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Genotypic and phenotypic characterization of industrial autochthonous Saccharomyces cerevisiae for the selection of well-adapted bioethanol-producing strains. Fungal Biol 2022; 126:658-673. [DOI: 10.1016/j.funbio.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
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2
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Gronchi N, De Bernardini N, Cripwell RA, Treu L, Campanaro S, Basaglia M, Foulquié-Moreno MR, Thevelein JM, Van Zyl WH, Favaro L, Casella S. Natural Saccharomyces cerevisiae Strain Reveals Peculiar Genomic Traits for Starch-to-Bioethanol Production: the Design of an Amylolytic Consolidated Bioprocessing Yeast. Front Microbiol 2022; 12:768562. [PMID: 35126325 PMCID: PMC8815085 DOI: 10.3389/fmicb.2021.768562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Natural yeast with superior fermentative traits can serve as a platform for the development of recombinant strains that can be used to improve the sustainability of bioethanol production from starch. This process will benefit from a consolidated bioprocessing (CBP) approach where an engineered strain producing amylases directly converts starch into ethanol. The yeast Saccharomyces cerevisiae L20, previously selected as outperforming the benchmark yeast Ethanol Red, was here subjected to a comparative genomic investigation using a dataset of industrial S. cerevisiae strains. Along with Ethanol Red, strain L20 was then engineered for the expression of α-amylase amyA and glucoamylase glaA genes from Aspergillus tubingensis by employing two different approaches (delta integration and CRISPR/Cas9). A correlation between the number of integrated copies and the hydrolytic abilities of the recombinants was investigated. L20 demonstrated important traits for the construction of a proficient CBP yeast. Despite showing a close relatedness to commercial wine yeast and the benchmark Ethanol Red, a unique profile of gene copy number variations (CNVs) was found in L20, mainly encoding membrane transporters and secretion pathway proteins but also the fermentative metabolism. Moreover, the genome annotation disclosed seven open reading frames (ORFs) in L20 that are absent in the reference S288C genome. Genome engineering was successfully implemented for amylase production. However, with equal amylase gene copies, L20 proved its proficiency as a good enzyme secretor by exhibiting a markedly higher amylolytic activity than Ethanol Red, in compliance to the findings of the genomic exploration. The recombinant L20 dT8 exhibited the highest amylolytic activity and produced more than 4 g/L of ethanol from 2% starch in a CBP setting without the addition of supplementary enzymes. Based on the performance of this strain, an amylase/glucoamylase ratio of 1:2.5 was suggested as baseline for further improvement of the CBP ability. Overall, L20 showed important traits for the future construction of a proficient CBP yeast. As such, this work shows that natural S. cerevisiae strains can be used for the expression of foreign secreted enzymes, paving the way to strain improvement for the starch-to-bioethanol route.
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Affiliation(s)
- Nicoletta Gronchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | | | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | | | - Marina Basaglia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | | | - Johan M Thevelein
- Department of Molecular Microbiology, VIB, KU Leuven, Leuven, Belgium
- NovelYeast Bv, Open Bio-Incubator, Erasmus High School, Jette, Belgium
| | - Willem H Van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Lorenzo Favaro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
| | - Sergio Casella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Legnaro, Italy
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Jacobus AP, Stephens TG, Youssef P, González-Pech R, Ciccotosto-Camp MM, Dougan KE, Chen Y, Basso LC, Frazzon J, Chan CX, Gross J. Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts. Front Microbiol 2021; 12:644089. [PMID: 33936002 PMCID: PMC8082247 DOI: 10.3389/fmicb.2021.644089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 01/05/2023] Open
Abstract
Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.
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Affiliation(s)
- Ana Paula Jacobus
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre Youssef
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Raul González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael M Ciccotosto-Camp
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine E Dougan
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Luiz Carlos Basso
- Biological Science Department, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo (USP), Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeferson Gross
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
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4
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Xiang P, Yang Y, Zhao Z, Wang J, Chen M, Chen A, Liu S. Performing flow injection chromatography using a narrow open tubular column. Anal Chim Acta 2020; 1109:19-26. [DOI: 10.1016/j.aca.2020.02.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
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5
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Tek EL, Sundstrom JF, Gardner JM, Oliver SG, Jiranek V. Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment. FEMS Microbiol Ecol 2019; 94:4831476. [PMID: 29394344 DOI: 10.1093/femsec/fix188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Abstract
Commercially available active dried wine yeasts are regularly used by winemakers worldwide to achieve reliable fermentations and obtain quality wine. This practice has led to increased evidence of traces of commercial wine yeast in the vineyard, winery and uninoculated musts. The mechanism(s) that enables commercial wine yeast to persist in the winery environment and the influence to native microbial communities on this persistence is poorly understood. This study has investigated the ability of commercial wine yeasts to form biofilms and adhere to plastic. The results indicate that the biofilms formed by commercial yeasts consist of cells with a combination of different lifestyles (replicative and non-replicative) and growth modes including invasive growth, bud elongation, sporulation and a mat sectoring-like phenotype. Invasive growth was greatly enhanced on grape pulp regardless of strain, while adhesion on plastic varied between strains. The findings suggest a possible mechanism that allows commercial yeast to colonise and survive in the winery environment, which may have implications for the indigenous microbiota profile as well as the population profile in uninoculated fermentations if their dissemination is not controlled.
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Affiliation(s)
- Ee Lin Tek
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Joanna F Sundstrom
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Gardner
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Stephen G Oliver
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Vladimir Jiranek
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, University of Adelaide, Waite Campus, Australia
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Viel A, Legras JL, Nadai C, Carlot M, Lombardi A, Crespan M, Migliaro D, Giacomini A, Corich V. The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination. Front Microbiol 2017; 8:1595. [PMID: 28883812 PMCID: PMC5573751 DOI: 10.3389/fmicb.2017.01595] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022] Open
Abstract
In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota.
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Affiliation(s)
- Alessia Viel
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Jean-Luc Legras
- SPO, INRA, SupAgro, Université de MontpellierMontpellier, France
| | - Chiara Nadai
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Milena Carlot
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy
| | - Angiolella Lombardi
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
| | - Manna Crespan
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria-Centro di Ricerca per la Viticoltura e l'enologiaConegliano, Italy
| | - Daniele Migliaro
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria-Centro di Ricerca per la Viticoltura e l'enologiaConegliano, Italy
| | - Alessio Giacomini
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy.,Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
| | - Viviana Corich
- Interdepartmental Centre for Research in Viticulture and Enology, University of PadovaConegliano, Italy.,Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of PadovaLegnaro, Italy
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7
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Bioethanol strains of Saccharomyces cerevisiae characterised by microsatellite and stress resistance. Braz J Microbiol 2016; 48:268-274. [PMID: 28057426 PMCID: PMC5470434 DOI: 10.1016/j.bjm.2016.09.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 09/19/2016] [Indexed: 11/22/2022] Open
Abstract
Strains of Saccharomyces cerevisiae may display characteristics that are typical of rough-type colonies, made up of cells clustered in pseudohyphal structures and comprised of daughter buds that do not separate from the mother cell post-mitosis. These strains are known to occur frequently in fermentation tanks with significant lower ethanol yield when compared to fermentations carried out by smooth strains of S. cerevisiae that are composed of dispersed cells. In an attempt to delineate genetic and phenotypic differences underlying the two phenotypes, this study analysed 10 microsatellite loci of 22 S. cerevisiae strains as well as stress resistance towards high concentrations of ethanol and glucose, low pH and cell sedimentation rates. The results obtained from the phenotypic tests by Principal-Component Analysis revealed that unlike the smooth colonies, the rough colonies of S. cerevisiae exhibit an enhanced resistance to stressful conditions resulting from the presence of excessive glucose and ethanol and high sedimentation rate. The microsatellite analysis was not successful to distinguish between the colony phenotypes as phenotypic assays. The relevant industrial strain PE-2 was observed in close genetic proximity to rough-colony although it does not display this colony morphology. A unique genetic pattern specific to a particular phenotype remains elusive.
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Barbosa EA, Souza MT, Diniz RHS, Godoy-Santos F, Faria-Oliveira F, Correa LFM, Alvarez F, Coutrim MX, Afonso RJCF, Castro IM, Brandão RL. Quality improvement and geographical indication of cachaça (Brazilian spirit) by using locally selected yeast strains. J Appl Microbiol 2016; 121:1038-51. [PMID: 27374976 DOI: 10.1111/jam.13216] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/21/2016] [Accepted: 06/26/2016] [Indexed: 11/29/2022]
Abstract
AIMS In order to improve the quality and to create a biological basis for obtainment of the protected denomination of origin (PDO), indigenous yeast were isolated and characterized for use in Salinas city (the Brazilian region of quality cachaça production). MATERIAL AND METHODS Seven thousand and two hundred yeast colonies from 15 Salinas city distilleries were screened based on their fermentative behaviour and the physicochemical composition of cachaça. Molecular polymorphic analyses were performed to characterize these isolates. RESULTS Two Saccharomyces cerevisiae strains (nos. 678 and 680) showed appropriate characteristics to use in the cachaça production: low levels of acetaldehyde and methanol, and high ethyl lactate/ethyl acetate ratio respectively. They also presented polymorphic characteristics more closely related between themselves even when compared to other strains from Salinas. CONCLUSIONS The application of selected yeast to cachaça production can contribute for the improvement of the quality product as well as be used as a natural marker for PDO. SIGNIFICANCE AND IMPACT OF THE STUDY This study suggests that the use of selected yeast strains could contribute to obtain a cachaça similar to those produced traditionally, while getting wide acceptation in the market, yet presenting more homogeneous organoleptic characteristics, and thus contributing to the PDO implementation.
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Affiliation(s)
- E A Barbosa
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Laboratório de Análises Físico - Químicas, Departamento de Química, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - M T Souza
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Laboratório de Análises Físico - Químicas, Departamento de Química, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - R H S Diniz
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - F Godoy-Santos
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - F Faria-Oliveira
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - L F M Correa
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - F Alvarez
- Cerlev - Projetos e Inovação na Biotecnologia da Fermentação Ltda., Ouro Preto, MG, Brazil
| | - M X Coutrim
- Campus Salinas, Instituto Federal Norte de Minas Gerais, Salinas, MG, Brazil
| | - R J C F Afonso
- Campus Salinas, Instituto Federal Norte de Minas Gerais, Salinas, MG, Brazil
| | - I M Castro
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - R L Brandão
- Laboratório de Biologia Celular e Molecular, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
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9
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Wrent P, Rivas EM, Peinado JM, de Silóniz MI. Development of an affordable typing method for Meyerozyma guilliermondii using microsatellite markers. Int J Food Microbiol 2015; 217:1-6. [PMID: 26476570 DOI: 10.1016/j.ijfoodmicro.2015.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/16/2015] [Accepted: 10/06/2015] [Indexed: 11/25/2022]
Abstract
Despite previously published methods, there is still a lack of rapid and affordable methods for genotyping the Meyerozyma guilliermondii yeast species. The development of microsatellite markers is a useful genotyping method in several yeast species. Using the Tandem Repeat Finder Software, a total of 19 microsatellite motifs (di-, tri-, and tetra- repetition) were found in silico in seven of the nine scaffolds published so far. Primer pairs were designed for all of them, although only four were used in this work. All microsatellite amplifications showed size polymorphism, and the results were identical when repeated. The combination of three microsatellite markers (sc15F/R, sc32 F/R and sc72 F/R) produced a different pattern for each of the Type Culture Collection strains of M. guilliermondii used to optimize the method. The three primer pairs can be used in the same PCR reaction, which reduces costs, in tandem with the fluorescent labeling of only the forward primer in each primer pair. Microsatellite typing was applied on 40 more M. guilliermondii strains. The results showed that no pattern is repeated between the different environmental niches. Four M. guilliermondii strains were only amplified with primer pair sc32 F/R, and subsequently identified as Meyerozyma caribbica by Taq I-RFLP of the 5.8S ITS rDNA. Most out-group species gave negative results even for physiologically similarly species such as Debaryomyces hansenii. The microsatellite markers used in this work were stable over time, which enables their use as a traceability tool.
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Affiliation(s)
- Petra Wrent
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - Eva-María Rivas
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - José M Peinado
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain
| | - María-Isabel de Silóniz
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis, 12, 28040 Madrid, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
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10
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Improving conversion yield of fermentable sugars into fuel ethanol in 1st generation yeast-based production processes. Curr Opin Biotechnol 2015; 33:81-6. [DOI: 10.1016/j.copbio.2014.12.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 11/22/2022]
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11
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Zhu Z, Chen H, Chen A, Lu JJ, Liu S, Zhao M. Simultaneously sizing and quantitating zeptomole-level DNA at high throughput in free solution. Chemistry 2014; 20:13945-50. [PMID: 25223843 PMCID: PMC4297202 DOI: 10.1002/chem.201403861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/11/2022]
Abstract
Determining the sizes and measuring the quantities of DNA molecules are fundamental tasks in molecular biology. DNA sizes are usually evaluated by gel electrophoresis, but this method cannot simultaneously size and quantitate a DNA at low zeptomole (zmol) levels of concentration. We have recently developed a new technique, called bare-narrow-capillary/hydrodynamic-chromatography or BaNC-HDC, for resolving DNA based on their sizes without using any sieving matrices. In this report, we utilize BaNC-HDC for measuring the sizes and quantities of DNA fragments at zmol to several-molecule levels of concentration. DNA ranging from a few base pairs to dozens of kilo base pairs are accurately sized and quantitated at a throughput of 15 samples per hour, and each sample contains dozens of DNA strands of different lengths. BaNC-HDC can be a cost-effective means and an excellent tool for high-throughput DNA sizing and quantitation at extremely low quantity level.
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Affiliation(s)
- Zaifang Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251 (USA)
| | - Huang Chen
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251 (USA)
| | - Apeng Chen
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251 (USA)
| | - Joann J. Lu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251 (USA)
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251 (USA)
| | - Meiping Zhao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (PR China)
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