201
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Chen S, Xie ZX, Yuan YJ. Discovering and genotyping genomic structural variations by yeast genome synthesis and inducible evolution. FEMS Yeast Res 2021; 20:5809967. [PMID: 32188997 DOI: 10.1093/femsyr/foaa012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022] Open
Abstract
Genomic structural variations (SVs) promote the evolution of Saccharomyces cerevisiae, and play an important role in phenotypic diversities. Yeast genomic structures can be remodeled by design and bottom-up synthesis. The synthesis of yeast genome creates novel copy number variations (CNVs) and SVs and develops new strategies to discover gene functions. Further, an inducible evolution system SCRaMbLE, consisted of 3,932 loxPsym sites, was incorporated on synthetic yeast genome. SCRaMbLE enables genomic rearrangements at will and rapidly generates chromosomal number variations, and massive SVs under customized conditions. The impacts of genetic variations on phenotypes can be revealed by genome analysis and chromosome restructuring. Yeast genome synthesis and SCRaMbLE provide a new research paradigm to explore the genotypic mechanisms of phenotype diversities, and can be used to improve biological traits and optimize industrial chassis.
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Affiliation(s)
- Si Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Ze-Xiong Xie
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, People's Republic of China
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202
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Dida F, Yi G. Empirical evaluation of methods for de novo genome assembly. PeerJ Comput Sci 2021; 7:e636. [PMID: 34307867 PMCID: PMC8279138 DOI: 10.7717/peerj-cs.636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/19/2021] [Indexed: 06/12/2023]
Abstract
Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and de novo assembly is a key initiative that has facilitated gene discovery and other studies. More powerful analytical algorithms are needed to work on the increasing amount of sequence data. We make a thorough comparison of the de novo assembly algorithms to allow new users to clearly understand the assembly algorithms: overlap-layout-consensus and de-Bruijn-graph, string-graph based assembly, and hybrid approach. We also address the computational efficacy of each algorithm's performance, challenges faced by the assem- bly tools used, and the impact of repeats. Our results compare the relative performance of the different assemblers and other related assembly differences with and without the reference genome. We hope that this analysis will contribute to further the application of de novo sequences and help the future growth of assembly algorithms.
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Affiliation(s)
- Firaol Dida
- Department of Multimedia Engineering, Dongguk University, Seoul, South Korea
| | - Gangman Yi
- Department of Multimedia Engineering, Dongguk University, Seoul, South Korea
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203
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Alsammar H, Delneri D. An update on the diversity, ecology and biogeography of the Saccharomyces genus. FEMS Yeast Res 2021; 20:5810663. [PMID: 32196094 PMCID: PMC7150579 DOI: 10.1093/femsyr/foaa013] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular mechanisms of eukaryotes. More recently, the increase in the discovery of wild strains, species and hybrids of the genus Saccharomyces has shifted the attention towards studies on genome evolution, ecology and biogeography, with the yeast becoming a model system for population genomic studies. The genus currently comprises eight species, some of clear industrial importance, while others are confined to natural environments, such as wild forests devoid from human domestication activities. To date, numerous studies showed that some Saccharomyces species form genetically diverged populations that are structured by geography, ecology or domestication activity and that the yeast species can also hybridize readily both in natural and domesticated environments. Much emphasis is now placed on the evolutionary process that drives phenotypic diversity between species, hybrids and populations to allow adaptation to different niches. Here, we provide an update of the biodiversity, ecology and population structure of the Saccharomyces species, and recapitulate the current knowledge on the natural history of Saccharomyces genus.
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Affiliation(s)
- Haya Alsammar
- Department of Biological Sciences, Faculty of Science, Kuwait University, P. O. Box 5969, Safat 13060, Kuwait
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, M1 7DN, UK
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204
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The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast. BIOLOGY 2021; 10:biology10070632. [PMID: 34356487 PMCID: PMC8301174 DOI: 10.3390/biology10070632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Metabolic engineering involves the sustainable production of high-value products. E. coli and yeast, in particular, are used for such processes. Using metabolic engineering, the biosynthetic pathways of these cells are altered to obtain a high production of desired products. Fatty acids (FAs) and their derivatives are products produced using metabolic engineering. However, classical methods used for engineering yeast metabolic pathways for the production of fatty acids and their derivatives face problems such as the low supply of key precursors and product tolerance. This review introduces the different ways FAs are being produced in E. coli and yeast and the genetic manipulations for enhanced production of FAs. The review also summarizes the latest techniques (i.e., CRISPR–Cas and synthetic biology) for developing FA-producing yeast cell factories. Abstract Metabolic engineering is a cutting-edge field that aims to produce simple, readily available, and inexpensive biomolecules by applying different genetic engineering and molecular biology techniques. Fatty acids (FAs) play an important role in determining the physicochemical properties of membrane lipids and are precursors of biofuels. Microbial production of FAs and FA-derived biofuels has several advantages in terms of sustainability and cost. Conventional yeast Saccharomyces cerevisiae is one of the models used for FA synthesis. Several genetic manipulations have been performed to enhance the citrate accumulation and its conversation into acetyl-CoA, a precursor for FA synthesis. Success has been achieved in producing different chemicals, including FAs and their derivatives, through metabolic engineering. However, several hurdles such as slow growth rate, low oleaginicity, and cytotoxicity are still need to be resolved. More robust research needs to be conducted on developing microbes capable of resisting diverse environments, chemicals, and cost-effective feed requirements. Redesigning microbes to produce FAs with cutting-edge synthetic biology and CRISPR techniques can solve these problems. Here, we reviewed the technological progression of metabolic engineering techniques and genetic studies conducted on S. cerevisiae, making it suitable as a model organism and a great candidate for the production of biomolecules, especially FAs.
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205
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Adebami GE, Kuila A, Ajunwa OM, Fasiku SA, Asemoloye MD. Genetics and metabolic engineering of yeast strains for efficient ethanol production. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Arindam Kuila
- Department of Bioscience and Biotechnology Banasthali University Vanasthali India
| | - Obinna M. Ajunwa
- Department of Microbiology Modibbo Adama University of Technology Yola Nigeria
| | - Samuel A. Fasiku
- Department of Biological Sciences Ajayi Crowther University Oyo Nigeria
| | - Michael D. Asemoloye
- Department of Pharmaceutical Science and Technology Tianjin University Tianjin China
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206
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Draft Genome Sequence of the Ectomycorrhizal Fungus Astraeus odoratus from Northern Thailand. Microbiol Resour Announc 2021; 10:e0004421. [PMID: 34197189 PMCID: PMC8248864 DOI: 10.1128/mra.00044-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We report the draft genome sequence of Astraeus odoratus, an edible ectomycorrhizal fungus from northern Thailand. The assembled genome has a size of 45.1 Mb and 13,403 annotated protein-coding genes. This reference genome will provide a better understanding of the biology of mushroom-forming ectomycorrhizal fungi in the family Diplocystidiaceae.
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207
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Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up. Microb Cell Fact 2021; 20:124. [PMID: 34193127 PMCID: PMC8246677 DOI: 10.1186/s12934-021-01617-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.
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208
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Meza E, Muñoz-Arellano AJ, Johansson M, Chen X, Petranovic D. Development of a method for heat shock stress assessment in yeast based on transcription of specific genes. Yeast 2021; 38:549-565. [PMID: 34182606 DOI: 10.1002/yea.3658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/22/2021] [Accepted: 06/22/2021] [Indexed: 11/11/2022] Open
Abstract
All living cells, including yeast cells, are challenged by different types of stresses in their environments and must cope with challenges such as heat, chemical stress, or oxidative damage. By reversibly adjusting the physiology while maintaining structural and genetic integrity, cells can achieve a competitive advantage and adapt environmental fluctuations. The yeast Saccharomyces cerevisiae has been extensively used as a model for study of stress responses due to the strong conservation of many essential cellular processes between yeast and human cells. We focused here on developing a tool to detect and quantify early responses using specific transcriptional responses. We analyzed the published transcriptional data on S. cerevisiae DBY strain responses to 10 different stresses in different time points. The principal component analysis (PCA) and the Pearson analysis were used to assess the stress response genes that are highly expressed in each individual stress condition. Except for these stress response genes, we also identified the reference genes in each stress condition, which would not be induced under stress condition and show stable transcriptional expression over time. We then tested our candidates experimentally in the CEN.PK strain. After data analysis, we identified two stress response genes (UBI4 and RRP) and two reference genes (MEX67 and SSY1) under heat shock (HS) condition. These genes were further verified by real-time PCR at mild (42°C), severe (46°C), to lethal temperature (50°C), respectively.
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Affiliation(s)
- Eugenio Meza
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ana Joyce Muñoz-Arellano
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Magnus Johansson
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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209
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Gonzalez R, Morales P. Truth in wine yeast. Microb Biotechnol 2021; 15:1339-1356. [PMID: 34173338 PMCID: PMC9049622 DOI: 10.1111/1751-7915.13848] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022] Open
Abstract
Evolutionary history and early association with anthropogenic environments have made Saccharomyces cerevisiae the quintessential wine yeast. This species typically dominates any spontaneous wine fermentation and, until recently, virtually all commercially available wine starters belonged to this species. The Crabtree effect, and the ability to grow under fully anaerobic conditions, contribute decisively to their dominance in this environment. But not all strains of Saccharomyces cerevisiae are equally suitable as starter cultures. In this article, we review the physiological and genetic characteristics of S. cerevisiae wine strains, as well as the biotic and abiotic factors that have shaped them through evolution. Limited genetic diversity of this group of yeasts could be a constraint to solving the new challenges of oenology. However, research in this field has for many years been providing tools to increase this diversity, from genetic engineering and classical genetic tools to the inclusion of other yeast species in the catalogues of wine yeasts. On occasion, these less conventional species may contribute to the generation of interspecific hybrids with S. cerevisiae. Thus, our knowledge about wine strains of S. cerevisiae and other wine yeasts is constantly expanding. Over the last decades, wine yeast research has been a pillar for the modernisation of oenology, and we can be confident that yeast biotechnology will keep contributing to solving any challenges, such as climate change, that we may face in the future.
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Affiliation(s)
- Ramon Gonzalez
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
| | - Pilar Morales
- Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de la Rioja, Universidad de La Rioja), Finca La Grajera, Carretera de Burgos, km 6, Logroño, La Rioja, 26071, Spain
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210
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Melkus G, Rucevskis P, Celms E, Čerāns K, Freivalds K, Kikusts P, Lace L, Opmanis M, Rituma D, Viksna J. Network motif-based analysis of regulatory patterns in paralogous gene pairs. J Bioinform Comput Biol 2021; 18:2040008. [PMID: 32698721 DOI: 10.1142/s0219720020400089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focus is the analysis of S. cerevisiae gene interaction graphs, which are of particular interest due to the ancestral whole-genome duplication (WGD) that allows to distinguish between paralogous transcription factors that are traceable to this duplication event and other paralogues. Similar analysis is also applied to E. coli and C. elegans networks. We compare paralogous gene pairs according to the presence and size of bi-fan arrays, classically associated in the literature with gene duplication, within other network motifs. We further extend this framework beyond transcription factor comparison to obtain topology-based similarity metrics based on the overlap of interaction neighborhoods applicable to most genes in a given organism. We observe that our network divergence metrics show considerably larger similarity between paralogues, especially those traceable to WGD. This is the case for both yeast and C. elegans, but not for E. coli regulatory network. While there is no obvious cross-species link between metrics, different classes of paralogues show notable differences in interaction overlap, with traceable duplications tending toward higher overlap compared to genes with shared protein families. Our findings indicate that divergence in paralogous interaction networks reflects a shared genetic origin, and that our approach may be useful for investigating structural similarity in the interaction networks of paralogous genes.
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Affiliation(s)
- Gatis Melkus
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Peteris Rucevskis
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Kārlis Čerāns
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Karlis Freivalds
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Paulis Kikusts
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Lelde Lace
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Mārtiņš Opmanis
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Darta Rituma
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Rainis blvd. 29, Riga, LV-1459, Latvia
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211
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Transcription at a Distance in the Budding Yeast Saccharomyces cerevisiae. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proper transcriptional regulation depends on the collaboration of multiple layers of control simultaneously. Cells tightly balance cellular resources and integrate various signaling inputs to maintain homeostasis during growth, development and stressors, among other signals. Many eukaryotes, including the budding yeast Saccharomyces cerevisiae, exhibit a non-random distribution of functionally related genes throughout their genomes. This arrangement coordinates the transcription of genes that are found in clusters, and can occur over long distances. In this work, we review the current literature pertaining to gene regulation at a distance in budding yeast.
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212
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213
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Berger B, Waterman MS, Yu YW. Levenshtein Distance, Sequence Comparison and Biological Database Search. IEEE TRANSACTIONS ON INFORMATION THEORY 2021; 67:3287-3294. [PMID: 34257466 PMCID: PMC8274556 DOI: 10.1109/tit.2020.2996543] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Levenshtein edit distance has played a central role-both past and present-in sequence alignment in particular and biological database similarity search in general. We start our review with a history of dynamic programming algorithms for computing Levenshtein distance and sequence alignments. Following, we describe how those algorithms led to heuristics employed in the most widely used software in bioinformatics, BLAST, a program to search DNA and protein databases for evolutionarily relevant similarities. More recently, the advent of modern genomic sequencing and the volume of data it generates has resulted in a return to the problem of local alignment. We conclude with how the mathematical formulation of Levenshtein distance as a metric made possible additional optimizations to similarity search in biological contexts. These modern optimizations are built around the low metric entropy and fractional dimensionality of biological databases, enabling orders of magnitude acceleration of biological similarity search.
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Affiliation(s)
- Bonnie Berger
- Department of Mathematics and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA, and also with the Department of Computer Science and AI Lab, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Michael S Waterman
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 USA
| | - Yun William Yu
- Department of Mathematics, University of Toronto, Toronto, ON M5S 2E4, Canada, and also with the Department of Computer and Mathematical Sciences, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada
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214
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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215
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Feng X, Marchisio MA. Novel S. cerevisiae Hybrid Synthetic Promoters Based on Foreign Core Promoter Sequences. Int J Mol Sci 2021; 22:ijms22115704. [PMID: 34071849 PMCID: PMC8198421 DOI: 10.3390/ijms22115704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Promoters are fundamental components of synthetic gene circuits. They are DNA segments where transcription initiation takes place. New constitutive and regulated promoters are constantly engineered in order to meet the requirements for protein and RNA expression into different genetic networks. In this work, we constructed and optimized new synthetic constitutive promoters for the yeast Saccharomyces cerevisiae. We started from foreign (e.g., viral) core promoters as templates. They are, usually, unfunctional in yeast but can be activated by extending them with a short sequence, from the CYC1 promoter, containing various transcription start sites (TSSs). Transcription was modulated by mutating the TATA box composition and varying its distance from the TSS. We found that gene expression is maximized when the TATA box has the form TATAAAA or TATATAA and lies between 30 and 70 nucleotides upstream of the TSS. Core promoters were turned into stronger promoters via the addition of a short UAS. In particular, the 40 nt bipartite UAS from the GPD promoter can enhance protein synthesis considerably when placed 150 nt upstream of the TATA box. Overall, we extended the pool of S. cerevisiae promoters with 59 new samples, the strongest overcoming the native TEF2 promoter.
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216
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Di Rosa MC, Guarino F, Conti Nibali S, Magrì A, De Pinto V. Voltage-Dependent Anion Selective Channel Isoforms in Yeast: Expression, Structure, and Functions. Front Physiol 2021; 12:675708. [PMID: 34093236 PMCID: PMC8171188 DOI: 10.3389/fphys.2021.675708] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial porins, also known as voltage-dependent anion selective channels (VDACs), are pore-forming molecules of the outer mitochondrial membranes, involved in the regulation of metabolic flux between cytosol and mitochondria. Playing such an essential role, VDAC proteins are evolutionary conserved and isoforms are present in numerous species. The quest for specific function(s) related to the raise of multiple isoforms is an intriguing theme. The yeast Saccharomyces cerevisiae genome is endowed with two different VDAC genes encoding for two distinct porin isoforms, definitely less characterized in comparison to mammalian counterpart. While yVDAC1 has been extensively studied, the second isoform, yVDAC2, is much less expressed, and has a still misunderstood function. This review will recapitulate the known and poorly known information in the literature, in the light of the growing interest about the features of VDAC isoforms in the cell.
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Affiliation(s)
- Maria Carmela Di Rosa
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,we.MitoBiotech S.R.L., Catania, Italy
| | - Stefano Conti Nibali
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Andrea Magrì
- we.MitoBiotech S.R.L., Catania, Italy.,Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,we.MitoBiotech S.R.L., Catania, Italy
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217
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Solieri L. The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology. World J Microbiol Biotechnol 2021; 37:96. [PMID: 33969449 DOI: 10.1007/s11274-021-03066-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/28/2021] [Indexed: 12/01/2022]
Abstract
Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.
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Affiliation(s)
- L Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.
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218
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Schmitt-Ulms G, Mehrabian M, Williams D, Ehsani S. The IDIP framework for assessing protein function and its application to the prion protein. Biol Rev Camb Philos Soc 2021; 96:1907-1932. [PMID: 33960099 DOI: 10.1111/brv.12731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023]
Abstract
The quest to determine the function of a protein can represent a profound challenge. Although this task is the mandate of countless research groups, a general framework for how it can be approached is conspicuously lacking. Moreover, even expectations for when the function of a protein can be considered to be 'known' are not well defined. In this review, we begin by introducing concepts pertinent to the challenge of protein function assignments. We then propose a framework for inferring a protein's function from four data categories: 'inheritance', 'distribution', 'interactions' and 'phenotypes' (IDIP). We document that the functions of proteins emerge at the intersection of inferences drawn from these data categories and emphasise the benefit of considering them in an evolutionary context. We then apply this approach to the cellular prion protein (PrPC ), well known for its central role in prion diseases, whose function continues to be considered elusive by many investigators. We document that available data converge on the conclusion that the function of the prion protein is to control a critical post-translational modification of the neural cell adhesion molecule in the context of epithelial-to-mesenchymal transition and related plasticity programmes. Finally, we argue that this proposed function of PrPC has already passed the test of time and is concordant with the IDIP framework in a way that other functions considered for this protein fail to achieve. We anticipate that the IDIP framework and the concepts analysed herein will aid the investigation of other proteins whose primary functional assignments have thus far been intractable.
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Affiliation(s)
- Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5T 0S8, Canada
| | - Sepehr Ehsani
- Theoretical and Philosophical Biology, Department of Philosophy, University College London, Bloomsbury, London, WC1E 6BT, U.K.,Ronin Institute for Independent Scholarship, Montclair, NJ, 07043, U.S.A
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219
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Heineike BM, El-Samad H. Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:642336. [PMID: 37744115 PMCID: PMC10512328 DOI: 10.3389/ffunb.2021.642336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.
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Affiliation(s)
- Benjamin M. Heineike
- Bioinformatics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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220
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Pretorius IS. Tasting the terroir of wine yeast innovation. FEMS Yeast Res 2021; 20:5674549. [PMID: 31830254 PMCID: PMC6964221 DOI: 10.1093/femsyr/foz084] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7000 year history is patterned by a tradition of innovation. Every value-adding innovation − whether in the vineyard, winery, supply chain or marketplace − that led to the invention of a new tradition spurred progress and created a brighter future from past developments. In a way, wine traditions can be defined as remembered innovations from the distant past − inherited knowledge and wisdom that withstood the test of time. Therefore, it should not be assumed a priori that tradition and innovation are polar opposites. The relations between the forces driven by the anchors of tradition and the wings of innovation do not necessarily involve displacement, conflict or exclusiveness. Innovation can strengthen wine tradition, and the reinvention of a tradition-bound practice, approach or concept can foster innovation. In cases where a paradigm-shifting innovation disrupts a tradition, the process of such an innovation transitioning into a radically new tradition can become protracted while proponents of divergent opinions duke it out. Sometimes these conflicting opinions are based on fact, and sometimes not. The imperfections of such a debate between the ‘ancients’ and the ‘moderns’ can, from time to time, obscure the line between myth and reality. Therefore, finding the right balance between traditions worth keeping and innovations worth implementing can be complex. The intent here is to harness the creative tension between science fiction and science fact when innovation's first-principles challenge the status quo by re-examining the foundational principles about a core traditional concept, such as terroir. Poignant questions are raised about the importance of the terroir (biogeography) of yeasts and the value of the microbiome of grapes to wine quality. This article imagines a metaphorical terroir free from cognitive biases where diverse perspectives can converge to uncork the effervescent power of territorial yeast populations as well as ‘nomadic’ yeast starter cultures. At the same time, this paper also engages in mental time-travel. A future scenario is imagined, explored, tested and debated where terroir-less yeast avatars are equipped with designer genomes to safely and consistently produce, individually or in combination with region-specific wild yeasts and or other starter cultures, high-quality wine according to the preferences of consumers in a range of markets. The purpose of this review is to look beyond the horizon and to synthesize a link between what we know now and what could be. This article informs readers where to look without suggesting what they must see as a way forward. In the context of one of the world's oldest fermentation industries − steeped in a rich history of tradition and innovation − the mantra here is: respect the past, lead the present and secure the future of wine.
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Affiliation(s)
- I S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, 19 Eastern Road, North Ryde, Sydney, NSW 2109, Australia
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221
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Liguori F, Amadio S, Volonté C. Where and Why Modeling Amyotrophic Lateral Sclerosis. Int J Mol Sci 2021; 22:ijms22083977. [PMID: 33921446 PMCID: PMC8070525 DOI: 10.3390/ijms22083977] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
Over the years, researchers have leveraged a host of different in vivo models in order to dissect amyotrophic lateral sclerosis (ALS), a neurodegenerative/neuroinflammatory disease that is heterogeneous in its clinical presentation and is multigenic, multifactorial and non-cell autonomous. These models include both vertebrates and invertebrates such as yeast, worms, flies, zebrafish, mice, rats, guinea pigs, dogs and, more recently, non-human primates. Despite their obvious differences and peculiarities, only the concurrent and comparative analysis of these various systems will allow the untangling of the causes and mechanisms of ALS for finally obtaining new efficacious therapeutics. However, harnessing these powerful organisms poses numerous challenges. In this context, we present here an updated and comprehensive review of how eukaryotic unicellular and multicellular organisms that reproduce a few of the main clinical features of the disease have helped in ALS research to dissect the pathological pathways of the disease insurgence and progression. We describe common features as well as discrepancies among these models, highlighting new insights and emerging roles for experimental organisms in ALS.
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Affiliation(s)
- Francesco Liguori
- Preclinical Neuroscience, IRCCS Santa Lucia Foundation, 00143 Rome, Italy; (F.L.); (S.A.)
| | - Susanna Amadio
- Preclinical Neuroscience, IRCCS Santa Lucia Foundation, 00143 Rome, Italy; (F.L.); (S.A.)
| | - Cinzia Volonté
- Preclinical Neuroscience, IRCCS Santa Lucia Foundation, 00143 Rome, Italy; (F.L.); (S.A.)
- Institute for Systems Analysis and Computer Science “A. Ruberti”, National Research Council (IASI—CNR), 00185 Rome, Italy
- Correspondence: ; Tel.: +39-06-50170-3084
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222
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Ancient DNA Research: Ongoing Challenges and Contribution to Medical Sciences. JOURNAL OF BASIC AND CLINICAL HEALTH SCIENCES 2021. [DOI: 10.30621/jbachs.854258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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223
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Perfect Match Genomic Landscape strategy: Refinement and customization of reference genomes. Proc Natl Acad Sci U S A 2021; 118:2025192118. [PMID: 33737447 PMCID: PMC8040819 DOI: 10.1073/pnas.2025192118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The accuracy of the nucleotide sequence of genomes is of utmost importance. The Perfect Match Genomic Landscape (PMGL) is a precise, sensitive, and nonstatistical strategy to detect genome variation. We used this strategy to refine reference genomes from microorganisms belonging to the three domains of life. Our studies show as well that the PMGL can be useful to detect variants in pathogen agents during a pandemic, and to isolate mutations generated during any desired stage of experimental evolution studies. We propose that the PMGL strategy could be the final step in the refinement of any haploid genome, independently of the methodology and algorithms used for its assembly. When addressing a genomic question, having a reliable and adequate reference genome is of utmost importance. This drives the necessity to refine and customize reference genomes (RGs). Our laboratory has recently developed a strategy, the Perfect Match Genomic Landscape (PMGL), to detect variation between genomes [K. Palacios-Flores et al.. Genetics 208, 1631–1641 (2018)]. The PMGL is precise and sensitive and, in contrast to most currently used algorithms, is nonstatistical in nature. Here we demonstrate the power of PMGL to refine and customize RGs. As a proof-of-concept, we refined different versions of the Saccharomyces cerevisiae RG. We applied the automatic PMGL pipeline to refine the genomes of microorganisms belonging to the three domains of life: the archaea Methanococcus maripaludis and Pyrococcus furiosus; the bacteria Escherichia coli, Staphylococcus aureus, and Bacillus subtilis; and the eukarya Schizosaccharomyces pombe, Aspergillus oryzae, and several strains of Saccharomyces paradoxus. We analyzed the reference genome of the virus SARS-CoV-2 and previously published viral genomes from patients’ samples with COVID-19. We performed a mutation-accumulation experiment in E. coli and show that the PMGL strategy can detect specific mutations generated at any desired step of the whole procedure. We propose that PMGL can be used as a final step for the refinement and customization of any haploid genome, independently of the strategies and algorithms used in its assembly.
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224
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Morita R, Shigeta Y, Harada R. Comprehensive predictions of secondary structures for comparative analysis in different species. J Struct Biol 2021; 213:107735. [PMID: 33831508 DOI: 10.1016/j.jsb.2021.107735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Protein structures are directly linked to biological functions. However, there is a gap of knowledge between the decoded genome and the structure. To bridge the gap, we focused on the secondary structure (SS). From a comprehensive analysis of predicted SS of proteins in different types of organisms, we have arrived at the following findings: The proportions of SS in genomes were different among phylogenic domains. The distributions of strand lengths indicated structural limitations in all of the species. Different from bacteria and archaea, eukaryotes have an abundance of α-helical and random coil proteins. Interestingly, there was a relationship between SS and post-translational modifications. By calculating hydrophobicity moments of helices and strands, highly amphipathic fragments of SS were found, which might be related to the biological functions. In conclusion, comprehensive predictions of SS will provide valuable perspectives to understand the entire protein structures in genomes and will help one to discover or design functional proteins.
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Affiliation(s)
- Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan.
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Ibaraki. Japan.
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225
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Aza P, Molpeceres G, de Salas F, Camarero S. Design of an improved universal signal peptide based on the α-factor mating secretion signal for enzyme production in yeast. Cell Mol Life Sci 2021; 78:3691-3707. [PMID: 33687500 PMCID: PMC8038962 DOI: 10.1007/s00018-021-03793-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae plays an important role in the heterologous expression of an array of proteins due to its easy manipulation, low requirements and ability for protein post-translational modifications. The implementation of the preproleader secretion signal of the α-factor mating pheromone from this yeast contributes to increase the production yields by targeting the foreign protein to the extracellular environment. The use of this signal peptide combined with enzyme-directed evolution allowed us to achieve the otherwise difficult functional expression of fungal laccases in S. cerevisiae, obtaining different evolved α-factor preproleader sequences that enhance laccase secretion. However, the design of a universal signal peptide to enhance the production of heterologous proteins in S. cerevisiae is a pending challenge. We describe here the optimisation of the α-factor preproleader to improve recombinant enzyme production in S. cerevisiae through two parallel engineering strategies: a bottom-up design over the native α-factor preproleader (αnat) and a top-down design over the fittest evolved signal peptide obtained in our lab (α9H2 leader). The goal was to analyse the effect of mutations accumulated in the signal sequence throughout iterations of directed evolution, or of other reported mutations, and their possible epistatic interactions. Both approaches agreed in the positive synergism of four mutations (Aα9D, Aα20T, Lα42S, Dα83E) contained in the final optimised leader (αOPT), which notably enhanced the secretion of several fungal oxidoreductases and hydrolases. Additionally, we suggest a guideline to further drive the heterologous production of a particular enzyme based on combinatorial saturation mutagenesis of positions 86th and 87th of the αOPT leader fused to the target protein.
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Affiliation(s)
- Pablo Aza
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Felipe de Salas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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226
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Lawson M, Elf J. Imaging-based screens of pool-synthesized cell libraries. Nat Methods 2021; 18:358-365. [PMID: 33589838 DOI: 10.1038/s41592-020-01053-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.
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Affiliation(s)
- Michael Lawson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Johan Elf
- Department of Cell and Molecular Biology Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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227
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Gómez-Muñoz C, García-Ortega LF, Montalvo-Arredondo J, Pérez-Ortega E, Damas-Buenrostro LC, Riego-Ruiz L. Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. G3-GENES GENOMES GENETICS 2021; 11:6188626. [PMID: 33768233 PMCID: PMC8495930 DOI: 10.1093/g3journal/jkab088] [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: 12/04/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022]
Abstract
Lager beer is made with the hybrid Saccharomyces pastorianus. Many publicly available S. pastorianus genome assemblies are highly fragmented due to the difficulties of assembling hybrid genomes, such as the presence of homeologous chromosomes from both parental types, and translocations between them. To improve the assembly of a previously sequenced lager yeast hybrid Saccharomyces sp. 790 and elucidate its genome structure, we proposed the use of alternative experimental evidence. We determined the phylogenetic position of Saccharomyces sp. 790 and established it as S. pastorianus 790. Then, we obtained from this yeast a bacterial artificial chromosome (BAC) genomic library with its BAC-end sequences (BESs). To analyze these data, we developed a pipeline (applicable to other assemblies) that classifies BES pairs alignments according to their orientation. For the case of S. pastorianus 790, paired-end BESs alignments validated parts of the assembly and unpaired-end ones suggested contig joins or misassemblies. Importantly, the BACs library was preserved and used for verification experiments. Unpaired-end alignments were used to upgrade the previous assembly and provided an improved detection of translocations. With this, we proposed a genome structure of S. pastorianus 790, which was similar to that of other lager yeasts; however, when we estimated chromosome copy number and experimentally measured its genome size, we discovered that one key difference is the outstanding S. pastorianus 790 ploidy level (allopentaploid). Altogether, our results show the value of combining bioinformatic analyses with experimental data such as long-insert clone information to improve a short-read assembly of a hybrid genome.
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Affiliation(s)
- Cintia Gómez-Muñoz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
| | - Luis Fernando García-Ortega
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico, 36824
| | - Javier Montalvo-Arredondo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216.,Dirección General Académica, Universidad Autónoma Agraria Antonio Narro, Saltillo, Mexico, 25315
| | | | | | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., San Luis Potosí, Mexico, 78216
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228
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Domenzain I, Li F, Kerkhoven EJ, Siewers V. Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. FEMS Yeast Res 2021; 21:foab002. [PMID: 33428734 PMCID: PMC7943257 DOI: 10.1093/femsyr/foab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public.
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Affiliation(s)
- Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Feiran Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
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229
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Polčic P, Machala Z. Effects of Non-Thermal Plasma on Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22052247. [PMID: 33668158 PMCID: PMC7956799 DOI: 10.3390/ijms22052247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 12/26/2022] Open
Abstract
Cold plasmas generated by various electrical discharges can affect cell physiology or induce cell damage that may often result in the loss of viability. Many cold plasma-based technologies have emerged in recent years that are aimed at manipulating the cells within various environments or tissues. These include inactivation of microorganisms for the purpose of sterilization, food processing, induction of seeds germination, but also the treatment of cells in the therapy. Mechanisms that underlie the plasma-cell interactions are, however, still poorly understood. Dissection of cellular pathways or structures affected by plasma using simple eukaryotic models is therefore desirable. Yeast Saccharomyces cerevisiae is a traditional model organism with unprecedented impact on our knowledge of processes in eukaryotic cells. As such, it had been also employed in studies of plasma-cell interactions. This review focuses on the effects of cold plasma on yeast cells.
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Affiliation(s)
- Peter Polčic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina CH1, Ilkovičova 6, 84215 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-2-60296-398
| | - Zdenko Machala
- Division of Environmental Physics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 84248 Bratislava, Slovakia;
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230
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Bereketoglu C, Nacar G, Sari T, Mertoglu B, Pradhan A. Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae. PeerJ 2021; 9:e10794. [PMID: 33614281 PMCID: PMC7882136 DOI: 10.7717/peerj.10794] [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: 11/18/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022] Open
Abstract
Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.
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Affiliation(s)
- Ceyhun Bereketoglu
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Iskenderun Technical University, Hatay, Turkey
| | - Gozde Nacar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Tugba Sari
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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231
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Invertebrate Models Untangle the Mechanism of Neurodegeneration in Parkinson's Disease. Cells 2021; 10:cells10020407. [PMID: 33669308 PMCID: PMC7920059 DOI: 10.3390/cells10020407] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, afflicting ~10 million people worldwide. Although several genes linked to PD are currently identified, PD remains primarily an idiopathic disorder. Neuronal protein α-synuclein is a major player in disease progression of both genetic and idiopathic forms of PD. However, it cannot alone explain underlying pathological processes. Recent studies demonstrate that many other risk factors can accelerate or further worsen brain dysfunction in PD patients. Several PD models, including non-mammalian eukaryotic organisms, have been developed to identify and characterize these factors. This review discusses recent findings in three PD model organisms, i.e., yeast, Drosophila, and Caenorhabditis elegans, that opened new mechanisms and identified novel contributors to this disorder. These non-mammalian models share many conserved molecular pathways and cellular processes with humans. New players affecting PD pathogenesis include previously unknown genes/proteins, novel signaling pathways, and low molecular weight substances. These findings might respond to the urgent need to discover novel drug targets for PD treatment and new biomarkers for early diagnostics of this disease. Since the study of neurodegeneration using simple eukaryotic organisms brought a huge amount of information, we include only the most recent or the most important relevant data.
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232
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Bonnet A, Lesage P. Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families. Curr Genet 2021; 67:347-357. [PMID: 33590295 DOI: 10.1007/s00294-021-01154-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Transposable elements are ubiquitous in genomes. Their successful expansion depends in part on their sites of integration in their host genome. In Saccharomyces cerevisiae, evolution has selected various strategies to target the five Ty LTR-retrotransposon families into gene-poor regions in a genome, where coding sequences occupy 70% of the DNA. The integration of Ty1/Ty2/Ty4 and Ty3 occurs upstream and at the transcription start site of the genes transcribed by RNA polymerase III, respectively. Ty5 has completely different integration site preferences, targeting heterochromatin regions. Here, we review the history that led to the identification of the cellular tethering factors that play a major role in anchoring Ty retrotransposons to their preferred sites. We also question the involvement of additional factors in the fine-tuning of the integration site selection, with several studies converging towards an importance of the structure and organization of the chromatin.
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Affiliation(s)
- Amandine Bonnet
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France.
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233
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Basile A, De Pascale F, Bianca F, Rossi A, Frizzarin M, De Bernardini N, Bosaro M, Baldisseri A, Antoniali P, Lopreiato R, Treu L, Campanaro S. Large-scale sequencing and comparative analysis of oenological Saccharomyces cerevisiae strains supported by nanopore refinement of key genomes. Food Microbiol 2021; 97:103753. [PMID: 33653526 DOI: 10.1016/j.fm.2021.103753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022]
Abstract
Saccharomyces cerevisiae has long been part of human activities related to the production of food and wine. The industrial demand for fermented beverages with well-defined and stable characteristics boosted the isolation and selection of strains conferring a distinctive aroma profile to the final product. To uncover variants characterizing oenological strains, the sequencing of 65 new S. cerevisiae isolates, and the comparison with other 503 publicly available genomes were performed. A hybrid approach based on short Illumina and long Oxford Nanopore reads allowed the in-depth investigation of eleven genomes and the identification of putative laterally transferred regions and structural variants. A comparative analysis between clusters of strains belonging to different datasets allowed the identification of novel relevant genetic features including single nucleotide polymorphisms, insertions and structural variants. Detection of oenological single nucleotide variants shed light on the existence of different levels of modulation for the mevalonate pathway relevant for the biosynthesis of aromatic compounds.
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Affiliation(s)
- Arianna Basile
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Fabio De Pascale
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Federico Bianca
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Alessandro Rossi
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Martina Frizzarin
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy; Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | | | - Matteo Bosaro
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Anna Baldisseri
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Paolo Antoniali
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, 35131, Padova, Italy; CRIBI Biotechnology Center, University of Padua, 35121, Padova, Italy
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234
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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235
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Soares EV, Soares HMVM. Harmful effects of metal(loid) oxide nanoparticles. Appl Microbiol Biotechnol 2021; 105:1379-1394. [PMID: 33521847 PMCID: PMC7847763 DOI: 10.1007/s00253-021-11124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/04/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023]
Abstract
Abstract The incorporation of nanomaterials (NMs), including metal(loid) oxide (MOx) nanoparticles (NPs), in the most diversified consumer products, has grown enormously in recent decades. Consequently, the contact between humans and these materials increased, as well as their presence in the environment. This fact has raised concerns and uncertainties about the possible risks of NMs to human health and the adverse effects on the environment. These concerns underline the need and importance of assessing its nanosecurity. The present review focuses on the main mechanisms underlying the MOx NPs toxicity, illustrated with different biological models: release of toxic ions, cellular uptake of NPs, oxidative stress, shading effect on photosynthetic microorganisms, physical restrain and damage of cell wall. Additionally, the biological models used to evaluate the potential hazardous of nanomaterials are briefly presented, with particular emphasis on the yeast Saccharomyces cerevisiae, as an alternative model in nanotoxicology. An overview containing recent scientific advances on cellular responses (toxic symptoms exhibited by yeasts) resulting from the interaction with MOx NPs (inhibition of cell proliferation, cell wall damage, alteration of function and morphology of organelles, presence of oxidative stress bio-indicators, gene expression changes, genotoxicity and cell dead) is critically presented. The elucidation of the toxic modes of action of MOx NPs in yeast cells can be very useful in providing additional clues about the impact of NPs on the physiology and metabolism of the eukaryotic cell. Current and future trends of MOx NPs toxicity, regarding their possible impacts on the environment and human health, are discussed. Key points • The potential hazardous effects of MOx NPs are critically reviewed. • An overview of the main mechanisms associated with MOx NPs toxicity is presented. • Scientific advances about yeast cell responses to MOx NPs are updated and discussed.
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Affiliation(s)
- Eduardo V Soares
- Bioengineering Laboratory-CIETI, ISEP-School of Engineering, Polytechnic Institute of Porto, rua Dr António Bernardino de Almeida, 431, 4249-015, Porto, Portugal. .,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Helena M V M Soares
- REQUIMTE/LAQV, Departamento de Engenharia Química, Faculdade de Engenharia, Universidade do Porto, rua Dr Roberto Frias, s/n, 4200-465, Porto, Portugal
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236
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Simons M. Synthetic biology as a technoscience: The case of minimal genomes and essential genes. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 85:127-136. [PMID: 33966767 DOI: 10.1016/j.shpsa.2020.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 06/12/2023]
Abstract
This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience.
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Affiliation(s)
- Massimiliano Simons
- Ghent University, Department of Philosophy and Moral Sciences, Blandijnberg 2, BE-9000, Ghent, Belgium.
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237
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Influence of fermentation conditions on the secretion of seripauperin 5 (PAU5) by industrial sparkling wine strains of Saccharomyces cerevisiae. Food Res Int 2021; 139:109912. [PMID: 33509479 DOI: 10.1016/j.foodres.2020.109912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 11/22/2022]
Abstract
The yeast mannoprotein seripauperin 5 (PAU5) from Saccharomyces cerevisiae is a negative gushing biomarker in sparkling wine with a direct gushing-reducing effect. The knowledge about the influence of the yeast strain and the fermentation conditions on the PAU5 content in the final product could reduce the gushing potential of sparkling wines and avoid economic losses for sparkling wine producers. The potential of 30 different commercially used (sparkling) wine S. cerevisiae strains to produce PAU5 was analyzed by RP-HPLC. The experiments revealed great differences between strains and identified three high-PAU5-producing yeast strains. The influence of different fermentation conditions was analyzed in two selected strains. Cultivation conditions of elevated temperature and lower inoculation density, as well as cultivation under diffuse daylight significantly enhanced PAU5 production by the tested S. cerevisiae strains as compared to standard conditions. However, cultivation as agitated cultures and co-cultivation with Metchnikowia pulcherrima or Torulaspora delbrueckii led to a reduction of PAU5 production as compared to standard conditions.
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238
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Gerstein AC, Sharp NP. The population genetics of ploidy change in unicellular fungi. FEMS Microbiol Rev 2021; 45:6121427. [PMID: 33503232 DOI: 10.1093/femsre/fuab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.
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Affiliation(s)
- Aleeza C Gerstein
- Dept. of Microbiology, Dept. of Statistics, University of Manitoba Canada
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239
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Orioli S, Henning Hansen CG, Arleth L. Ab initio determination of the shape of membrane proteins in a nanodisc. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:176-193. [DOI: 10.1107/s2059798320015405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
New software, called Marbles, is introduced that employs SAXS intensities to predict the shape of membrane proteins embedded into membrane nanodiscs. To gain computational speed and efficient convergence, the strategy is based on a hybrid approach that allows one to account for the contribution of the nanodisc to the SAXS intensity through a semi-analytical model, while the embedded membrane protein is treated as a set of beads, similarly to as in well known ab initio methods. The reliability and flexibility of this approach is proved by benchmarking the code, implemented in C++ with a Python interface, on a toy model and two proteins with very different geometry and size.
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240
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Young MJ, Imperial RJ, Lakhi S, Court DA. A non-radioactive DNA synthesis assay demonstrates that elements of the Sigma 1278b Mip1 mitochondrial DNA polymerase domain and C-terminal extension facilitate robust enzyme activity. Yeast 2021; 38:262-275. [PMID: 33270277 DOI: 10.1002/yea.3541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 11/06/2022] Open
Abstract
The yeast DNA polymerase gamma, Mip1, is a useful tool to investigate the impact of orthologous human disease variants on mitochondrial DNA (mtDNA) replication. However, Mip1 is characterized by a C-terminal extension (CTE) that is not found on orthologous metazoan DNA polymerases, and the CTE is required for robust enzymatic activity. Two MIP1 alleles exist in standard yeast strains, encoding Mip1[S] or Mip1[Σ]. Mip1[S] is associated with reduced mtDNA stability and increased error rates in vivo. Although the Mip1[S] allele was initially identified in S288c, the Mip1[Σ] allele is widely present among available yeast genome sequences, suggesting that it is the wild-type (WT) allele. We developed a novel non-radioactive polymerase gamma assay to assess Mip1 functioning at its intracellular location, the mitochondrial membrane. Membrane fractions were isolated from yeast cells expressing full-length or CTE truncation variants of Mip1[S] or a chimeric Mip1[S] isoform harboring the Mip1[Σ]-specific T661 residue (cMip1 T661). Relative incorporation of digoxigenin (DIG)-11-deoxyuridine monophosphate (DIG-dUMP) by cMip1 T661 was higher than that by Mip1[S]. A cMip1 T661variant lacking 175 C-terminal residues maintained WT levels of DIG-dUMP incorporation, whereas the C-terminal variant lacking 205 residues displayed a significant decrease in incorporation. Newly synthesized DIG-labeled DNA decreased during later phases of reactions carried out at 37°C, suggesting temperature-sensitive destabilization of the polymerase domain and/or increased shuttling of the nascent DNA into the exonuclease domain. Comparative analysis of Mip1 enzyme functions using our novel assay has further demonstrated the importance of the CTE and T661 encoded by MIP1[Σ] in yeast mtDNA replication.
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Affiliation(s)
- Matthew J Young
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Robin J Imperial
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Truman Medical Center, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Suman Lakhi
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deborah A Court
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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241
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Bernauer L, Radkohl A, Lehmayer LGK, Emmerstorfer-Augustin A. Komagataella phaffii as Emerging Model Organism in Fundamental Research. Front Microbiol 2021; 11:607028. [PMID: 33505376 PMCID: PMC7829337 DOI: 10.3389/fmicb.2020.607028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 01/11/2023] Open
Abstract
Komagataella phaffii (Pichia pastoris) is one of the most extensively applied yeast species in pharmaceutical and biotechnological industries, and, therefore, also called the biotech yeast. However, thanks to more advanced strain engineering techniques, it recently started to gain attention as model organism in fundamental research. So far, the most studied model yeast is its distant cousin, Saccharomyces cerevisiae. While these data are of great importance, they limit our knowledge to one organism only. Since the divergence of the two species 250 million years ago, K. phaffii appears to have evolved less rapidly than S. cerevisiae, which is why it remains more characteristic of the common ancient yeast ancestors and shares more features with metazoan cells. This makes K. phaffii a valuable model organism for research on eukaryotic molecular cell biology, a potential we are only beginning to fully exploit. As methylotrophic yeast, K. phaffii has the intriguing property of being able to efficiently assimilate methanol as a sole source of carbon and energy. Therefore, major efforts have been made using K. phaffii as model organism to study methanol assimilation, peroxisome biogenesis and pexophagy. Other research topics covered in this review range from yeast genetics including mating and sporulation behavior to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. In this review article, we compare data obtained from K. phaffii with S. cerevisiae and other yeasts whenever relevant, elucidate major differences, and, most importantly, highlight the big potential of using K. phaffii in fundamental research.
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Affiliation(s)
- Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | - Astrid Radkohl
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | | | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
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242
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Sousa-Silva M, Vieira D, Soares P, Casal M, Soares-Silva I. Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii. J Fungi (Basel) 2021; 7:36. [PMID: 33435379 PMCID: PMC7827542 DOI: 10.3390/jof7010036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.
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Affiliation(s)
- Maria Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Daniel Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Isabel Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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243
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Luo Z, Yu K, Xie S, Monti M, Schindler D, Fang Y, Zhao S, Liang Z, Jiang S, Luan M, Xiao C, Cai Y, Dai J. Compacting a synthetic yeast chromosome arm. Genome Biol 2021; 22:5. [PMID: 33397424 PMCID: PMC7780613 DOI: 10.1186/s13059-020-02232-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction. RESULTS We develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified. CONCLUSIONS We develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
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Affiliation(s)
- Zhouqing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Kang Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shangqian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Present Address: Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Yuan Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhenzhen Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Meiwei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yizhi Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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244
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Human Fungal Pathogens: Diversity, Genomics, and Preventions. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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245
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Afolaranmi O, Salako O, Okunade K, James A, Fagbenro G. Integrating genomics education into Nigerian undergraduate medical training - A narrative review. JOURNAL OF CLINICAL SCIENCES 2021. [DOI: 10.4103/jcls.jcls_6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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246
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Abstract
DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides the repair reaction by using a homologous DNA template. The budding yeast Saccharomyces cerevisiae is an excellent model system with which to study this repair mechanism and the resulting patterns of genomic change resulting from it. In this chapter, we describe an approach that utilizes whole-genome sequencing data to support the analysis of tracts of loss-of-heterozygosity (LOH) that can arise from mitotic recombination in the context of the entire diploid yeast genome. The workflow and the discussion in this chapter are intended to enable classically trained molecular biologists and geneticists with limited experience in computational methods to conceptually understand and execute the steps of genome-wide LOH analysis as well as to adapt and apply them to their own specific studies and experimental models.
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Affiliation(s)
- Lydia R Heasley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Nadia M V Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA.
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247
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Selbmann L, Benkő Z, Coleine C, de Hoog S, Donati C, Druzhinina I, Emri T, Ettinger CL, Gladfelter AS, Gorbushina AA, Grigoriev IV, Grube M, Gunde-Cimerman N, Karányi ZÁ, Kocsis B, Kubressoian T, Miklós I, Miskei M, Muggia L, Northen T, Novak-Babič M, Pennacchio C, Pfliegler WP, Pòcsi I, Prigione V, Riquelme M, Segata N, Schumacher J, Shelest E, Sterflinger K, Tesei D, U’Ren JM, Varese GC, Vázquez-Campos X, Vicente VA, Souza EM, Zalar P, Walker AK, Stajich JE. Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES. Life (Basel) 2020; 10:life10120362. [PMID: 33352712 PMCID: PMC7767062 DOI: 10.3390/life10120362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/01/2023] Open
Abstract
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
- Section of Mycology, Italian National Antarctic Museum (MNA), 16121 Genoa, Italy
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
| | - Zsigmond Benkő
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy;
| | - Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, 6532 Nijmegen, The Netherlands;
| | - Claudio Donati
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
| | - Irina Druzhinina
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China;
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Cassie L. Ettinger
- Genome Center, University of California, Davis, CA 95616, USA;
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Amy S. Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA;
| | - Anna A. Gorbushina
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
- Department of Earth Sciences & Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin 10115 Berlin, Germany
| | - Igor V. Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Martin Grube
- Institute of Biology, University of Graz, Graz A-8010, Austria;
| | - Nina Gunde-Cimerman
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Zsolt Ákos Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Beatrix Kocsis
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Tania Kubressoian
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Márton Miskei
- Department of Biochemistry and Molecular Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary;
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, 34121 Trieste, Italy;
| | - Trent Northen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Monika Novak-Babič
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Christa Pennacchio
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; (I.V.G.); (T.N.); (C.P.)
| | - Walter P. Pfliegler
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Istvàn Pòcsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary; (Z.B.); (T.E.); (B.K.); (W.P.P.); (I.P.)
| | - Valeria Prigione
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22980, Mexico;
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy;
| | - Julia Schumacher
- Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany; (A.A.G.); (J.S.)
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2UP, UK;
| | - Katja Sterflinger
- Institute of Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna 22180, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 22180, Austria;
| | - Jana M. U’Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA;
| | - Giovanna C. Varese
- Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy; (V.P.); (G.C.V.)
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2006, Australia;
| | - Vania A. Vicente
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Emanuel M. Souza
- Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil; (V.A.V.); (E.M.S.)
| | - Polona Zalar
- Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (N.G.-C.); (M.N.-B.); (P.Z.)
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada;
| | - Jason E. Stajich
- Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA;
- Correspondence: (L.S.); (J.E.S.); Tel.: +39-0761-357012 (L.S.); +1-951-827-2363 (J.E.S.)
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248
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Perruchon O, Schmitz-Afonso I, Grondin C, Casaregola S, Afonso C, Elomri A. Combination of UHPLC-MS/MS-molecular networking approach and FTICR-MS for the metabolic profiling of Saccharomyces cerevisiae. J Pharm Biomed Anal 2020; 195:113857. [PMID: 33385718 DOI: 10.1016/j.jpba.2020.113857] [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: 09/11/2020] [Revised: 11/18/2020] [Accepted: 12/16/2020] [Indexed: 01/25/2023]
Abstract
Natural products are a reliable source of bioactive molecules and represent an industrial and pharmaceutical stake. Indeed, the model yeast species Saccharomyces cerevisiae is a well-known eukaryotic organism largely used as a biotechnological tool, but still a topical subject of study. In this work, the exploration of Saccharomyces cerevisiae is taken further through an untargeted metabolomics workflow. The aim is to enrich databases and bring new information about the standard S. cerevisiae strain in a given medium. Analytical methods and bioinformatics tools were combined in a high-throughput methodology useable to dereplicate many types of biological extracts and cartography secondary metabolites. Ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analyses were carried out and spectral data were pre-processed to build molecular networks. Annotations were attributed to compounds through comparison with databases and manual investigation of networks. Ultra-high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) brought additional information thanks to a higher dynamic range and enhanced UHPLC-MS/MS results by unveiling ambiguities and bringing accurate molecular formulae. Therefore, accurate and reliable annotated features resulted from the UHPLC-MS/MS data while FTICR-MS provided an overall cartography of metabolites thanks to van Krevelen diagrams. Various small molecules such as amino acids derivatives and indole alkaloids have been determined for the first time in this yeast. The complementarity of FTICR-MS and UHPLC-MS/MS for secondary metabolite annotation brought this new mapping of S. cerevisiae.
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Affiliation(s)
- Olivier Perruchon
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Rouen 76000, France
| | | | - Cécile Grondin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, CIRM-Levures, 78350, Jouy-en-Josas, France
| | - Serge Casaregola
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, CIRM-Levures, 78350, Jouy-en-Josas, France
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Rouen 76000, France
| | - Abdelhakim Elomri
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Rouen 76000, France.
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249
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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250
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Daran JMG. Entering GATTACA: yeast genomes: analysis, insights and applications. FEMS Yeast Res 2020; 20:6041023. [PMID: 33332537 DOI: 10.1093/femsyr/foaa064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
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