1
|
Weller CA, Andreev I, Chambers MJ, Park M, Bloom JS, Sadhu MJ. Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity. Genome Res 2023; 33:729-740. [PMID: 37127330 PMCID: PMC10317115 DOI: 10.1101/gr.277515.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.
Collapse
Affiliation(s)
- Cory A Weller
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ilya Andreev
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael J Chambers
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Morgan Park
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Meru J Sadhu
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| |
Collapse
|
2
|
Pan H, Mei D, Xu C, Han S, Wang Y. Bisymmetric coherent acoustic tweezers based on modulation of surface acoustic waves for dynamic and reconfigurable cluster manipulation of particles and cells. LAB ON A CHIP 2023; 23:215-228. [PMID: 36420975 DOI: 10.1039/d2lc00812b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Acoustic tweezers based on surface acoustic waves (SAWs) have raised great interest in the fields of tissue engineering, targeted therapy, and drug delivery. Generally, the complex structure and array layout design of interdigital electrodes would restrict the applications of acoustic tweezers. Here, we present a novel approach by using bisymmetric coherent acoustic tweezers to modulate the shape of acoustic pressure fields with high flexibility and accuracy. Experimental tests were conducted to perform the precise, contactless, and biocompatible cluster manipulation of polystyrene microparticles and yeast cells. Stripe, dot, quadratic lattice, hexagonal lattice, interleaved stripe, oblique stripe, and many other complex arrays were achieved by real-time modulation of amplitudes and phase relations of coherent SAWs to demonstrate the capability of the device for the cluster manipulation of particles and cells. Furthermore, rapid switching among various arrays, shape regulation, geometric parameter modulation of array units, and directional translation of microparticles and cells were implemented. This study demonstrated a favorable technique for flexible and versatile manipulation and patterning of cells and biomolecules, and it has the advantages of high manipulation accuracy and adjustability, thus it is expected to be utilized in the fields of targeted cellular assembly, biological 3D printing, and targeted release of drugs.
Collapse
Affiliation(s)
- Hemin Pan
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Deqing Mei
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Chengyao Xu
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Shuo Han
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yancheng Wang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, 310027, China.
| |
Collapse
|
3
|
Selective drivers of simple multicellularity. Curr Opin Microbiol 2022; 67:102141. [PMID: 35247708 DOI: 10.1016/j.mib.2022.102141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/21/2022]
Abstract
In order to understand the evolution of multicellularity, we must understand how and why selection favors the first steps in this process: the evolution of simple multicellular groups. Multicellularity has evolved many times in independent lineages with fundamentally different ecologies, yet no work has yet systematically examined these diverse selective drivers. Here we review recent developments in systematics, comparative biology, paleontology, synthetic biology, theory, and experimental evolution, highlighting ten selective drivers of simple multicellularity. Our survey highlights the many ecological opportunities available for simple multicellularity, and stresses the need for additional work examining how these first steps impact the subsequent evolution of complex multicellularity.
Collapse
|
4
|
Chen Z, Niu Y, Chen C, Li H. Optimization of bioethanol fermentation productivity in Saccharomyces cerevisiae by regulation of social behavior. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
5
|
Evaluation of yeasts from Ecuadorian chicha by their performance as starters for alcoholic fermentations in the food industry. Int J Food Microbiol 2020; 317:108462. [DOI: 10.1016/j.ijfoodmicro.2019.108462] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 12/25/2022]
|
6
|
Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc Natl Acad Sci U S A 2018; 115:11030-11035. [PMID: 30297402 DOI: 10.1073/pnas.1806268115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. Here, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.
Collapse
|
7
|
Genetic signatures of microbial altruism and cheating in social amoebas in the wild. Proc Natl Acad Sci U S A 2018; 115:3096-3101. [PMID: 29507206 DOI: 10.1073/pnas.1720324115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many microbes engage in social interactions. Some of these have come to play an important role in the study of cooperation and conflict, largely because, unlike most animals, they can be genetically manipulated and experimentally evolved. However, whereas animal social behavior can be observed and assessed in natural environments, microbes usually cannot, so we know little about microbial social adaptations in nature. This has led to some difficult-to-resolve controversies about social adaptation even for well-studied traits such as bacterial quorum sensing, siderophore production, and biofilms. Here we use molecular signatures of population genetics and molecular evolution to address controversies over the existence of altruism and cheating in social amoebas. First, we find signatures of rapid adaptive molecular evolution that are consistent with social conflict being a significant force in nature. Second, we find population-genetic signatures of purifying selection to support the hypothesis that the cells that form the sterile stalk evolve primarily through altruistic kin selection rather than through selfish direct reproduction. Our results show how molecular signatures can provide insight into social adaptations that cannot be observed in their natural context, and they support the hypotheses that social amoebas in the wild are both altruists and cheaters.
Collapse
|
8
|
Bruce JB, Cooper GA, Chabas H, West SA, Griffin AS. Cheating and resistance to cheating in natural populations of the bacteriumPseudomonas fluorescens. Evolution 2017; 71:2484-2495. [DOI: 10.1111/evo.13328] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Affiliation(s)
- John B. Bruce
- Department of Zoology; University of Oxford; Oxford UK
| | - Guy A. Cooper
- Department of Zoology; University of Oxford; Oxford UK
| | - Hélène Chabas
- CEFE UMR 5175, CNRS-Université de Montpellier; Université Paul-Valéry Montpellier; Montpellier Cedex 5 France
| | | | | |
Collapse
|
9
|
Abstract
Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyces strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes.
Collapse
|
10
|
Xia W, Nielly-Thibault L, Charron G, Landry CR, Kasimer D, Anderson JB, Kohn LM. Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland. Mol Ecol 2017; 26:995-1007. [PMID: 27988980 DOI: 10.1111/mec.13954] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/28/2016] [Indexed: 12/23/2022]
Abstract
Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km2 in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies.
Collapse
Affiliation(s)
- Wenjing Xia
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Lou Nielly-Thibault
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Guillaume Charron
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Dahlia Kasimer
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - James B Anderson
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| | - Linda M Kohn
- Departments of Ecology and Evolutionary Biology and Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga, ON, L5L 1C6, Canada
| |
Collapse
|
11
|
Kowallik V, Greig D. A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:833-841. [PMID: 27481438 DOI: 10.1111/1758-2229.12446] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Although we understand the genetics of the laboratory model yeast Saccharomyces cerevisiae very well, we know little about the natural ecology and environment that shaped its genome. Most isolates of Saccharomyces paradoxus, the wild relative of S. cerevisiae, come from oak trees, but it is not known whether this is because oak is their primary habitat. We surveyed leaf litter in a forest in Northern Germany and found a strong correlation between isolation success of wild Saccharomyces and the proximity of the nearest oak. We compared the four most common tree genera and found Saccharomyces most frequently in oak litter. Interestingly, we show that Saccharomyces is much more abundant in oak leaf litter than on oak bark, suggesting that it grows in litter or soil rather than on the surfaces of oaks themselves. The distribution and abundance of Saccharomyces over the course of a year shows that oak leaf litter provides a stable habitat for the yeast, although there was significant tree-to-tree variation. Taken together, our results suggest that leaf litter rather than tree surfaces provide the better habitat for wild Saccharomyces, with oak being the preferred tree genus. 99.5% of all strains (633/636) isolated were S. paradoxus.
Collapse
Affiliation(s)
- Vienna Kowallik
- Experimental Evolution Group, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Duncan Greig
- Experimental Evolution Group, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
12
|
Leimar O, Dall SRX, Hammerstein P, McNamara JM. Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments. PLoS Comput Biol 2016; 12:e1005006. [PMID: 27341199 PMCID: PMC4920369 DOI: 10.1371/journal.pcbi.1005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/27/2016] [Indexed: 12/23/2022] Open
Abstract
There are many situations where relatives interact while at the same time there is genetic polymorphism in traits influencing survival and reproduction. Examples include cheater-cooperator polymorphism and polymorphic microbial pathogens. Environmental heterogeneity, favoring different traits in nearby habitats, with dispersal between them, is one general reason to expect polymorphism. Currently, there is no formal framework of social evolution that encompasses genetic polymorphism. We develop such a framework, thus integrating theories of social evolution into the evolutionary ecology of heterogeneous environments. We allow for adaptively maintained genetic polymorphism by applying the concept of genetic cues. We analyze a model of social evolution in a two-habitat situation with limited dispersal between habitats, in which the average relatedness at the time of helping and other benefits of helping can differ between habitats. An important result from the analysis is that alleles at a polymorphic locus play the role of genetic cues, in the sense that the presence of a cue allele contains statistical information for an organism about its current environment, including information about relatedness. We show that epistatic modifiers of the cue polymorphism can evolve to make optimal use of the information in the genetic cue, in analogy with a Bayesian decision maker. Another important result is that the genetic linkage between a cue locus and modifier loci influences the evolutionary interest of modifiers, with tighter linkage leading to greater divergence between social traits induced by different cue alleles, and this can be understood in terms of genetic conflict. The theory of kin selection explains the evolution of helping when relatives interact. It can be used when individuals in a social group have different sexes, ages or phenotypic qualities, but the theory has not been worked out for situations where there is genetic polymorphism in helping. That kind of polymorphism, for instance cheater-cooperator polymorphism in microbes, has attracted much interest. We include these phenomena into a general framework of social evolution. Our framework is built on the idea of genetic cues, which means that an individual uses its genotype at a polymorphic locus as a statistical predictor of the current social conditions, including the expected relatedness in a social group. We allow for multilocus determination of the phenotype, in the form of modifiers of the effects of the alleles at a cue locus, and we find that there can be genetic conflicts between modifier loci that are tightly linked versus unlinked to the cue locus.
Collapse
Affiliation(s)
- Olof Leimar
- Department of Zoology, Stockholm University, Stockholm, Sweden
- * E-mail:
| | - Sasha R. X. Dall
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Peter Hammerstein
- Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany
| | - John M. McNamara
- School of Mathematics, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
13
|
Cámara E, Albiol J, Ferrer P. Droplet digital PCR-aided screening and characterization of Pichia pastoris multiple gene copy strains. Biotechnol Bioeng 2016; 113:1542-51. [PMID: 26704939 DOI: 10.1002/bit.25916] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 01/25/2023]
Abstract
Pichia (syn. Komagataella) pastoris is a widely used yeast platform for heterologous protein production. Expression cassettes are usually stably integrated into the genome of this host via homologous recombination. Although increasing gene dosage is a powerful strategy to improve recombinant protein production, an excess in the number of gene copies often leads to decreased product yields and increased metabolic burden, particularly for secreted proteins. We have constructed a series of strains harboring different copy numbers of a Rhizopus oryzae lipase gene (ROL), aiming to find the optimum gene dosage for secreted Rol production. In order to accurately determine ROL gene dosage, we implemented a novel protocol based on droplet digital PCR (ddPCR), and cross validated it with conventional real-time PCR. Gene copy number determination based on ddPCR allowed for an accurate ranking of transformants according to their ROL gene dosage. Results indicated that ddPCR was particularly superior at lower gene dosages (one to five copies) over quantitative real-time PCR (qPCR). This facilitated the determination of the optimal ROL gene dosage as low as two copies. The ranking of ROL gene dosage versus Rol yield was consistent at both small scale and bioreactor chemostat cultures, thereby easing clone characterization in terms of gene dosage dependent physiological effects, which could be discriminated even among strains differing by only one ROL copy. A selected two-copy strain showed twofold increase in Rol specific production in a chemostat culture over the single copy strain. Conversely, strains harboring more than two copies of the ROL gene showed decreased product and biomass yields, as well as altered substrate consumption specific rates, compared to the reference (one-copy) strain. Biotechnol. Bioeng. 2016;113: 1542-1551. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Elena Cámara
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
| |
Collapse
|
14
|
Dashko S, Liu P, Volk H, Butinar L, Piškur J, Fay JC. Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations. Front Microbiol 2016; 7:215. [PMID: 26941733 PMCID: PMC4764737 DOI: 10.3389/fmicb.2016.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/09/2016] [Indexed: 11/23/2022] Open
Abstract
Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance.
Collapse
Affiliation(s)
- Sofia Dashko
- Wine Research Center, University of Nova GoricaVipava, Slovenia; Department of Biology, Lund UniversityLund, Sweden
| | - Ping Liu
- Department of Genetics and Center for Genome Sciences and System Biology, Washington University St. Louis, MO, USA
| | - Helena Volk
- Wine Research Center, University of Nova Gorica Vipava, Slovenia
| | - Lorena Butinar
- Wine Research Center, University of Nova Gorica Vipava, Slovenia
| | - Jure Piškur
- Wine Research Center, University of Nova GoricaVipava, Slovenia; Department of Biology, Lund UniversityLund, Sweden
| | - Justin C Fay
- Department of Genetics and Center for Genome Sciences and System Biology, Washington University St. Louis, MO, USA
| |
Collapse
|
15
|
Marques WL, Raghavendran V, Stambuk BU, Gombert AK. Sucrose and Saccharomyces cerevisiae: a relationship most sweet. FEMS Yeast Res 2015; 16:fov107. [PMID: 26658003 DOI: 10.1093/femsyr/fov107] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 12/16/2022] Open
Abstract
Sucrose is an abundant, readily available and inexpensive substrate for industrial biotechnology processes and its use is demonstrated with much success in the production of fuel ethanol in Brazil. Saccharomyces cerevisiae, which naturally evolved to efficiently consume sugars such as sucrose, is one of the most important cell factories due to its robustness, stress tolerance, genetic accessibility, simple nutrient requirements and long history as an industrial workhorse. This minireview is focused on sucrose metabolism in S. cerevisiae, a rather unexplored subject in the scientific literature. An analysis of sucrose availability in nature and yeast sugar metabolism was performed, in order to understand the molecular background that makes S. cerevisiae consume this sugar efficiently. A historical overview on the use of sucrose and S. cerevisiae by humans is also presented considering sugarcane and sugarbeet as the main sources of this carbohydrate. Physiological aspects of sucrose consumption are compared with those concerning other economically relevant sugars. Also, metabolic engineering efforts to alter sucrose catabolism are presented in a chronological manner. In spite of its extensive use in yeast-based industries, a lot of basic and applied research on sucrose metabolism is imperative, mainly in fields such as genetics, physiology and metabolic engineering.
Collapse
Affiliation(s)
- Wesley Leoricy Marques
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
| | | | - Boris Ugarte Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis-SC, 88040-900, Brazil
| | - Andreas Karoly Gombert
- Department of Chemical Engineering, University of São Paulo, São Paulo-SP, 05424-970, Brazil School of Food Engineering, University of Campinas, Campinas-SP, 13083-862, Brazil
| |
Collapse
|
16
|
Hu W, Suo F, Du LL. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. Genome Biol Evol 2015; 7:3496-510. [PMID: 26615217 PMCID: PMC4700965 DOI: 10.1093/gbe/evv238] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
Collapse
Affiliation(s)
- Wen Hu
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
| |
Collapse
|
17
|
Luján AM, Gómez P, Buckling A. Siderophore cooperation of the bacterium Pseudomonas fluorescens in soil. Biol Lett 2015; 11:20140934. [PMID: 25694506 PMCID: PMC4360104 DOI: 10.1098/rsbl.2014.0934] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
While social interactions play an important role for the evolution of bacterial siderophore production in vitro, the extent to which siderophore production is a social trait in natural populations is less clear. Here, we demonstrate that siderophores act as public goods in a natural physical environment of Pseudomonas fluorescens: soil-based compost. We show that monocultures of siderophore producers grow better than non-producers in soil, but non-producers can exploit others' siderophores, as shown by non-producers' ability to invade populations of producers when rare. Despite this rare advantage, non-producers were unable to outcompete producers, suggesting that producers and non-producers may stably coexist in soil. Such coexistence is predicted to arise from the spatial structure associated with soil, and this is supported by increased fitness of non-producers when grown in a shaken soil–water mix. Our results suggest that both producers and non-producers should be observed in soil, as has been observed in marine environments and in clinical populations.
Collapse
Affiliation(s)
- Adela M Luján
- ESI, Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Pedro Gómez
- ESI, Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Angus Buckling
- ESI, Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| |
Collapse
|
18
|
Rivero D, Berná L, Stefanini I, Baruffini E, Bergerat A, Csikász-Nagy A, De Filippo C, Cavalieri D. Hsp12p and PAU
genes are involved in ecological interactions between natural yeast strains. Environ Microbiol 2015; 17:3069-81. [DOI: 10.1111/1462-2920.12950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Damaríz Rivero
- Department of Neurosciences, Psychology, Drug Research and Child Health; University of Florence; Florence Italy
| | - Luisa Berná
- Molecular Biology Unit; Institut Pasteur; Montevideo Uruguay
| | - Irene Stefanini
- Centre for Research and Innovation; Fondazione Edmund Mach; San Michele all'Adige Trento Italy
| | | | - Agnes Bergerat
- Department of Pathology; Boston University School of Medicine; Boston USA
| | - Attila Csikász-Nagy
- Centre for Research and Innovation; Fondazione Edmund Mach; San Michele all'Adige Trento Italy
| | - Carlotta De Filippo
- Centre for Research and Innovation; Fondazione Edmund Mach; San Michele all'Adige Trento Italy
| | - Duccio Cavalieri
- Department of Neurosciences, Psychology, Drug Research and Child Health; University of Florence; Florence Italy
| |
Collapse
|
19
|
Kowallik V, Miller E, Greig D. The interaction of Saccharomyces paradoxus with its natural competitors on oak bark. Mol Ecol 2015; 24:1596-610. [PMID: 25706044 PMCID: PMC4405091 DOI: 10.1111/mec.13120] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 12/30/2022]
Abstract
The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.
Collapse
Affiliation(s)
- Vienna Kowallik
- Max Planck Institute for Evolutionary Biology, August Thienemann Strasse 2, 24306, Plön, Germany
| | | | | |
Collapse
|
20
|
Precarious development: the uncertain social life of cellular slime molds. Proc Natl Acad Sci U S A 2015; 112:2639-40. [PMID: 25713343 DOI: 10.1073/pnas.1500708112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
|