive capacity of Saccharomyces cerevisiae in industrial lignocellulose fermentation. Metab Eng 2020; 61:160-170. [DOI: 10.1016/j.ymben.2020.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
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12
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Cunha JT, Soares PO, Baptista SL, Costa CE, Domingues L. Engineered Saccharomyces cerevisiae for lignocellulosic valorization: a review and perspectives on bioethanol production. Bioengineered 2020; 11:883-903. [PMID: 32799606 PMCID: PMC8291843 DOI: 10.1080/21655979.2020.1801178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biorefinery concept, consisting in using renewable biomass with economical and energy goals, appeared in response to the ongoing exhaustion of fossil reserves. Bioethanol is the most prominent biofuel and has been considered one of the top chemicals to be obtained from biomass. Saccharomyces cerevisiae, the preferred microorganism for ethanol production, has been the target of extensive genetic modifications to improve the production of this alcohol from renewable biomasses. Additionally, S. cerevisiae strains from harsh industrial environments have been exploited due to their robust traits and improved fermentative capacity. Nevertheless, there is still not an optimized strain capable of turning second generation bioprocesses economically viable. Considering this, and aiming to facilitate and guide the future development of effective S. cerevisiae strains, this work reviews genetic engineering strategies envisioning improvements in 2nd generation bioethanol production, with special focus in process-related traits, xylose consumption, and consolidated bioprocessing. Altogether, the genetic toolbox described proves S. cerevisiae to be a key microorganism for the establishment of a bioeconomy, not only for the production of lignocellulosic bioethanol, but also having potential as a cell factory platform for overall valorization of renewable biomasses.
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Affiliation(s)
- Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar , Braga, Portugal
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13
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Puligundla P, Smogrovicova D, Mok C, Obulam VSR. Recent developments in high gravity beer-brewing. INNOV FOOD SCI EMERG 2020. [DOI: 10.1016/j.ifset.2020.102399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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De S, Rebnegger C, Moser J, Tatto N, Graf AB, Mattanovich D, Gasser B. Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. FEMS Yeast Res 2020; 20:5884885. [PMID: 32766781 PMCID: PMC7419694 DOI: 10.1093/femsyr/foaa044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here, we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5-1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5-1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5-1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.
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Affiliation(s)
- Sonakshi De
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Josef Moser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Nadine Tatto
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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15
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Gorter de Vries AR, Pronk JT, Daran JMG. Lager-brewing yeasts in the era of modern genetics. FEMS Yeast Res 2020; 19:5573808. [PMID: 31553794 PMCID: PMC6790113 DOI: 10.1093/femsyr/foz063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
The yeast Saccharomyces pastorianus is responsible for the annual worldwide production of almost 200 billion liters of lager-type beer. S. pastorianus is a hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus that has been studied for well over a century. Scientific interest in S. pastorianus intensified upon the discovery, in 2011, of its S. eubayanus ancestor. Moreover, advances in whole-genome sequencing and genome editing now enable deeper exploration of the complex hybrid and aneuploid genome architectures of S. pastorianus strains. These developments not only provide novel insights into the emergence and domestication of S. pastorianus but also generate new opportunities for its industrial application. This review paper combines historical, technical and socioeconomic perspectives to analyze the evolutionary origin and genetics of S. pastorianus. In addition, it provides an overview of available methods for industrial strain improvement and an outlook on future industrial application of lager-brewing yeasts. Particular attention is given to the ongoing debate on whether current S. pastorianus originates from a single or multiple hybridization events and to the potential role of genome editing in developing industrial brewing yeast strains.
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Affiliation(s)
- Arthur R Gorter de Vries
- 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
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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16
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Bartle L, Sumby K, Sundstrom J, Jiranek V. The microbial challenge of winemaking: yeast-bacteria compatibility. FEMS Yeast Res 2020; 19:5513997. [PMID: 31187141 DOI: 10.1093/femsyr/foz040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/10/2019] [Indexed: 12/25/2022] Open
Abstract
The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.
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Affiliation(s)
- Louise Bartle
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Krista Sumby
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Joanna Sundstrom
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, PMB1, Glen Osmond, SA, 5064, Australia
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17
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Yeast Flocculin: Methods for Quantitative Analysis of Flocculation in Yeast Cells. Methods Mol Biol 2020. [PMID: 32306350 DOI: 10.1007/978-1-0716-0430-4_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Flocculation, the clump forming property of yeast, has long been appreciated in breweries and utilized as an off-cost method to enable the reuse of yeast cells. Members of the flocculin protein family were identified as the adherent proteins on the cell surface responsible for flocculation, and their properties have been investigated. Crystal structures of the adhesion domain of flocculins revealed their unique mode of ligand binding where a calcium ion is located in the middle of the interface between flocculin and the interacting sugar. Here we describe the most commonly used flocculation assay. The method is simple and easy, yet it is the most direct and reliable assay to evaluate the flocculation cellular phenotype.
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18
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Varela C, Bartel C, Nandorfy DE, Borneman A, Schmidt S, Curtin C. Identification of flocculant wine yeast strains with improved filtration-related phenotypes through application of high-throughput sedimentation rate assays. Sci Rep 2020; 10:2738. [PMID: 32066762 PMCID: PMC7026045 DOI: 10.1038/s41598-020-59579-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/30/2020] [Indexed: 11/24/2022] Open
Abstract
In most yeast-driven biotechnological applications, biomass is separated from the aqueous phase after fermentation or production has finished. During winemaking, yeasts are removed after fermentation by racking, filtration, or centrifugation, which add costs to the overall process and may reduce product yield. Theoretically, clarification and filtration can be aided through use of yeast strains that form flocs due to cell-cell binding, a process known as flocculation. However, because early flocculation can cause stuck/sluggish fermentations, this phenotype is not common amongst commercially available wine yeasts. In this study we sought to identify wine strains that exhibit late-fermentation flocculant behaviour using two complementary approaches; a high-throughput sedimentation rate assay of individual strains and a competitive sedimentation assay using a barcoded yeast collection. Amongst 103 wine strains, several exhibited strong sedimentation at the end of the wine fermentation process under various environmental conditions. Two of these strains, AWRI1688 and AWRI1759, were further characterised during red winemaking trials. Shiraz wines produced with both strains displayed improved filtration-related properties. AWRI1759 produced wines with greater filterability, whereas AWRI1688 enabled the recovery of larger wine volumes after racking. Thus, this study demonstrates the effective use of sedimentation screening assays to identify wine yeasts with practical winemaking applications.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia. .,Department of Wine & Food Science, University of Adelaide, Glen Osmond, SA 5064, Adelaide, Australia.
| | - Caroline Bartel
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | | | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Simon Schmidt
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Chris Curtin
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.,College of Agricultural Sciences, Oregon State University, Wiegand Hall, 3051 SW Campus Way, Corvallis, OR, 97331, USA
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19
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Sarang MC, Nerurkar AS. Amyloid protein produced by B. cereus CR4 possesses bioflocculant activity and has potential application in microalgae harvest. Biotechnol Lett 2019; 42:79-91. [PMID: 31720978 DOI: 10.1007/s10529-019-02758-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/08/2019] [Indexed: 11/29/2022]
Abstract
Bacillus cereus CR4 from the flocs of activated sludge was found to produce an extracellular bioflocculant, which was characterized as amyloid protein and demonstrated to have potential application in microalgae recovery. Cell surface amyloid production was demonstrated by fluorescence, confocal and scanning electron microscopy. Birefringence, spectral shift assay, TEM, FTIR and CD spectra confirmed the amyloid nature of the purified protein that demonstrated flocculation. The gene for amyloid protein of B. cereus CR4 was found to be related to tasA gene of amyloid protein produced by Bacillus subtilis. The results demonstrated that the amyloid protein produced by B. cereus CR4 possessed a novel bioflocculant activity which at pH below 4.5 reached to a maximum of 86.87%. The amyloid bioflocculant producing B. cereus CR4 has a potential in biotechnological application like Scenedesmus biomass recovery.
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Affiliation(s)
- M C Sarang
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India
| | - A S Nerurkar
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, India.
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20
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Reinmets K, Dehkharghani A, Guasto JS, Fuchs SM. Microfluidic quantification and separation of yeast based on surface adhesion. LAB ON A CHIP 2019; 19:3481-3489. [PMID: 31524206 DOI: 10.1039/c9lc00275h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fungal adhesion is fundamental to processes ranging from infections to food production to bioengineering. Yet, robust, population-scale quantification methods for yeast surface adhesion are lacking. We developed a microfluidic assay to discriminate and separate genetically-related yeast strains based on adhesion strength, and to quantify effects of ionic strength and substrate hydrophobicity on adhesion. This approach will enable the rapid screening and fractionation of yeast based on adhesive properties for genetic protein engineering, anti-fouling surfaces, and a host of other applications.
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21
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Su Y, Chen J, Huang Y. Disruption of ppr3, ppr4, ppr6 or ppr10 induces flocculation and filamentous growth in Schizosaccharomyces pombe. FEMS Microbiol Lett 2019; 365:5033677. [PMID: 29878109 DOI: 10.1093/femsle/fny141] [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: 04/07/2018] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are major players in mitochondrial and chloroplast RNA metabolism, which is essential for normal organellar function. The fission yeast Schizosaccharomyces pombe has 10 PPR proteins. We have previously reported that loss of ppr3, ppr4, ppr6 or ppr10 perturbs iron homeostasis leading to accumulation of reactive oxygen species and apoptotic cell death. In the present study, we show that loss of ppr3, ppr4, ppr6 or ppr10 can cause non-sexual flocculation and filamentous growth of cells. Furthermore, expression of a number of genes encoding cell-surface flocculins and cell wall-remodeling enzymes are induced in these ppr-deletion mutants. We also show that Δppr10 cells, and, to a lesser extent, Δppr4 and Δppr6 cells, exhibited increased tolerance to H2O2 toxicity compared with the wild-type strain. Finally, we found that overexpression of genes involved in iron uptake and/or iron homeostasis could cause the flocculation of wild-type cells. Our findings suggest that an elevated level of intracellular iron in the mutant caused by loss of ppr3, ppr4, ppr6 or ppr10 may result in flocculation and filamentous growth in S. pombe.
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Affiliation(s)
- Yang Su
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jie Chen
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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22
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Cell Aggregation and Aerobic Respiration Are Important for Zymomonas mobilis ZM4 Survival in an Aerobic Minimal Medium. Appl Environ Microbiol 2019; 85:AEM.00193-19. [PMID: 30877116 DOI: 10.1128/aem.00193-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/09/2019] [Indexed: 12/30/2022] Open
Abstract
Zymomonas mobilis produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to the yeast Saccharomyces cerevisiae for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals than single cells. While spontaneous floc-forming Z. mobilis mutants have been described, little is known about the natural conditions that induce Z. mobilis floc formation or about the genetic factors involved. Here we found that wild-type Z. mobilis forms flocs in response to aerobic growth conditions but only in a minimal medium. We identified a cellulose synthase gene cluster and a single diguanylate cyclase that are essential for both floc formation and survival in a minimal aerobic medium. We also found that NADH dehydrogenase 2, a key component of the aerobic respiratory chain, is important for survival in a minimal aerobic medium, providing a physiological role for this enzyme, which has previously been found to be disadvantageous in a rich aerobic medium. Supplementation of the minimal medium with vitamins also promoted survival but did not inhibit floc formation.IMPORTANCE The bacterium Zymomonas mobilis is best known for its anaerobic fermentative lifestyle, in which it converts glucose into ethanol at a yield surpassing that of yeast. However, Z. mobilis also has an aerobic lifestyle, which has confounded researchers with its attributes of poor growth, accumulation of toxic acetic acid and acetaldehyde, and respiratory enzymes that are detrimental for aerobic growth. Here we show that a major Z. mobilis respiratory enzyme and the ability to form multicellular aggregates, called flocs, are important for survival, but only during aerobic growth in a medium containing a minimum set of nutrients required for growth. Supplements, such as vitamins or yeast extract, promote aerobic growth and, in some cases, inhibit floc formation. We propose that Z. mobilis likely requires aerobic respiration and floc formation in order to survive in natural environments that lack protective factors found in supplements such as yeast extract.
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23
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Vergara-Álvarez I, Quiroz-Figueroa F, Tamayo-Ordóñez MC, Oliva-Hernández AA, Larralde-Corona CP, Narváez-Zapata JA. Flocculation and Expression of FLO Genes of a Saccharomyces cerevisiae Mezcal Strain with High Stress Tolerance. Food Technol Biotechnol 2019; 57:544-553. [PMID: 32123516 PMCID: PMC7029389 DOI: 10.17113/ftb.57.04.19.6063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mezcal is a distillate produced by spontaneous fermentation of the must obtained from stalks of Agave spp. plants that are cooked and pressed. Agave must contains a high amount of fructose and phenolic compounds, and fermentation usually occurs under stressful (and uncontrolled) environmental conditions. Yeasts capable of growing under such conditions usually display advantageous biological and industrial traits for stress tolerance such as flocculation. In this study, seven Saccharomyces cerevisiae strains isolated from mezcal must were exposed to temperatures ranging between 10 and 40 °C, and to different sugar sources (fructose or glucose). Yeasts grown in fructose increased their stress tolerance, determined by colony count in a microdrop assay, under low temperature (10 °C) compared to the growth at 40 °C on solid cultures. The most stress-tolerant mezcal strain (Sc3Y8) and a commercial wine (Fermichamp) strain, used as control, were grown under fermentation conditions and exposed to long-term temperature stress to determine their performance and their potential for flocculation. Compared to glucose, fermentation on fructose increased the metabolite accumulation at the end of culture, particularly at 40 °C, with 2.3, 1.3 and 3.4 times more glycerol (8.6 g/L), ethanol (43.6 g/L) and acetic acid (7.3 g/L), respectively. Using confocal microscopy analysis, we detected morphological changes such as aggregation and wall recognition at the level of budding scars in yeast, particularly in the Sc3Y8 strain when it was exposed to 40 °C. The analysis confirmed that this mezcal strain was positive for flocculation in the presence of Ca2+ ions. Analysis of FLO1, FLO5 and FLO11 gene expression implicated in flocculation in both Saccharomyces strains showed a strong transcriptional induction, mainly of the FLO5 gene in the mezcal Sc3Y8 strain.
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Affiliation(s)
- Israel Vergara-Álvarez
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico.,Aix-Marseille University, LCB (UMR7283), CNRS, Marseille, France
| | - Francisco Quiroz-Figueroa
- National Polytechnic Institute (Instituto Politécnico Nacional), CIIDIR-IPN Unidad Sinaloa, Blvd. Juan de Dios Bátiz Paredes no. 250, Col. San Joachin, C.P. 81101 Guasave (Sinaloa), Mexico
| | - María Concepción Tamayo-Ordóñez
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico.,Genetic Engineering Laboratory, Department of Biotechnology, Faculty of Chemical Sciences, Autonomous University of Coahuila, Saltillo Unit, Mexico
| | - Amanda Alejandra Oliva-Hernández
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
| | - Claudia Patricia Larralde-Corona
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
| | - José Alberto Narváez-Zapata
- National Polytechnic Institute (Instituto Politécnico Nacional), Center for Genomic Biotechnology, Blvd del Maestro s/n esq, Elías Piña Col. Narciso Mendoza, C.P. 88710, Reynosa (Tamaulipas), Mexico
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24
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Wang FZ, Zhang L. Flocculating Protein Flo1p from Saccharomyces cerevisiae W303-1A. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683819010198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Abstract
Due to increasing demands for microalgal biomass and products originating from microalgae, large-scale production systems are necessary. However, current microalgal production technologies are not cost-effective and are hindered by various bottlenecks, one of which is the harvesting of microalgal biomass. Cell separation is difficult because of the low sedimentation velocity of microalgae, their colloidal character with repelling negative surface charges, and low biomass concentrations in culture broths; therefore, large volumes need to be processed in order to concentrate the cells. Flocculation is considered to be one of the most suitable methods for harvesting microalgal biomass. This article provides an overview of flocculation methods suitable for microalgal harvesting, their mechanisms, advantages and drawbacks. Special attention is paid to the role of surface charge in the mechanism of flocculation. The novelty of the review lies in the interconnection between the context of technological applications and physico-chemical surface phenomena.
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26
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Moreno-García J, Martín-García FJ, Ogawa M, García-Martínez T, Moreno J, Mauricio JC, Bisson LF. FLO1, FLO5 and FLO11 Flocculation Gene Expression Impacts Saccharomyces cerevisiae Attachment to Penicillium chrysogenum in a Co-immobilization Technique. Front Microbiol 2018; 9:2586. [PMID: 30429833 PMCID: PMC6220091 DOI: 10.3389/fmicb.2018.02586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/10/2018] [Indexed: 11/14/2022] Open
Abstract
A reoccurring flaw of most yeast immobilization systems that limits the potential of the technique is leakage of the cells from the matrix. Leakage may be due to weakly adherent cells, deterioration of the matrix, or to new growth and loss of non-adherent daughter cells. Yeast biocapsules are a spontaneous, cost effective system of immobilization whereby Saccharomyces cerevisiae cells are attached to the hyphae of Penicillium chrysogenum, creating hollow spheres that allow recovery and reutilization. This attachment is based on naturally occurring adherent properties of the yeast cell surface. We hypothesized that proteins associated with flocculation might play a role in adherence to fungal hyphae. To test this hypothesis, yeast strains with overexpressed and deleted flocculation genes (FLO1, FLO5, and FLO11) were evaluated for biocapsule formation to observe the impact of gene expression on biocapsule diameter, number, volume, dry mass, and percent immobilized versus non-immobilized cells. Overexpression of all three genes enhanced immobilization and resulted in larger diameter biocapsules. In particular, overexpression of FLO11 resulted in a five fold increase of absorbed cells versus the wild type isogenic strain. In addition, deletion of FLO1 and FLO11 significantly decreased the number of immobilized yeast cells compared to the wild type BY4742. These results confirm the role of natural adherent properties of yeast cells in attachment to fungal hyphae and offer the potential to create strongly adherent cells that will produce adherent progeny thereby reducing the potential for cell leakage from the matrix.
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Affiliation(s)
- Jaime Moreno-García
- Department of Microbiology, University of Córdoba, Córdoba, Spain
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Minami Ogawa
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Juan Moreno
- Department of Agricultural Chemistry, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Microbiology, University of Córdoba, Córdoba, Spain
| | - Linda F. Bisson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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27
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Abstract
Physical contact between yeast species, in addition to better-understood and reported metabolic interactions, has recently been proposed to significantly impact the relative fitness of these species in cocultures. Such data have been generated by using membrane bioreactors, which physically separate two yeast species. However, doubts persist about the degree that the various membrane systems allow for continuous and complete metabolic contact, including the exchange of proteins. Here, we provide independent evidence for the importance of physical contact by using a genetic system to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Such adhesion is controlled by a family of structurally related cell wall proteins encoded by the FLO gene family. As previously shown, the expression of specific members of the FLO gene family in Saccharomyces cerevisiae dramatically changes the coadhesion patterns between this yeast and other yeast species. Here, we use this differential aggregation mediated by FLO genes as a model to assess the impact of physical contact between different yeast species on the relative fitness of these species in simplified ecosystems. The identity of the FLO gene has a marked effect on the persistence of specific non-Saccharomyces yeasts over the course of extended growth periods in batch cultures. Remarkably, FLO1 and FLO5 expression often result in opposite outcomes. The data provide clear evidence for the role of physical contact in multispecies yeast ecosystems and suggest that FLO gene expression may be a major factor in such interactions.IMPORTANCE The impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard but suffer from numerous limitations. Here, we provide independent evidence for the importance of physical contact by using a genetic system, based on the FLO gene family, to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Our results show that interspecies contact significantly impacts population dynamics and the survival of individual species. Remarkably, different members of the FLO gene family often lead to very different population outcomes, further suggesting that FLO gene expression may be a major factor in such interactions.
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28
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Fungal Light-Oxygen-Voltage Domains for Optogenetic Control of Gene Expression and Flocculation in Yeast. mBio 2018; 9:mBio.00626-18. [PMID: 30065085 PMCID: PMC6069114 DOI: 10.1128/mbio.00626-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Optogenetic switches permit accurate control of gene expression upon light stimulation. These synthetic switches have become a powerful tool for gene regulation, allowing modulation of customized phenotypes, overcoming the obstacles of chemical inducers, and replacing their use by an inexpensive resource: light. In this work, we implemented FUN-LOV, an optogenetic switch based on the photon-regulated interaction of WC-1 and VVD, two LOV (light-oxygen-voltage) blue-light photoreceptors from the fungus Neurospora crassa. When tested in yeast, FUN-LOV yields light-controlled gene expression with exquisite temporal resolution and a broad dynamic range of over 1,300-fold, as measured by a luciferase reporter. We also tested the FUN-LOV switch for heterologous protein expression in Saccharomyces cerevisiae, where Western blot analysis confirmed strong induction upon light stimulation, surpassing by 2.5 times the levels achieved with a classic GAL4/galactose chemical-inducible system. Additionally, we utilized FUN-LOV to control the ability of yeast cells to flocculate. Light-controlled expression of the flocculin-encoding gene FLO1, by the FUN-LOV switch, yielded flocculation in light (FIL), whereas the light-controlled expression of the corepressor TUP1 provided flocculation in darkness (FID). Altogether, the results reveal the potential of the FUN-LOV optogenetic switch to control two biotechnologically relevant phenotypes such as heterologous protein expression and flocculation, paving the road for the engineering of new yeast strains for industrial applications. Importantly, FUN-LOV’s ability to accurately manipulate gene expression, with a high temporal dynamic range, can be exploited in the analysis of diverse biological processes in various organisms. Optogenetic switches are molecular devices which allow the control of different cellular processes by light, such as gene expression, providing a versatile alternative to chemical inducers. Here, we report a novel optogenetic switch (FUN-LOV) based on the LOV domain interaction of two blue-light photoreceptors (WC-1 and VVD) from the fungus N. crassa. In yeast cells, FUN-LOV allowed tight regulation of gene expression, with low background in darkness and a highly dynamic and potent control by light. We used FUN-LOV to optogenetically manipulate, in yeast, two biotechnologically relevant phenotypes, heterologous protein expression and flocculation, resulting in strains with potential industrial applications. Importantly, FUN-LOV can be implemented in diverse biological platforms to orthogonally control a multitude of cellular processes.
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29
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Nguyen PV, Hlaváček O, Maršíková J, Váchová L, Palková Z. Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity of yeast colony biofilms. PLoS Genet 2018; 14:e1007495. [PMID: 29965985 PMCID: PMC6044549 DOI: 10.1371/journal.pgen.1007495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/13/2018] [Accepted: 06/16/2018] [Indexed: 12/26/2022] Open
Abstract
Yeast biofilms are complex multicellular structures, in which the cells are well protected against drugs and other treatments and thus highly resistant to antifungal therapies. Colony biofilms represent an ideal system for studying molecular mechanisms and regulations involved in development and internal organization of biofilm structure as well as those that are involved in fungal domestication. We have identified here antagonistic functional interactions between transcriptional regulators Cyc8p and Tup1p that modulate the life-style of natural S. cerevisiae strains between biofilm and domesticated mode. Herein, strains with different levels of Cyc8p and Tup1p regulators were constructed, analyzed for processes involved in colony biofilm development and used in the identification of modes of regulation of Flo11p, a key adhesin in biofilm formation. Our data show that Tup1p and Cyc8p regulate biofilm formation in the opposite manner, being positive and negative regulators of colony complexity, cell-cell interaction and adhesion to surfaces. Notably, in-depth analysis of regulation of expression of Flo11p adhesin revealed that Cyc8p itself is the key repressor of FLO11 expression, whereas Tup1p counteracts Cyc8p's repressive function and, in addition, counters Flo11p degradation by an extracellular protease. Interestingly, the opposing actions of Tup1p and Cyc8p concern processes crucial to the biofilm mode of yeast multicellularity, whereas other multicellular processes such as cell flocculation are co-repressed by both regulators. This study provides insight into the mechanisms regulating complexity of the biofilm lifestyle of yeast grown on semisolid surfaces.
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Affiliation(s)
- Phu Van Nguyen
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Otakar Hlaváček
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Maršíková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
- * E-mail:
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30
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Di Gianvito P, Perpetuini G, Tittarelli F, Schirone M, Arfelli G, Piva A, Patrignani F, Lanciotti R, Olivastri L, Suzzi G, Tofalo R. Impact of Saccharomyces cerevisiae strains on traditional sparkling wines production. Food Res Int 2018; 109:552-560. [DOI: 10.1016/j.foodres.2018.04.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/16/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
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31
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Fischer S, Büchner K, Becker T. Induced expression of the alcohol acetyltransferase geneATF1in industrial yeastSaccharomyces pastorianusTUM 34/70. Yeast 2018; 35:531-541. [DOI: 10.1002/yea.3319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022] Open
Affiliation(s)
- S. Fischer
- Technical University of Munich, Institute of Brewing and Beverage Technology; Research Group Beverage and Ceral Biotechnology; Weihenstephaner Steig 20 85354 Freising Germany
| | - K.R. Büchner
- Technical University of Munich, Institute of Brewing and Beverage Technology; Research Group Beverage and Ceral Biotechnology; Weihenstephaner Steig 20 85354 Freising Germany
| | - T. Becker
- Technical University of Munich, Institute of Brewing and Beverage Technology; Research Group Beverage and Ceral Biotechnology; Weihenstephaner Steig 20 85354 Freising Germany
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Srivastava A, Seo SH, Ko SR, Ahn CY, Oh HM. Bioflocculation in natural and engineered systems: current perspectives. Crit Rev Biotechnol 2018; 38:1176-1194. [DOI: 10.1080/07388551.2018.1451984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ankita Srivastava
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seong-Hyun Seo
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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Steenwyk JL, Rokas A. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation. Front Microbiol 2018; 9:288. [PMID: 29520259 PMCID: PMC5826948 DOI: 10.3389/fmicb.2018.00288] [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: 12/12/2017] [Accepted: 02/07/2018] [Indexed: 11/13/2022] Open
Abstract
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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Kopecká J, Němec M, Matoulková D, Čejka P, Jelínková M, Felsberg J, Sigler K. Effect of Growth Conditions on Flocculation and Cell Surface Hydrophobicity of Brewing Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2015-0324-01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jana Kopecká
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Miroslav Němec
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Dagmar Matoulková
- Research Institute of Brewing and Malting, Lípová 15, 120 44 Prague, Czech Republic
| | - Pavel Čejka
- Research Institute of Brewing and Malting, Lípová 15, 120 44 Prague, Czech Republic
| | - Markéta Jelínková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jürgen Felsberg
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Karel Sigler
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Karabín M, Jelínek L, Kotrba P, Cejnar R, Dostálek P. Enhancing the performance of brewing yeasts. Biotechnol Adv 2017; 36:691-706. [PMID: 29277309 DOI: 10.1016/j.biotechadv.2017.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/23/2017] [Accepted: 12/20/2017] [Indexed: 12/26/2022]
Abstract
Beer production is one of the oldest known traditional biotechnological processes, but is nowadays facing increasing demands not only for enhanced product quality, but also for improved production economics. Targeted genetic modification of a yeast strain is one way to increase beer quality and to improve the economics of beer production. In this review we will present current knowledge on traditional approaches for improving brewing strains and for rational metabolic engineering. These research efforts will, in the near future, lead to the development of a wider range of industrial strains that should increase the diversity of commercial beers.
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Affiliation(s)
- Marcel Karabín
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Lukáš Jelínek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Kotrba
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Rudolf Cejnar
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Dostálek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic.
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Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3 (BETHESDA, MD.) 2017; 7:1475-1485. [PMID: 28292787 PMCID: PMC5427499 DOI: 10.1534/g3.117.040105] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023]
Abstract
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S. cerevisiae wine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as the SNO gene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.
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Affiliation(s)
- Jacob Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth. Metab Eng 2017; 41:46-56. [DOI: 10.1016/j.ymben.2017.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/10/2017] [Accepted: 03/08/2017] [Indexed: 12/20/2022]
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Deed RC, Fedrizzi B, Gardner RC. Saccharomyces cerevisiae FLO1 Gene Demonstrates Genetic Linkage to Increased Fermentation Rate at Low Temperatures. G3 (BETHESDA, MD.) 2017; 7:1039-1048. [PMID: 28143947 PMCID: PMC5345705 DOI: 10.1534/g3.116.037630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/25/2017] [Indexed: 01/14/2023]
Abstract
Low fermentation temperatures are of importance to food and beverage industries working with Saccharomyces cerevisiae Therefore, the identification of genes demonstrating a positive impact on fermentation kinetics is of significant interest. A set of 121 mapped F1 progeny, derived from a cross between haploid strains BY4716 (a derivative of the laboratory yeast S288C) and wine yeast RM11-1a, were fermented in New Zealand Sauvignon Blanc grape juice at 12.5°. Analyses of five key fermentation kinetic parameters among the F1 progeny identified a quantitative trait locus (QTL) on chromosome I with a significant degree of linkage to maximal fermentation rate (Vmax) at low temperature. Independent deletions of two candidate genes within the region, FLO1 and SWH1, were constructed in the parental strains (with S288C representing BY4716). Fermentation of wild-type and deletion strains at 12.5 and 25° confirmed that the genetic linkage to Vmax corresponds to the S288C version of the FLO1 allele, as the absence of this allele reduced Vmax by ∼50% at 12.5°, but not at 25°. Reciprocal hemizygosity analysis (RHA) between S288C and RM11-1a FLO1 alleles did not confirm the prediction that the S288C version of FLO1 was promoting more rapid fermentation in the opposing strain background, suggesting that the positive effect on Vmax derived from S288C FLO1 may only provide an advantage in haploids, or is dependent on strain-specific cis or trans effects. This research adds to the growing body of evidence demonstrating the role of FLO1 in providing stress tolerance to S. cerevisiae during fermentation.
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Affiliation(s)
- Rebecca C Deed
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
- School of Biological Sciences, University of Auckland, 1010, New Zealand
| | - Bruno Fedrizzi
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
| | - Richard C Gardner
- School of Biological Sciences, University of Auckland, 1010, New Zealand
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Molecular Basis for Strain Variation in the Saccharomyces cerevisiae Adhesin Flo11p. mSphere 2016; 1:mSphere00129-16. [PMID: 27547826 PMCID: PMC4989245 DOI: 10.1128/msphere.00129-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022] Open
Abstract
As a nonmotile organism, Saccharomyces cerevisiae employs the cell surface flocculin Flo11/Muc1 as an important means of adapting to environmental change. However, there is a great deal of strain variation in the expression of Flo11-dependent phenotypes, including flocculation. In this study, we investigated the molecular basis of this strain-specific phenotypic variability. Our data indicate that strain-specific differences in the level of flocculation result from significant sequence differences in the FLO11 alleles and do not depend on quantitative differences in FLO11 expression or on surface hydrophobicity. We further have shown that beads coated with amino-terminal domain peptide bind preferentially to homologous cells. These data show that variability in the structure of the Flo11 adhesion domain may thus be an important determinant of membership in microbial communities and hence may drive selection and evolution. FLO11 encodes a yeast cell wall flocculin that mediates a variety of adhesive phenotypes in Saccharomyces cerevisiae. Flo11p is implicated in many developmental processes, including flocculation, formation of pseudohyphae, agar invasion, and formation of microbial mats and biofilms. However, Flo11p mediates different processes in different yeast strains. To investigate the mechanisms by which FLO11 determines these differences in colony morphology, flocculation, and invasion, we studied gene structure, function, and expression levels. Nonflocculent Saccharomyces cerevisiae Σ1278b cells exhibited significantly higher FLO11 mRNA expression, especially in the stationary phase, than highly flocculent S. cerevisiae var. diastaticus. The two strains varied in cell surface hydrophobicity, and Flo11p contributed significantly to surface hydrophobicity in S. cerevisiae var. diastaticus but not in strain Σ1278b. Sequencing of the FLO11 gene in S. cerevisiae var. diastaticus revealed strain-specific differences, including a 15-amino-acid insertion in the adhesion domain. Flo11p adhesion domains from strain Σ1278b and S. cerevisiae var. diastaticus were expressed and used to coat magnetic beads. The adhesion domain from each strain bound preferentially to homologous cells, and the preferences were independent of the cells in which the adhesion domains were produced. These results are consistent with the idea that strain-specific variations in the amino acid sequences in the adhesion domains cause different Flo11p flocculation activities. The results also imply that strain-specific differences in expression levels, posttranslational modifications, and allelic differences outside the adhesion domains have little effect on flocculation. IMPORTANCE As a nonmotile organism, Saccharomyces cerevisiae employs the cell surface flocculin Flo11/Muc1 as an important means of adapting to environmental change. However, there is a great deal of strain variation in the expression of Flo11-dependent phenotypes, including flocculation. In this study, we investigated the molecular basis of this strain-specific phenotypic variability. Our data indicate that strain-specific differences in the level of flocculation result from significant sequence differences in the FLO11 alleles and do not depend on quantitative differences in FLO11 expression or on surface hydrophobicity. We further have shown that beads coated with amino-terminal domain peptide bind preferentially to homologous cells. These data show that variability in the structure of the Flo11 adhesion domain may thus be an important determinant of membership in microbial communities and hence may drive selection and evolution.
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Quorum-sensing in yeast and its potential in wine making. Appl Microbiol Biotechnol 2016; 100:7841-52. [DOI: 10.1007/s00253-016-7758-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 10/21/2022]
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Tofalo R, Perpetuini G, Di Gianvito P, Arfelli G, Schirone M, Corsetti A, Suzzi G. Characterization of specialized flocculent yeasts to improve sparkling wine fermentation. J Appl Microbiol 2016; 120:1574-84. [DOI: 10.1111/jam.13113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 02/10/2016] [Accepted: 02/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- R. Tofalo
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Perpetuini
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - P. Di Gianvito
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Arfelli
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - M. Schirone
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - A. Corsetti
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Suzzi
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
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Flocculation-Related Gene Identification by Whole-Genome Sequencing of Thauera aminoaromatica MZ1T Floc-Defective Mutants. Appl Environ Microbiol 2015; 82:1646-52. [PMID: 26712552 PMCID: PMC4784049 DOI: 10.1128/aem.02917-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/18/2015] [Indexed: 01/12/2023] Open
Abstract
Thauera aminoaromatica MZ1T, a floc-forming bacterium isolated from an industrial activated-sludge wastewater treatment plant, overproduces exopolysaccharide (EPS), leading to viscous bulking. This phenomenon results in poor sludge settling and dewatering during the clarification process. To identify genes responsible for bacterial flocculation, a whole-genome phenotypic-sequencing technique was applied. Genomic DNA of MZ1T flocculation-deficient mutants was subjected to massively parallel sequencing. The resultant high-quality reads were assembled and compared to the reference genome of the wild type (WT). We identified nine nonsynonymous mutations and one nonsense mutation putatively involved in EPS biosynthesis. Complementation of the nonsense mutation located in an EPS deacetylase gene restored the flocculating phenotype. The Fourier transform infrared (FTIR) spectra of EPS isolated from the wild type showed a reduced C=O peak of the N-acetyl group at 1,665 cm−1 compared to the spectra of MZ1T floc-deficient mutant EPS, suggesting that the WT EPS was partially deacetylated. Gene expression analysis also demonstrated that the putative deacetylase gene transcript increased before flocculation occurred. These data suggest that targeting deacetylation processes via direct chemical modification of EPS or enzyme inhibition may prove useful in combating viscous bulking in this and related bacteria.
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Transcription Factor SomA Is Required for Adhesion, Development and Virulence of the Human Pathogen Aspergillus fumigatus. PLoS Pathog 2015; 11:e1005205. [PMID: 26529322 PMCID: PMC4631450 DOI: 10.1371/journal.ppat.1005205] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/13/2015] [Indexed: 11/19/2022] Open
Abstract
The transcription factor Flo8/Som1 controls filamentous growth in Saccharomyces cerevisiae and virulence in the plant pathogen Magnaporthe oryzae. Flo8/Som1 includes a characteristic N-terminal LUG/LUH-Flo8-single-stranded DNA binding (LUFS) domain and is activated by the cAMP dependent protein kinase A signaling pathway. Heterologous SomA from Aspergillus fumigatus rescued in yeast flo8 mutant strains several phenotypes including adhesion or flocculation in haploids and pseudohyphal growth in diploids, respectively. A. fumigatus SomA acts similarly to yeast Flo8 on the promoter of FLO11 fused with reporter gene (LacZ) in S. cerevisiae. FLO11 expression in yeast requires an activator complex including Flo8 and Mfg1. Furthermore, SomA physically interacts with PtaB, which is related to yeast Mfg1. Loss of the somA gene in A. fumigatus resulted in a slow growth phenotype and a block in asexual development. Only aerial hyphae without further differentiation could be formed. The deletion phenotype was verified by a conditional expression of somA using the inducible Tet-on system. A adherence assay with the conditional somA expression strain indicated that SomA is required for biofilm formation. A ptaB deletion strain showed a similar phenotype supporting that the SomA/PtaB complex controls A. fumigatus biofilm formation. Transcriptional analysis showed that SomA regulates expression of genes for several transcription factors which control conidiation or adhesion of A. fumigatus. Infection assays with fertilized chicken eggs as well as with mice revealed that SomA is required for pathogenicity. These data corroborate a complex control function of SomA acting as a central factor of the transcriptional network, which connects adhesion, spore formation and virulence in the opportunistic human pathogen A. fumigatus. Invasive fungal infections affecting immunocompromised patients are emerging worldwide. Among various human fungal pathogens, Aspergillus fumigatus is one of the most common molds causing severe invasive aspergillosis in immunocompromised patients. The conidia, which can evade from innate immunity and adhere to epithelial cells of alveoli in human lungs will start to germinate and cause the disease. Currently, the understanding of the molecular mechanisms of adherence of fungal cells to hosts is scarce. The transcription factor Flo8 controls adhesion to biotic or abiotic surfaces and morphological development in baker’s yeast. Flo8 homologues in the dimorphic human pathogenic yeast Candida albicans or the filamentous plant pathogen Magnaporthe oryzae are required for development and virulence. We found in this study that the Flo8 homologue SomA of A. fumigatus is required for adhesion and conidiation. Two independent invasive aspergillosis assays using chicken eggs or mouse demonstrated that deletion of the corresponding gene resulted in attenuated virulence. SomA represents an important fungal transcription factor at the interface between adherence, asexual spore formation and pathogenicity in an important opportunistic human pathogen.
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Flocculation inSaccharomyces cerevisiaeis regulated by RNA/DNA helicase Sen1p. FEBS Lett 2015; 589:3165-74. [DOI: 10.1016/j.febslet.2015.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/13/2022]
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Rossouw D, Bagheri B, Setati ME, Bauer FF. Co-Flocculation of Yeast Species, a New Mechanism to Govern Population Dynamics in Microbial Ecosystems. PLoS One 2015; 10:e0136249. [PMID: 26317200 PMCID: PMC4552943 DOI: 10.1371/journal.pone.0136249] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Flocculation has primarily been studied as an important technological property of Saccharomyces cerevisiae yeast strains in fermentation processes such as brewing and winemaking. These studies have led to the identification of a group of closely related genes, referred to as the FLO gene family, which controls the flocculation phenotype. All naturally occurring S. cerevisiae strains assessed thus far possess at least four independent copies of structurally similar FLO genes, namely FLO1, FLO5, FLO9 and FLO10. The genes appear to differ primarily by the degree of flocculation induced by their expression. However, the reason for the existence of a large family of very similar genes, all involved in the same phenotype, has remained unclear. In natural ecosystems, and in wine production, S. cerevisiae growth together and competes with a large number of other Saccharomyces and many more non-Saccharomyces yeast species. Our data show that many strains of such wine-related non-Saccharomyces species, some of which have recently attracted significant biotechnological interest as they contribute positively to fermentation and wine character, were able to flocculate efficiently. The data also show that both flocculent and non-flocculent S. cerevisiae strains formed mixed species flocs (a process hereafter referred to as co-flocculation) with some of these non-Saccharomyces yeasts. This ability of yeast strains to impact flocculation behaviour of other species in mixed inocula has not been described previously. Further investigation into the genetic regulation of co-flocculation revealed that different FLO genes impact differently on such adhesion phenotypes, favouring adhesion with some species while excluding other species from such mixed flocs. The data therefore strongly suggest that FLO genes govern the selective association of S. cerevisiae with specific species of non-Saccharomyces yeasts, and may therefore be drivers of ecosystem organisational patterns. Our data provide, for the first time, insights into the role of the FLO gene family beyond intraspecies cellular association, and suggest a wider evolutionary role for the FLO genes. Such a role would explain the evolutionary persistence of a large multigene family of genes with apparently similar function.
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Affiliation(s)
- Debra Rossouw
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Bahareh Bagheri
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Mathabatha Evodia Setati
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Florian Franz Bauer
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
- * E-mail:
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Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability. PLoS One 2015; 10:e0122709. [PMID: 25884705 PMCID: PMC4401569 DOI: 10.1371/journal.pone.0122709] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12 h, 24 h and 96 h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations.
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48
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Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. mBio 2015; 6:mBio.00427-15. [PMID: 25873380 PMCID: PMC4453552 DOI: 10.1128/mbio.00427-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.
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Díaz-Santos E, Vila M, de la Vega M, León R, Vigara J. Study of bioflocculation induced by Saccharomyces bayanus var. uvarum and flocculating protein factors in microalgae. ALGAL RES 2015. [DOI: 10.1016/j.algal.2014.12.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Alvarez F, Correa LFDM, Araújo TM, Mota BEF, da Conceição LEFR, Castro IDM, Brandão RL. Variable flocculation profiles of yeast strains isolated from cachaça distilleries. Int J Food Microbiol 2014; 190:97-104. [PMID: 25209588 DOI: 10.1016/j.ijfoodmicro.2014.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 08/04/2014] [Accepted: 08/09/2014] [Indexed: 10/24/2022]
Abstract
In cachaça production, the use of yeast cells as starters with predictable flocculation behavior facilitates the cell recovery at the end of each fermentation cycle. Therefore, the aim of this work was to explain the behavior of cachaça yeast strains in fermentation vats containing sugarcane through the determination of biochemical and molecular parameters associated with flocculation phenotypes. By analyzing thirteen cachaça yeast strains isolated from different distilleries, our results demonstrated that neither classic biochemical measurements (e.g., percentage of flocculation, EDTA sensitivity, cell surface hydrophobicity, and sugar residues on the cell wall) nor modern molecular approaches, such as polymerase chain reaction (PCR) and real-time PCR (q-PCR), were sufficient to distinctly classify the cachaça yeast strains according to their flocculation behavior. It seems that flocculation is indeed a strain-specific phenomenon that is difficult to explain and/or categorize by the available methodologies.
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Affiliation(s)
- Florencia Alvarez
- Cerlev - Projetos e Inovação na Biotecnologia da Fermentação Ltda, Rua Amaro Lanari 59, Saramenha, 35.400-000 Ouro Preto, MG, Brazil
| | - Lygia Fátima da Mata Correa
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Thalita Macedo Araújo
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Bruno Eduardo Fernandes Mota
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | | | - Ieso de Miranda Castro
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Brazil.
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