1
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Pangestu R, Kahar P, Ogino C, Kondo A. Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation. Yeast 2024; 41:192-206. [PMID: 38081785 DOI: 10.1002/yea.3917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/23/2023] [Indexed: 04/09/2024] Open
Abstract
While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.
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Affiliation(s)
- Radityo Pangestu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
- National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation (STIN), Kobe University, Kobe, Hyogo, Japan
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2
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Nasalingkhan C, Sirinonthanawech N, Noree C. Robust assembly of the aldehyde dehydrogenase Ald4p in Saccharomyces cerevisiae. Biol Open 2023; 12:bio060070. [PMID: 37767855 PMCID: PMC10602002 DOI: 10.1242/bio.060070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023] Open
Abstract
As part of our studies of yeast aldehyde dehydrogenase (Ald4p) assembly, we identified a population of transformants (SWORD strain) that show more robust filament formation of GFP-tagged Ald4p (Ald4p-GFP) than that of a wild type ALD4::GFP strain. Sequencing of the ALD4 gene in the SWORD strain showed that the increased assembly was not due to changes to the ALD4 coding sequence, suggesting that a second mutation site was altering Ald4p assembly. Using short-read whole-genome sequencing, we identified spontaneous mutations in FLO9. Introduction of the SWORD allele of FLO9 into a wild-type ALD4::GFP yeast strain revealed that the changes to FLO9 were a contributor to the increased length of Ald4p-GFP filaments we observe in the SWORD strain and that this effect was not due to an increase in Ald4p protein levels. However, the expression of the FLO9 (SWORD) allele in wild-type yeast did not fully recapitulate the length control defect we observed in SWORD strains, arguing that there are additional genes contributing to the filament length phenotype. For our future work, this FLO9 from SWORD will be tested whether it could show global effect, promoting the assembly of some other filament-forming enzymes.
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Affiliation(s)
- Channarong Nasalingkhan
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Naraporn Sirinonthanawech
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
| | - Chalongrat Noree
- Institute of Molecular Biosciences, Mahidol University, 25/25 Phuttamonthon 4 Road, Salaya, Phuttamonthon, Nakhon Pathom 73170Thailand
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3
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Park K, Lim JY, Kim JH, Lee J, Shin S, Park HM. LAMMER Kinase Modulates Cell Cycle by Phosphorylating the MBF Repressor, Yox1, in Schizosaccharomyces pombe. MYCOBIOLOGY 2023; 51:372-378. [PMID: 37929004 PMCID: PMC10621261 DOI: 10.1080/12298093.2023.2262806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Lkh1, a LAMMER kinase homolog in the fission yeast Schizosaccharomyces pombe, acts as a negative regulator of filamentous growth and flocculation. It is also involved in the response to oxidative stress. The lkh1-deletion mutant displays slower cell growth, shorter cell size, and abnormal DNA content compared to the wild type. These phenotypes suggest that Lkh1 controls cell size and cell cycle progression. When we performed microarray analysis using the lkh1-deletion mutant, we found that only four of the up-regulated genes in the lkh1-deletion were associated with the cell cycle. Interestingly, all of these genes are regulated by the Mlu1 cell cycle box binding factor (MBF), which is a transcription complex responsible for regulating the expression of cell cycle genes during the G1/S phase. Transcription analyses of the MBF-dependent cell-cycle genes, including negative feedback regulators, confirmed the up-regulation of these genes by the deletion of lkh1. Pull-down assay confirmed the interaction between Lkh1 and Yox1, which is a negative feedback regulator of MBF. This result supports the involvement of LAMMER kinase in cell cycle regulation by modulating MBF activity. In vitro kinase assay and NetPhosK 2.0 analysis with the Yox1T40,41A mutant allele revealed that T40 and T41 residues are the phosphorylation sites mediated by Lkh1. These sites affect the G1/S cell cycle progression of fission yeast by modulating the activity of the MBF complex.
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Affiliation(s)
- Kibum Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Joo-Yeon Lim
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN, USA
| | - Je-Hoon Kim
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jieun Lee
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Songju Shin
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hee-Moon Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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4
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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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5
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Belpaire TER, Pešek J, Lories B, Verstrepen KJ, Steenackers HP, Ramon H, Smeets B. Permissive aggregative group formation favors coexistence between cooperators and defectors in yeast. THE ISME JOURNAL 2022; 16:2305-2312. [PMID: 35778439 PMCID: PMC9477849 DOI: 10.1038/s41396-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 06/01/2023]
Abstract
In Saccharomyces cerevisiae, the FLO1 gene encodes flocculins that lead to formation of multicellular flocs, that offer protection to the constituent cells. Flo1p was found to preferentially bind to fellow cooperators compared to defectors lacking FLO1 expression, enriching cooperators within the flocs. Given this dual function in cooperation and kin recognition, FLO1 has been termed a "green beard gene". Because of the heterophilic nature of the Flo1p bond however, we hypothesize that kin recognition is permissive and depends on the relative stability of the FLO1+/flo1- versus FLO1+/FLO1+ detachment force F. We combine single-cell measurements of adhesion, individual cell-based simulations of cluster formation, and in vitro flocculation to study the impact of relative bond stability on the evolutionary stability of cooperation. We identify a trade-off between both aspects of the green beard mechanism, with reduced relative bond stability leading to increased kin recognition at the expense of cooperative benefits. We show that the fitness of FLO1 cooperators decreases as their frequency in the population increases, arising from the observed permissive character (F+- = 0.5 F++) of the Flo1p bond. Considering the costs associated with FLO1 expression, this asymmetric selection often results in a stable coexistence between cooperators and defectors.
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Affiliation(s)
- Tom E R Belpaire
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium.
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium.
| | - Jiří Pešek
- Team SIMBIOTX, Inria Saclay, 91120, Palaiseau, France
| | - Bram Lories
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Kevin J Verstrepen
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- Laboratory of Systems Biology, VIB-KU Leuven Center for Microbiology, 3001, Leuven, Belgium
| | - Hans P Steenackers
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Herman Ramon
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium
| | - Bart Smeets
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium
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6
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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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7
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Alkalbani NS, Osaili TM, Al-Nabulsi AA, Olaimat AN, Liu SQ, Shah NP, Apostolopoulos V, Ayyash MM. Assessment of Yeasts as Potential Probiotics: A Review of Gastrointestinal Tract Conditions and Investigation Methods. J Fungi (Basel) 2022; 8:jof8040365. [PMID: 35448596 PMCID: PMC9027893 DOI: 10.3390/jof8040365] [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: 02/22/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Probiotics are microorganisms (including bacteria, yeasts and moulds) that confer various health benefits to the host, when consumed in sufficient amounts. Food products containing probiotics, called functional foods, have several health-promoting and therapeutic benefits. The significant role of yeasts in producing functional foods with promoted health benefits is well documented. Hence, there is considerable interest in isolating new yeasts as potential probiotics. Survival in the gastrointestinal tract (GIT), salt tolerance and adherence to epithelial cells are preconditions to classify such microorganisms as probiotics. Clear understanding of how yeasts can overcome GIT and salt stresses and the conditions that support yeasts to grow under such conditions is paramount for identifying, characterising and selecting probiotic yeast strains. This study elaborated the adaptations and mechanisms underlying the survival of probiotic yeasts under GIT and salt stresses. This study also discussed the capability of yeasts to adhere to epithelial cells (hydrophobicity and autoaggregation) and shed light on in vitro methods used to assess the probiotic characteristics of newly isolated yeasts.
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Affiliation(s)
- Nadia S. Alkalbani
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Tareq M. Osaili
- Department Clinical Nutrition and Dietetics, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates;
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Anas A. Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P. O. Box 330127, Zarqa 13133, Jordan;
| | - Shao-Quan Liu
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, S14 Level 5, Science Drive 2, Singapore 117542, Singapore;
| | - Nagendra P. Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong 999077, China;
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia;
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Mutamed M. Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
- Correspondence:
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8
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:6440159. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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9
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Sun L, Zhang C, Chen J, Zhao X, Bai F, Zhong S. Combining oligomer build-up with alanine scanning to determine the flocculation protein mutants for enhancing oligosaccharide binding. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.2015068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lu Sun
- School of Bioengineering, Dalian University of Technology, Liaoning, People’s Republic of China
| | - Chenhong Zhang
- School of Bioengineering, Dalian University of Technology, Liaoning, People’s Republic of China
| | - Jiemin Chen
- School of Bioengineering, Dalian University of Technology, Liaoning, People’s Republic of China
| | - Xinqing Zhao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Fengwu Bai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Shijun Zhong
- School of Bioengineering, Dalian University of Technology, Liaoning, People’s Republic of China
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10
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Wang D, Li W, Zhang X, Liang S, Lin Y. Green Process: Improved Semi-Continuous Fermentation of Pichia pastoris Based on the Principle of Vitality Cell Separation. Front Bioeng Biotechnol 2021; 9:777774. [PMID: 34917600 PMCID: PMC8669635 DOI: 10.3389/fbioe.2021.777774] [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: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
The large-scale fermentation of Pichia pastoris for recombinant protein production would be time consuming and produce a large amount of waste yeast. Here we introduce a novel semi-continuous fermentation process for P. pastoris GS115 that can separate vitality cells from broth and recycle the cells to produce high-secretory recombinant pectate lyase. It is based on differences in cell sedimentation coefficients with the formation of salt bridges between metal ions and various cell states. Compared to batch-fed cultivation and general semi-continuous culture, the novel process has significant advantages, such as consuming fewer resources, taking less time, and producing less waste yeast. Sedimentation with the addition of Fe3+ metal ions consumed 14.8 ± 0.0% glycerol, 97.8 ± 1.3% methanol, 55.0 ± 0.9 inorganic salts, 81.5 ± 0.0% time cost, and 77.0 ± 0.1% waste yeast versus batch-fed cultivation to produce an equal amount of protein; in addition, the cost of solid-liquid separation was lower for cells in the collected fermentation broth. The process is economically and environmentally efficient for producing recombinant proteins.
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Affiliation(s)
- Denggang Wang
- South China University of Technology, Guangzhou, China
| | - Wenjie Li
- South China University of Technology, Guangzhou, China
| | - Xinying Zhang
- South China University of Technology, Guangzhou, China
| | - Shuli Liang
- South China University of Technology, Guangzhou, China
| | - Ying Lin
- South China University of Technology, Guangzhou, China
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11
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Willaert RG, Kayacan Y, Devreese B. The Flo Adhesin Family. Pathogens 2021; 10:pathogens10111397. [PMID: 34832553 PMCID: PMC8621652 DOI: 10.3390/pathogens10111397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins. Next, the structure, function, and adhesion mechanisms of the Flo adhesins whose structure has been solved are discussed in detail. Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. These yeasts are discussed in relation to their adhesion characteristics and involvement in infections.
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Affiliation(s)
- Ronnie G. Willaert
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Correspondence: ; Tel.: +32-2629-1846
| | - Yeseren Kayacan
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bart Devreese
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Laboratory for Microbiology, Gent University (UGent), 9000 Gent, Belgium
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12
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Lipke PN, Mathelié-Guinlet M, Viljoen A, Dufrêne YF. A New Function for Amyloid-Like Interactions: Cross-Beta Aggregates of Adhesins form Cell-to-Cell Bonds. Pathogens 2021; 10:pathogens10081013. [PMID: 34451476 PMCID: PMC8398270 DOI: 10.3390/pathogens10081013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022] Open
Abstract
Amyloid structures assemble through a repeating type of bonding called "cross-β", in which identical sequences in many protein molecules form β-sheets that interdigitate through side chain interactions. We review the structural characteristics of such bonds. Single cell force microscopy (SCFM) shows that yeast expressing Als5 adhesin from Candida albicans demonstrate the empirical characteristics of cross-β interactions. These properties include affinity for amyloid-binding dyes, birefringence, critical concentration dependence, repeating structure, and inhibition by anti-amyloid agents. We present a model for how cross-β bonds form in trans between two adhering cells. These characteristics also apply to other fungal adhesins, so the mechanism appears to be an example of a new type of cell-cell adhesion.
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Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: ; Tel.: +1-(917)-696-4862
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
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13
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Lebleux M, Denimal E, De Oliveira D, Marin A, Desroche N, Alexandre H, Weidmann S, Rousseaux S. Prediction of Genetic Groups within Brettanomyces bruxellensis through Cell Morphology Using a Deep Learning Tool. J Fungi (Basel) 2021; 7:jof7080581. [PMID: 34436120 PMCID: PMC8396822 DOI: 10.3390/jof7080581] [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: 06/28/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
Abstract
Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly strain-dependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict their stress resistance capacities. Few predictive tools are available to reveal intraspecific diversity within B. bruxellensis species; also, they require expertise and can be expensive. In this study, a Random Amplified Polymorphic DNA (RAPD) adapted PCR method was used with three different primers to discriminate 74 different B. bruxellensis isolates. High correlation between the results of this method using the primer OPA-09 and those of a previous microsatellite analysis was obtained, allowing us to cluster the isolates among four genetic groups more quickly and cheaply than microsatellite analysis. To make analysis even faster, we further investigated the correlation suggested in a previous study between genetic groups and cell polymorphism using the analysis of optical microscopy images via deep learning. A Convolutional Neural Network (CNN) was trained to predict the genetic group of B. bruxellensis isolates with 96.6% accuracy. These methods make intraspecific discrimination among B. bruxellensis species faster, simpler and less costly. These results open up very promising new perspectives in oenology for the study of microbial ecosystems.
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Affiliation(s)
- Manon Lebleux
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
- Correspondence:
| | - Emmanuel Denimal
- AgroSup Dijon, Direction Scientifique, Appui à la Recherche, 26 Boulevard Docteur Petitjean, F-21000 Dijon, France;
| | - Déborah De Oliveira
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Ambroise Marin
- Plateau D’imagerie DimaCell, Esplanade Erasme, Agrosup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France;
| | | | - Hervé Alexandre
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Stéphanie Weidmann
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Sandrine Rousseaux
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
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14
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Man-Specific Lectins from Plants, Fungi, Algae and Cyanobacteria, as Potential Blockers for SARS-CoV, MERS-CoV and SARS-CoV-2 (COVID-19) Coronaviruses: Biomedical Perspectives. Cells 2021; 10:cells10071619. [PMID: 34203435 PMCID: PMC8305077 DOI: 10.3390/cells10071619] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Betacoronaviruses, responsible for the “Severe Acute Respiratory Syndrome” (SARS) and the “Middle East Respiratory Syndrome” (MERS), use the spikes protruding from the virion envelope to attach and subsequently infect the host cells. The coronavirus spike (S) proteins contain receptor binding domains (RBD), allowing the specific recognition of either the dipeptidyl peptidase CD23 (MERS-CoV) or the angiotensin-converting enzyme ACE2 (SARS-Cov, SARS-CoV-2) host cell receptors. The heavily glycosylated S protein includes both complex and high-mannose type N-glycans that are well exposed at the surface of the spikes. A detailed analysis of the carbohydrate-binding specificity of mannose-binding lectins from plants, algae, fungi, and bacteria, revealed that, depending on their origin, they preferentially recognize either complex type N-glycans, or high-mannose type N-glycans. Since both complex and high-mannose glycans substantially decorate the S proteins, mannose-specific lectins are potentially useful glycan probes for targeting the SARS-CoV, MERS-CoV, and SARS-CoV-2 virions. Mannose-binding legume lectins, like pea lectin, and monocot mannose-binding lectins, like snowdrop lectin or the algal lectin griffithsin, which specifically recognize complex N-glycans and high-mannose glycans, respectively, are particularly adapted for targeting coronaviruses. The biomedical prospects of targeting coronaviruses with mannose-specific lectins are wide-ranging including detection, immobilization, prevention, and control of coronavirus infection.
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15
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Fukuda APM, Camandona VDL, Francisco KJM, Rios-Anjos RM, Lucio do Lago C, Ferreira-Junior JR. Simulated microgravity accelerates aging in Saccharomyces cerevisiae. LIFE SCIENCES IN SPACE RESEARCH 2021; 28:32-40. [PMID: 33612178 DOI: 10.1016/j.lssr.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/01/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
The human body experiences physiological changes under microgravity environment that phenocopy aging on Earth. These changes include early onset osteoporosis, skeletal muscle atrophy, cardiac dysfunction, and immunosenescence, and such adaptations to the space environment may pose some risk to crewed missions to Mars. To investigate the effect of microgravity on aging, many model organisms have been used such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and mice. Herein we report that the budding yeast Saccharomyces cerevisiae show decreased replicative lifespan (RLS) under simulated microgravity in a clinostat. The reduction of yeast lifespan is not a result of decreased tolerance to heat shock or oxidative stress and could be overcome either by deletion of FOB1 or calorie restriction, two known interventions that extend yeast RLS. Deletion of the sirtuin gene SIR2 worsens the simulated microgravity effect on RLS, and together with the fob1Δ mutant phenotype, it suggests that simulated microgravity augments the formation of extrachromosomal rDNA circles, which accumulate in yeast during aging. We also show that the chronological lifespan in minimal medium was not changed when cells were grown in the clinostat. Our data suggest that the reduction in longevity due to simulated microgravity is conserved in yeast, worms, and flies, and these findings may have potential implications for future crewed missions in space, as well as the use of microgravity as a model for human aging.
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Affiliation(s)
| | | | | | | | - Claudimir Lucio do Lago
- Departamento de Química Fundamental - Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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16
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Flocculation Type and the Lg-FLO1 Gene of Bottom-Fermenting Yeast Are Derived from Top-Fermenting Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1843944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Chen BL, Mhuantong W, Ho SH, Chang JS, Zhao XQ, Bai FW. Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11. BMC Genomics 2020; 21:743. [PMID: 33109102 PMCID: PMC7590803 DOI: 10.1186/s12864-020-07142-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications. RESULTS We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies. CONCLUSIONS The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.
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Affiliation(s)
- Bai-Ling Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung City, Taiwan.,Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung City, Taiwan.,Department of Chemical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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18
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Ji H, Xu K, Dong X, Sun D, Peng R, Lin S, Zhang K, Jin L. Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii. J Biosci Bioeng 2020; 130:588-595. [PMID: 32798135 DOI: 10.1016/j.jbiosc.2020.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/11/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022]
Abstract
The non-conventional yeast Pichia kudriavzevii is considered to be a promising biotechnological host for the production of organic acids under low-pH conditions. However, little is known about the low-pH stress response in P. kudriavzevii, which significantly restricts its future development. In this study, P. kudriavzevii N-X showed great tolerance to low-pH stress, but the cell aggregation upon extremely acidic conditions might be unfavorable for low-pH fermentation. We therefore conducted RNA-Seq to compare global gene expression of P. kudriavzevii N-X in response to different pH stresses. Totally 434 genes were identified to be differentially expressed genes (DEGs), and annotation and enrichment analysis suggested that multiple genes associated with regulation of membrane lipid composition, filamentous growth and arginine metabolism were differentially expressed. The increased specific activity of arginase and intracellular ammonia concentration of P. kudriavzevii cultured at pH 2.0 further implied potential roles of arginine in response to extreme low-pH conditions. Extracellular supplementation of 5 mM arginine resulted in increased pHi and cell growth at pH 2.0, meanwhile the cell aggregation was partially suppressed. Additionally, overexpression of ARG J involving in arginine synthesis can also enhance the cell growth and reduce the aggregation effect. These results suggested that increasing arginine flux might be an alternative approach in the developing of P. kudriavzevii as a platform host for production of organic acids under low-pH conditions.
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Affiliation(s)
- Hao Ji
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China.
| | - Ke Xu
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang 325006, PR China
| | - Da Sun
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Renyi Peng
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Kailun Zhang
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Libo Jin
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
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19
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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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20
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Zhu Z, Wang Y, Zhou X, Yang L, Meng G, Zhang Z. SWAV: a web-based visualization browser for sliding window analysis. Sci Rep 2020; 10:149. [PMID: 31924845 PMCID: PMC6954255 DOI: 10.1038/s41598-019-57038-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/19/2019] [Indexed: 01/23/2023] Open
Abstract
Sliding window analysis has been extensively applied in evolutionary biology. With the development of the high-throughput DNA sequencing of organisms at the population level, an application that is dedicated to visualizing population genetic test statistics at the genomic level is needed. We have developed the sliding window analysis viewer (SWAV), which is a web-based program that can be used to integrate, view and browse test statistics and perform genome annotation. In addition to browsing, SAV can mark, generate and customize statistical images and search by sequence alignment, position or gene name. These features facilitate the effectiveness of sliding window analysis. As an example application, yeast and silkworm resequencing data are analyzed with SWAV. The SWAV package, user manual and usage demo are available at http://swav.popgenetics.net.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.
| | - Yawang Wang
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.,Khoury College of Computer Sciences, Northeastern University, Seattle, 98109, WA, USA
| | - Xichuan Zhou
- The School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, China
| | - Liuqing Yang
- Department of Medical Ultrasonics, Chongqing Occupational Disease Prevention Hospital, Chongqing, 400060, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
| | - Ze Zhang
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
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21
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Cortesão M, Schütze T, Marx R, Moeller R, Meyer V. Fungal Biotechnology in Space: Why and How? GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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22
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Godara A, Rodriguez MAG, Weatherston JD, Peabody GL, Wu HJ, Kao KC. Beneficial mutations for carotenoid production identified from laboratory-evolved Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:1793-1804. [PMID: 31595456 DOI: 10.1007/s10295-019-02241-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/26/2019] [Indexed: 01/26/2023]
Abstract
Adaptive laboratory evolution (ALE) is a powerful tool used to increase strain fitness in the presence of environmental stressors. If production and strain fitness can be coupled, ALE can be used to increase product formation. In earlier work, carotenoids hyperproducing mutants were obtained using an ALE strategy. Here, de novo mutations were identified in hyperproducers, and reconstructed mutants were explored to determine the exact impact of each mutation on production and tolerance. A single mutation in YMRCTy1-3 conferred increased carotenoid production, and when combined with other beneficial mutations led to further increased β-carotene production. Findings also suggest that the ALE strategy selected for mutations that confer increased carotenoid production as primary phenotype. Raman spectroscopy analysis and total lipid quantification revealed positive correlation between increased lipid content and increased β-carotene production. Finally, we demonstrated that the best combinations of mutations identified for β-carotene production were also beneficial for production of lycopene.
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Affiliation(s)
- Avinash Godara
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Joshua D Weatherston
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Hung-Jen Wu
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Katy C Kao
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA. .,Department of Chemical and Materials Engineering, San Jose State University, One Washington Square, San Jose, CA, 95129, USA.
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23
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Sariki SK, Kumawat R, Singh V, Tomar RS. Flocculation ofSaccharomyces cerevisiaeis dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway. Mol Microbiol 2019; 112:1350-1369. [DOI: 10.1111/mmi.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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24
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Abstract
Understanding how and why cells cooperate to form multicellular organisms is a central aim of evolutionary biology. Multicellular groups can form through clonal development (where daughter cells stick to mother cells after division) or by aggregation (where cells aggregate to form groups). These different ways of forming groups directly affect relatedness between individual cells, which in turn can influence the degree of cooperation and conflict within the multicellular group. It is hard to study the evolution of multicellularity by focusing only on obligately multicellular organisms, like complex animals and plants, because the factors that favour multicellular cooperation cannot be disentangled, as cells cannot survive and reproduce independently. We support the use of Saccharomyces cerevisiae as an ideal model for studying the very first stages of the evolution of multicellularity. This is because it can form multicellular groups both clonally and through aggregation and uses a family of proteins called ‘flocculins’ that determine the way in which groups form, making it particularly amenable to laboratory experiments. We briefly review current knowledge about multicellularity in S. cerevisiae and then propose a framework for making predictions about the evolution of multicellular phenotypes in yeast based on social evolution theory. We finish by explaining how S. cerevisiae is a particularly useful experimental model for the analysis of open questions concerning multicellularity.
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Affiliation(s)
- R M Fisher
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - B Regenberg
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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25
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Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F. Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan. MICROBIAL CELL 2019; 6:397-413. [PMID: 31528631 PMCID: PMC6717879 DOI: 10.15698/mic2019.09.690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Emily Cook
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Eugene Kroll
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Adam Rosebrock
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Present address: Stony Brook School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Amy Caudy
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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26
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Cao P, Wall D. Direct visualization of a molecular handshake that governs kin recognition and tissue formation in myxobacteria. Nat Commun 2019; 10:3073. [PMID: 31300643 PMCID: PMC6626042 DOI: 10.1038/s41467-019-11108-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Many organisms regulate their social life through kin recognition, but the underlying mechanisms are poorly understood. Here, we use a social bacterium, Myxococcus xanthus, to investigate kin recognition at the molecular level. By direct visualization of a cell surface receptor, TraA, we show how these myxobacteria identify kin and transition towards multicellularity. TraA is fluid on the cell surface, and homotypic interactions between TraA from juxtaposed cells trigger the receptors to coalesce, representing a ‘molecular handshake’. Polymorphisms within TraA govern social recognition such that receptors cluster only between individuals bearing compatible alleles. TraA clusters, which resemble eukaryotic gap junctions, direct the robust exchange of cellular goods that allows heterogeneous populations to transition towards homeostasis. This work provides a conceptual framework for how microbes use a fluid outer membrane receptor to recognize and assemble kin cells into a cooperative multicellular community that resembles a tissue. Many organisms, including the bacterium Myxococcus xanthus, regulate their social life through kin recognition. Here, Cao and Wall show that these bacteria use a polymorphic and fluid cell-surface receptor to recognize and assemble kin cells into a cooperative multicellular community that resembles a tissue.
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Affiliation(s)
- Pengbo Cao
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, 1000 E University Avenue, Laramie, WY, 82071, USA.
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27
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Alonso-Del-Real J, Pérez-Torrado R, Querol A, Barrio E. Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization. Environ Microbiol 2019; 21:1627-1644. [PMID: 30672093 DOI: 10.1111/1462-2920.14536] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Grape must is a sugar-rich habitat for a complex microbiota which is replaced by Saccharomyces cerevisiae strains during the first fermentation stages. Interest on yeast competitive interactions has recently been propelled due to the use of alternative yeasts in the wine industry to respond to new market demands. The main issue resides in the persistence of these yeasts due to the specific competitive activity of S. cerevisiae. To gather deeper knowledge of the molecular mechanisms involved, we performed a comparative transcriptomic analysis during fermentation carried out by a wine S. cerevisiae strain and a strain representative of the cryophilic S. kudriavzevii, which exhibits high genetic and physiological similarities to S. cerevisiae, but also differences of biotechnological interest. In this study, we report that transcriptomic response to the presence of a competitor is stronger in S. cerevisiae than in S. kudriavzevii. Our results demonstrate that a wine S. cerevisiae industrial strain accelerates nutrient uptake and utilization to outcompete the co-inoculated yeast, and that this process requires cell-to-cell contact to occur. Finally, we propose that this competitive phenotype evolved recently, during the adaptation of S. cerevisiae to man-manipulated fermentative environments, since a non-wine S. cerevisiae strain, isolated from a North American oak, showed a remarkable low response to competition.
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Affiliation(s)
- Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, València, Spain
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28
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Espinosa A, Paz-Y-Miño-C G. Discrimination Experiments in Entamoeba and Evidence from Other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals. J Eukaryot Microbiol 2019; 66:354-368. [PMID: 30055104 PMCID: PMC6349510 DOI: 10.1111/jeu.12673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023]
Abstract
Entamoeba histolytica is one of the least understood protists in terms of taxa, clone, and kin discrimination/recognition ability. However, the capacity to tell apart same or self (clone/kin) from different or nonself (nonclone/nonkin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = noncooperators that benefit from others' investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa, clone, and kin discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica's life cycle, host infestation, and implications of these features of the amebas' natural history for human health (including mitigation of amebiasis).
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Affiliation(s)
- Avelina Espinosa
- Department of Biology, Roger Williams University, Bristol, Rhode Island
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
| | - Guillermo Paz-Y-Miño-C
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
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29
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A Highly Polymorphic Receptor Governs Many Distinct Self-Recognition Types within the Myxococcales Order. mBio 2019; 10:mBio.02751-18. [PMID: 30755513 PMCID: PMC6372800 DOI: 10.1128/mbio.02751-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many biological species distinguish self from nonself by using different mechanisms. Higher animals recognize close kin via complex processes that often involve the five senses, cognition, and learning, whereas some microbes achieve self-recognition simply through the activity of a single genetic locus. Here we describe a single locus, traA, in myxobacteria that governs cell-cell recognition within natural populations. We found that traA is widespread across the order Myxococcales. TraA is highly polymorphic among diverse myxobacterial isolates, and such polymorphisms determine selectivity in self-recognition. Through bioinformatic and experimental analyses, we showed that traA governs many distinct recognition groups within Myxococcales. This report provides an example in which a single locus influences social recognition across a wide phylogenetic range of natural populations. Self-recognition underlies sociality in many group-living organisms. In bacteria, cells use various strategies to recognize kin to form social groups and, in some cases, to transition into multicellular life. One strategy relies on a single genetic locus that encodes a variable phenotypic tag (“greenbeard”) for recognizing other tag bearers. Previously, we discovered a polymorphic cell surface receptor called TraA that directs self-identification through homotypic interactions in the social bacterium Myxococcus xanthus. Recognition by TraA leads to cellular resource sharing in a process called outer membrane exchange (OME). A second gene in the traA operon, traB, is also required for OME but is not involved in recognition. Our prior studies of TraA identified only six recognition groups among closely related M. xanthus isolates. Here we hypothesize that the number of traA polymorphisms and, consequently, the diversity of recognition in wild isolates are much greater. To test this hypothesis, we expand the scope of TraA characterization to the order Myxococcales. From genomic sequences within the three suborders of Myxococcales, we identified 90 traA orthologs. Sequence analyses and functional characterization of traAB loci suggest that OME is well maintained among diverse myxobacterial taxonomic groups. Importantly, TraA orthologs are highly polymorphic within their variable domain, the region that confers selectivity in self-recognition. We experimentally defined 10 distinct recognition groups and, based on phylogenetic and experimental analyses, predicted >60 recognition groups among the 90 traA alleles. Taken together, our findings revealed a widespread greenbeard locus that mediates the diversity of self-recognition across the order Myxococcales.
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30
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Barre A, Bourne Y, Van Damme EJM, Rougé P. Overview of the Structure⁻Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi. Int J Mol Sci 2019; 20:E254. [PMID: 30634645 PMCID: PMC6359319 DOI: 10.3390/ijms20020254] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 01/05/2023] Open
Abstract
To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the "broad sugar-binding specificity" toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure⁻function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Yves Bourne
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Els J M Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
| | - Pierre Rougé
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
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31
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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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32
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Di Gianvito P, Tesnière C, Suzzi G, Blondin B, Tofalo R. Different genetic responses to oenological conditions between a flocculent wine yeast and its FLO5 deleted strain: Insights from the transcriptome. Food Res Int 2018; 114:178-186. [DOI: 10.1016/j.foodres.2018.07.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/06/2018] [Accepted: 07/30/2018] [Indexed: 01/26/2023]
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33
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Kock M, Brückner S, Wozniak N, Maestre-Reyna M, Veelders M, Schlereth J, Mösch HU, Essen LO. Structural and Functional Characterization of PA14/Flo5-Like Adhesins From Komagataella pastoris. Front Microbiol 2018; 9:2581. [PMID: 30425696 PMCID: PMC6218569 DOI: 10.3389/fmicb.2018.02581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/10/2018] [Indexed: 12/19/2022] Open
Abstract
Cell–cell and cell-substrate based adhesion of yeasts are major determinants of their adoption of different life styles. Genome-mining of ascomycetous GPI-anchored cell wall proteins with lectin-like PA14 domains identified a unique class of putative adhesins in the clade of methylotrophic Komagataella yeasts, many of which are known to colonize plants and insects involving yet unknown adhesion mechanisms. Here, we report the functional and structural analysis of two of its members: KpFlo1 (=Cea1), that is highly specific for terminal N-acetylglucosamine moieties, and KpFlo2, which represents an orphan lectin with intact binding site but unknown specificity. Crystal structures of the Cea1 adhesion domain complexed to N-acetylglucosamine and N,N′-diacetylchitobiose reveal a Ca2+-dependent binding mode that differs from other members of the PA14/Flo5 adhesin family. Heterologous expression of Cea1A in Saccharomyces cerevisiae promotes cellular adhesion to non-reducing ends of non-crystalline chitin. Overall, our data suggest that high-affinity recognition of β-GlcNAc-capped glycans by Cea1 enable Komagataella species to interact with surface cues present in fungi and insects.
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Affiliation(s)
- Michael Kock
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Stefan Brückner
- Department of Genetics, Faculty of Biology, Philipps University of Marburg, Marburg, Germany
| | - Nina Wozniak
- Department of Genetics, Faculty of Biology, Philipps University of Marburg, Marburg, Germany
| | | | - Maik Veelders
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Julia Schlereth
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Hans-Ulrich Mösch
- Department of Genetics, Faculty of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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34
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Willaert RG. Adhesins of Yeasts: Protein Structure and Interactions. J Fungi (Basel) 2018; 4:jof4040119. [PMID: 30373267 PMCID: PMC6308950 DOI: 10.3390/jof4040119] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
The ability of yeast cells to adhere to other cells or substrates is crucial for many yeasts. The budding yeast Saccharomyces cerevisiae can switch from a unicellular lifestyle to a multicellular one. A crucial step in multicellular lifestyle adaptation is self-recognition, self-interaction, and adhesion to abiotic surfaces. Infectious yeast diseases such as candidiasis are initiated by the adhesion of the yeast cells to host cells. Adhesion is accomplished by adhesin proteins that are attached to the cell wall and stick out to interact with other cells or substrates. Protein structures give detailed insights into the molecular mechanism of adhesin-ligand interaction. Currently, only the structures of a very limited number of N-terminal adhesion domains of adhesins have been solved. Therefore, this review focuses on these adhesin protein families. The protein architectures, protein structures, and ligand interactions of the flocculation protein family of S. cerevisiae; the epithelial adhesion family of C. glabrata; and the agglutinin-like sequence protein family of C. albicans are reviewed and discussed.
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Affiliation(s)
- Ronnie G Willaert
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), IJRG VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Research Group Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
- Department Bioscience Engineering, University Antwerp, 2020 Antwerp, Belgium.
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35
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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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36
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Kontár S, Varečka L, Híreš M, Kryštofová S, Šimkovič M. Light-induced conidiation of Trichoderma spp. strains is accompanied by development-dependent changes in the Ca 2+ binding to cell walls. Can J Microbiol 2018; 64:856-864. [PMID: 29906398 DOI: 10.1139/cjm-2017-0747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect of light on the binding of Ca2+ to mycelia and to cell walls isolated from aerial mycelia of three strains of Trichoderma spp. was studied. Two independent methods were used to measure the total Ca2+ content in mycelia and the Ca2+ bound to cell walls isolated from aerial mycelia. The results of these methods showed that the light-induced formation and maturation of conidia in Trichoderma spp. is accompanied by increased Ca2+ deposition in mycelia and cell walls. Moreover, the cultivation of Trichoderma atroviride F-534 in the presence of 45Ca2+ under circadian illumination showed that radioactivity was exclusively localized in the light-induced conidial rings of aerial mycelia. The fluorescence microscopy of chlortetracycline-stained mycelia showed that the major fraction of Ca2+ was accumulated in conidia and fructification structures, or some intracellular compartments in T. atroviride F-534 grown under circadian illumination, while only a limited amount of Ca2+ was associated with hyphal surfaces. In addition, the study of 45Ca2+ binding to cell walls revealed that T. atroviride F-534 displays both increased 45Ca2+ binding capacity and elevated affinity to 45Ca2+ binding upon illumination. The results indicate that conidia formation and (or) maturation is associated with changes in Ca2+ homeostasis.
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Affiliation(s)
- Szilvia Kontár
- a Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic.,b Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - L'udovít Varečka
- a Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic
| | - Michal Híreš
- a Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic
| | - Svetlana Kryštofová
- a Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic
| | - Martin Šimkovič
- a Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic
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37
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Beheshti A, Miller J, Kidane Y, Berrios D, Gebre SG, Costes SV. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies. Radiat Res 2018; 189:553-559. [DOI: 10.1667/rr15062.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Afshin Beheshti
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Jack Miller
- Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Yared Kidane
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Daniel Berrios
- USRA, NASA Ames Research Center, Moffett Field, Calfornia 94035
| | - Samrawit G. Gebre
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, California 94035
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38
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Lipke PN. What We Do Not Know about Fungal Cell Adhesion Molecules. J Fungi (Basel) 2018; 4:jof4020059. [PMID: 29772751 PMCID: PMC6023273 DOI: 10.3390/jof4020059] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022] Open
Abstract
There has been extensive research on structure and function of fungal cell adhesion molecules, but the most of the work has been about adhesins in Candida albicans and Saccharomyces cerevisiae. These yeasts are members of a single ascomycete order, and adhesion molecules from the six other fungal phyla are only sparsely described in the literature. In these other phyla, most of the research is at the cellular level, rather than at the molecular level, so there has been little characterization of the adhesion molecules themselves. A catalog of known adhesins shows some common features: high Ser/Thr content, tandem repeats, N- and O-glycosylations, GPI anchors, dibasic sequence motifs, and potential amyloid-forming sequences. However, none of these features is universal. Known ligands include proteins and glycans on homologous cells and host cells. Existing and novel tools can exploit the availability of genome sequences to identify and characterize new fungal adhesins. These include bioinformatics tools and well-established yeast surface display models, which could be coupled with an adhesion substrate array. Thus, new knowledge could be exploited to answer key questions in fungal ecology, animal and plant pathogenesis, and roles of biofilms in infection and biomass turnover.
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Affiliation(s)
- Peter N Lipke
- Biology Department, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA.
- The Graduate Center, City University of New York, New York, NY 10016, USA.
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Liu CG, Li ZY, Hao Y, Xia J, Bai FW, Mehmood MA. Computer Simulation Elucidates Yeast Flocculation and Sedimentation for Efficient Industrial Fermentation. Biotechnol J 2018; 13:e1700697. [DOI: 10.1002/biot.201700697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/31/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Zhi-Yang Li
- School of Information Science and Technology; Dalian Maritime University; Dalian Liaoning 116023 China
| | - Yue Hao
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture; Institute of Apicultural Research; Chinese Academy of Agricultural Sciences; Beijing 100093 China
| | - Juan Xia
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Muhammad Aamer Mehmood
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
- Department of Bioinformatics & Biotechnology; Bioenergy Research Centre; Government College University Faisalabad; Faisalabad-38000 Pakistan
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40
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Amyloid-Like β-Aggregates as Force-Sensitive Switches in Fungal Biofilms and Infections. Microbiol Mol Biol Rev 2017; 82:82/1/e00035-17. [PMID: 29187516 DOI: 10.1128/mmbr.00035-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cellular aggregation is an essential step in the formation of biofilms, which promote fungal survival and persistence in hosts. In many of the known yeast cell adhesion proteins, there are amino acid sequences predicted to form amyloid-like β-aggregates. These sequences mediate amyloid formation in vitro. In vivo, these sequences mediate a phase transition from a disordered state to a partially ordered state to create patches of adhesins on the cell surface. These β-aggregated protein patches are called adhesin nanodomains, and their presence greatly increases and strengthens cell-cell interactions in fungal cell aggregation. Nanodomain formation is slow (with molecular response in minutes and the consequences being evident for hours), and strong interactions lead to enhanced biofilm formation. Unique among functional amyloids, fungal adhesin β-aggregation can be triggered by the application of physical shear force, leading to cellular responses to flow-induced stress and the formation of robust biofilms that persist under flow. Bioinformatics analysis suggests that this phenomenon may be widespread. Analysis of fungal abscesses shows the presence of surface amyloids in situ, a finding which supports the idea that phase changes to an amyloid-like state occur in vivo. The amyloid-coated fungi bind the damage-associated molecular pattern receptor serum amyloid P component, and there may be a consequential modulation of innate immune responses to the fungi. Structural data now suggest mechanisms for the force-mediated induction of the phase change. We summarize and discuss evidence that the sequences function as triggers for protein aggregation and subsequent cellular aggregation, both in vitro and in vivo.
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FLO5 gene controls flocculation phenotype and adhesive properties in a Saccharomyces cerevisiae sparkling wine strain. Sci Rep 2017; 7:10786. [PMID: 28883485 PMCID: PMC5589750 DOI: 10.1038/s41598-017-09990-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Flocculation is an important feature for yeast survival in adverse conditions. The natural diversity of flocculating genes in Saccharomyces cerevisiae can also be exploited in several biotechnological applications. Flocculation is mainly regulated by the expression of genes belonging to the FLO family. These genes have a similar function, but their specific contribution to flocculation ability is still unclear. In this study, the distribution of FLO1, FLO5 and FLO8 genes in four S. cerevisiae wine strains was investigated. Subsequently, both FLO1 and FLO5 genes were separately deleted in a flocculent S. cerevisiae wine strain. After gene disruption, flocculation ability and agar adhesion were evaluated. FLO1 and FLO5 genes inheritance was also monitored. All strains presented different lengths for FLO1 and FLO5 genes. Results confirm that in S. cerevisiae strain F6789, the FLO5 gene drives flocculation and influences adhesive properties. Flocculation ability monitoring after a cross with a non-flocculent strain revealed that FLO5 is the gene responsible for flocculation development.
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Church M, Smith KC, Alhussain MM, Pennings S, Fleming AB. Sas3 and Ada2(Gcn5)-dependent histone H3 acetylation is required for transcription elongation at the de-repressed FLO1 gene. Nucleic Acids Res 2017; 45:4413-4430. [PMID: 28115623 PMCID: PMC5416777 DOI: 10.1093/nar/gkx028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/19/2017] [Indexed: 01/12/2023] Open
Abstract
The Saccharomyces cerevisiae FLO1 gene encodes a cell wall protein that imparts cell-cell adhesion. FLO1 transcription is regulated via the antagonistic activities of the Tup1-Cyc8 co-repressor and Swi-Snf co-activator complexes. Tup1-Cyc8 represses transcription through the organization of strongly positioned, hypoacetylated nucleosomes across gene promoters. Swi-Snf catalyzes remodeling of these nucleosomes in a mechanism involving histone acetylation that is poorly understood. Here, we show that FLO1 de-repression is accompanied by Swi-Snf recruitment, promoter histone eviction and Sas3 and Ada2(Gcn5)-dependent histone H3K14 acetylation. In the absence of H3K14 acetylation, Swi-Snf recruitment and histone eviction proceed, but transcription is reduced, suggesting these processes, while essential, are not sufficient for de-repression. Further analysis in the absence of H3K14 acetylation reveals RNAP II recruitment at the FLO1 promoter still occurs, but RNAP II is absent from the gene-coding region, demonstrating Sas3 and Ada2-dependent histone H3 acetylation is required for transcription elongation. Analysis of the transcription kinetics at other genes reveals shared mechanisms coupled to a distinct role for histone H3 acetylation, essential at FLO1, downstream of initiation. We propose histone H3 acetylation in the coding region provides rate-limiting control during the transition from initiation to elongation which dictates whether the gene is permissive for transcription.
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Affiliation(s)
- Michael Church
- School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Kim C Smith
- School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Mohamed M Alhussain
- School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Sari Pennings
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Alastair B Fleming
- School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, College Green, Dublin 2, Ireland
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Nydam ML, Stephenson EE, Waldman CE, De Tomaso AW. Balancing selection on allorecognition genes in the colonial ascidian Botryllus schlosseri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 69:60-74. [PMID: 28024871 DOI: 10.1016/j.dci.2016.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
Allorecognition is the capability of an organism to recognize its own or related tissues. The colonial ascidian Botryllus schlosseri, which comprises five genetically distinct and divergent species (Clades A-E), contains two adjacent genes that control allorecognition: fuhcsec and fuhctm. These genes have been characterized extensively in Clade A and are highly polymorphic. Using alleles from 10 populations across the range of Clade A, we investigated the type and strength of selection maintaining this variation. Both fuhc genes exhibit higher within-population variation and lower population differentiation measures (FST) than neutral loci. The fuhc genes contain a substantial number of codons with >95% posterior probability of dN/dS > 1. fuhcsec and fuhctm also have polymorphisms shared between Clade A and Clade E that were present prior to speciation (trans-species polymorphisms). These results provide robust evidence that the fuhc genes are evolving under balancing selection.
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Affiliation(s)
- Marie L Nydam
- Division of Science and Mathematics, Centre College, 600 W. Walnut Street, Danville, KY 40422, United States.
| | - Emily E Stephenson
- Division of Science and Mathematics, Centre College, 600 W. Walnut Street, Danville, KY 40422, United States; Centre for Infectious Disease Research, P.O. Box 34681, Lusaka, 10101, Zambia.
| | - Claire E Waldman
- Division of Science and Mathematics, Centre College, 600 W. Walnut Street, Danville, KY 40422, United States.
| | - Anthony W De Tomaso
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, United States.
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Self-identity reprogrammed by a single residue switch in a cell surface receptor of a social bacterium. Proc Natl Acad Sci U S A 2017; 114:3732-3737. [PMID: 28320967 DOI: 10.1073/pnas.1700315114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The ability to recognize close kin confers survival benefits on single-celled microbes that live in complex and changing environments. Microbial kinship detection relies on perceptible cues that reflect relatedness between individuals, although the mechanisms underlying recognition in natural populations remain poorly understood. In myxobacteria, cells identify related individuals through a polymorphic cell surface receptor, TraA. Recognition of compatible receptors leads to outer membrane exchange among clonemates and fitness consequences. Here, we investigated how a single receptor creates a diversity in recognition across myxobacterial populations. We first show that TraA requires its partner protein TraB to function in cell-cell adhesion. Recognition is shown to be traA allele-specific, where polymorphisms within TraA dictate binding selectivity. We reveal the malleability of TraA recognition, and seemingly minor changes to its variable region reprogram recognition outcomes. Strikingly, we identify a single residue (A/P205) as a molecular switch for TraA recognition. Substitutions at this position change the specificity of a diverse panel of environmental TraA receptors. In addition, we engineered a receptor with unique specificity by simply creating an A205P substitution, suggesting that modest changes in TraA can lead to diversification of new recognition groups in nature. We hypothesize that the malleable property of TraA has allowed it to evolve and create social barriers between myxobacterial populations and in turn avoid adverse interactions with relatives.
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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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Force Sensitivity in Saccharomyces cerevisiae Flocculins. mSphere 2016; 1:mSphere00128-16. [PMID: 27547825 PMCID: PMC4989244 DOI: 10.1128/msphere.00128-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022] Open
Abstract
The Saccharomyces cerevisiae flocculins mediate the formation of cellular aggregates and biofilm-like mats, useful in clearing yeast from fermentations. An important property of fungal adhesion proteins, including flocculins, is the ability to form catch bonds, i.e., bonds that strengthen under tension. This strengthening is based, at least in part, on increased avidity of binding due to clustering of adhesins in cell surface nanodomains. This clustering depends on amyloid-like β-aggregation of short amino acid sequences in the adhesins. In Candida albicans adhesin Als5, shear stress from vortex mixing can unfold part of the protein to expose aggregation-prone sequences, and then adhesins aggregate into nanodomains. We therefore tested whether shear stress from mixing can increase flocculation activity by potentiating similar protein remodeling and aggregation in the flocculins. The results demonstrate the applicability of the Als adhesin model and provide a rational framework for the enhancement or inhibition of flocculation in industrial applications. Many fungal adhesins have short, β-aggregation-prone sequences that play important functional roles, and in the Candida albicans adhesin Als5p, these sequences cluster the adhesins after exposure to shear force. Here, we report that Saccharomyces cerevisiae flocculins Flo11p and Flo1p have similar β-aggregation-prone sequences and are similarly stimulated by shear force, despite being nonhomologous. Shear from vortex mixing induced the formation of small flocs in cells expressing either adhesin. After the addition of Ca2+, yeast cells from vortex-sheared populations showed greatly enhanced flocculation and displayed more pronounced thioflavin-bright surface nanodomains. At high concentrations, amyloidophilic dyes inhibited Flo1p- and Flo11p-mediated agar invasion and the shear-induced increase in flocculation. Consistent with these results, atomic force microscopy of Flo11p showed successive force-distance peaks characteristic of sequentially unfolding tandem repeat domains, like Flo1p and Als5p. Flo11p-expressing cells bound together through homophilic interactions with adhesion forces of up to 700 pN and rupture lengths of up to 600 nm. These results are consistent with the potentiation of yeast flocculation by shear-induced formation of high-avidity domains of clustered adhesins at the cell surface, similar to the activation of Candida albicans adhesin Als5p. Thus, yeast adhesins from three independent gene families use similar force-dependent interactions to drive cell adhesion. IMPORTANCE The Saccharomyces cerevisiae flocculins mediate the formation of cellular aggregates and biofilm-like mats, useful in clearing yeast from fermentations. An important property of fungal adhesion proteins, including flocculins, is the ability to form catch bonds, i.e., bonds that strengthen under tension. This strengthening is based, at least in part, on increased avidity of binding due to clustering of adhesins in cell surface nanodomains. This clustering depends on amyloid-like β-aggregation of short amino acid sequences in the adhesins. In Candida albicans adhesin Als5, shear stress from vortex mixing can unfold part of the protein to expose aggregation-prone sequences, and then adhesins aggregate into nanodomains. We therefore tested whether shear stress from mixing can increase flocculation activity by potentiating similar protein remodeling and aggregation in the flocculins. The results demonstrate the applicability of the Als adhesin model and provide a rational framework for the enhancement or inhibition of flocculation in industrial applications.
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Dahiya P, Bhat DS, Thakur JK. Expression of AtMed15 of Arabidopsis in yeast causes flocculation and increases ethanol production in yeast culture. Sci Rep 2016; 6:27967. [PMID: 27306498 PMCID: PMC4910046 DOI: 10.1038/srep27967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/27/2016] [Indexed: 12/30/2022] Open
Abstract
Mediator, a multiprotein complex involved in transcription of class II genes, was first discovered in yeast and then characterized in many metazoans revealing a striking structural conservation of the complex. However, sequences of Mediator subunits are not well conserved raising a question on the functional conservation of these individual subunits. In this study, expression of Med15 of Arabidopsis (AtMed15) in gal11∆ yeast could not complement the function of ScGal11 in galactose metabolism and resistance against cycloheximide. Surprisingly, AtMed15 changed the morphology of the yeast cells. The cells adhered strongly on the surface of the agar media, and showed robust flocculation in the liquid media without affecting the growth. The AtMed15-induced adhesion and flocculation were observed in different carbon sources. Calcium-assisted cell wall-bound mannan-binding proteins were found to be involved in this flocculation, which was unaffected by wide fluctuation of pH or temperatures revealing its constitutive robust nature. Expression of few flocculation related Flo genes was up-regulated in these cells. Interestingly, there was significant increase in ethanol production by the yeast expressing AtMed15. Robust and constitutive flocculation and increased ethanol production by yeast cells harbouring AtMed15 indicate an opportunity of its important usage in biotechnology industries.
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Affiliation(s)
- Pradeep Dahiya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Divya S Bhat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Bizzarri M, Giudici P, Cassanelli S, Solieri L. Chimeric Sex-Determining Chromosomal Regions and Dysregulation of Cell-Type Identity in a Sterile Zygosaccharomyces Allodiploid Yeast. PLoS One 2016; 11:e0152558. [PMID: 27065237 PMCID: PMC4827841 DOI: 10.1371/journal.pone.0152558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022] Open
Abstract
Allodiploidization is a fundamental yet evolutionarily poorly characterized event, which impacts genome evolution and heredity, controlling organismal development and polyploid cell-types. In this study, we investigated the sex determination system in the allodiploid and sterile ATCC 42981 yeast, a member of the Zygosaccharomyces rouxii species complex, and used it to study how a chimeric mating-type gene repertoire contributes to hybrid reproductive isolation. We found that ATCC 42981 has 7 MAT-like (MTL) loci, 3 of which encode α-idiomorph and 4 encode a-idiomorph. Two phylogenetically divergent MAT expression loci were identified on different chromosomes, accounting for a hybrid a/α genotype. Furthermore, extra a-idimorph-encoding loci (termed MTLa copies 1 to 3) were recognized, which shared the same MATa1 ORFs but diverged for MATa2 genes. Each MAT expression locus was linked to a HML silent cassette, while the corresponding HMR loci were located on another chromosome. Two putative parental sex chromosome pairs contributed to this unusual genomic architecture: one came from an as-yet-undescribed taxon, which has the NCYC 3042 strain as a unique representative, while the other did not match any MAT-HML and HMR organizations previously described in Z. rouxii species. This chimeric rearrangement produces two copies of the HO gene, which encode for putatively functional endonucleases essential for mating-type switching. Although both a and α coding sequences, which are required to obtain a functional cell-type a1-α2 regulator, were present in the allodiploid ATCC 42981 genome, the transcriptional circuit, which regulates entry into meiosis in response to meiosis-inducing salt stress, appeared to be turned off. Furthermore, haploid and α-specific genes, such as MATα1 and HO, were observed to be actively transcribed and up-regulated under hypersaline stress. Overall, these evidences demonstrate that ATCC 42981 is unable to repress haploid α-specific genes and to activate meiosis in response to stress. We argue that sequence divergence within the chimeric a1-α2 heterodimer could be involved in the generation of negative epistasis, contributing to the allodiploid sterility and the dysregulation of cell identity.
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Affiliation(s)
- Melissa Bizzarri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
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