1
|
Sun G, Zhang C, Shan X, Zhang Z, Wang W, Lu W, Dai Z, E L, Wang Y, Ma Z, Hou X. Conjunctive BSA-Seq and BSR-Seq to Map the Genes of Yellow Leaf Mutations in Hot Peppers ( Capsicum annuum L.). Genes (Basel) 2024; 15:1115. [PMID: 39336705 PMCID: PMC11430990 DOI: 10.3390/genes15091115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/17/2024] [Accepted: 08/22/2024] [Indexed: 09/30/2024] Open
Abstract
Yellow leaf mutations have been widely used to study the chloroplast structures, the pigment synthesis, the photosynthesis mechanisms and the chlorophyll biosynthesis pathways across various species. For this study, a spontaneous mutant with the yellow leaf color named 96-140YBM was employed to explore the primary genetic elements that lead to the variations in the leaf color of hot peppers. To identify the pathways and genes associated with yellow leaf phenotypes, we applied sequencing-based Bulked Segregant Analysis (BSA-Seq) combined with BSR-Seq. We identified 4167 differentially expressed genes (DEGs) in the mutant pool compared with the wild-type pool. The results indicated that DEGs were involved in zeatin biosynthesis, plant hormone signal transduction, signal transduction mechanisms, post-translational modification and protein turnover. A total of 437 candidates were identified by the BSA-Seq, while the BSR-Seq pinpointed four candidate regions in chromosomes 8 and 9, containing 222 candidate genes. Additionally, the combination of BSA-Seq and BSR-Seq showed that there were 113 overlapping candidate genes between the two methods, among which 8 common candidates have been previously reported to be related to the development of chloroplasts, the photomorphogenesis and chlorophyll formation of plant chloroplasts and chlorophyll biogenesis. qRT-PCR analysis of the 8 common candidates showed higher expression levels in the mutant pool compared with the wild-type pool. Among the overlapping candidates, the DEG analysis showed that the CaKAS2 and CaMPH2 genes were down-regulated in the mutant pool compared to the wild type, suggesting that these genes may be key contributors to the yellow leaf phenotype of 96-140YBM. This research will deepen our understanding of the genetic basis of leaf color formation and provide valuable information for the breeding of hot peppers with diverse leaf colors.
Collapse
Affiliation(s)
- Guosheng Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
| | - Xi Shan
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Zhenchao Zhang
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Wenlong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
| | - Wenjun Lu
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Zhongliang Dai
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Liu E
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
| | - Yaolong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
| | - Zhihu Ma
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, 1# Hongjing Road, Jurong 212400, China; (X.S.); (Z.Z.); (W.L.); (Z.D.)
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (G.S.); (C.Z.); (W.W.); (L.E.); (Y.W.)
| |
Collapse
|
2
|
Wang H, Zeng W, Huang X, Liu Z, Sun Y, Zhang L. MTTLm 6A: A multi-task transfer learning approach for base-resolution mRNA m 6A site prediction based on an improved transformer. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:272-299. [PMID: 38303423 DOI: 10.3934/mbe.2024013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
N6-methyladenosine (m6A) is a crucial RNA modification involved in various biological activities. Computational methods have been developed for the detection of m6A sites in Saccharomyces cerevisiae at base-resolution due to their cost-effectiveness and efficiency. However, the generalization of these methods has been hindered by limited base-resolution datasets. Additionally, RMBase contains a vast number of low-resolution m6A sites for Saccharomyces cerevisiae, and base-resolution sites are often inferred from these low-resolution results through post-calibration. We propose MTTLm6A, a multi-task transfer learning approach for base-resolution mRNA m6A site prediction based on an improved transformer. First, the RNA sequences are encoded by using one-hot encoding. Then, we construct a multi-task model that combines a convolutional neural network with a multi-head-attention deep framework. This model not only detects low-resolution m6A sites, it also assigns reasonable probabilities to the predicted sites. Finally, we employ transfer learning to predict base-resolution m6A sites based on the low-resolution m6A sites. Experimental results on Saccharomyces cerevisiae m6A and Homo sapiens m1A data demonstrate that MTTLm6A respectively achieved area under the receiver operating characteristic (AUROC) values of 77.13% and 92.9%, outperforming the state-of-the-art models. At the same time, it shows that the model has strong generalization ability. To enhance user convenience, we have made a user-friendly web server for MTTLm6A publicly available at http://47.242.23.141/MTTLm6A/index.php.
Collapse
Affiliation(s)
- Honglei Wang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
- School of Information Engineering, Xuzhou College of Industrial Technology, Xuzhou, China
| | - Wenliang Zeng
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Xiaoling Huang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Zhaoyang Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Yanjing Sun
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| |
Collapse
|
3
|
Vargas BDO, dos Santos JR, Pereira GAG, de Mello FDSB. An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae. PeerJ 2023; 11:e16340. [PMID: 38047029 PMCID: PMC10691383 DOI: 10.7717/peerj.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 12/05/2023] Open
Abstract
Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
Collapse
Affiliation(s)
- Beatriz de Oliveira Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jade Ribeiro dos Santos
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | | |
Collapse
|
4
|
Procópio DP, Lee JW, Shin J, Tramontina R, Ávila PF, Brenelli LB, Squina FM, Damasio A, Rabelo SC, Goldbeck R, Franco TT, Leak D, Jin YS, Basso TO. Metabolic engineering of Saccharomyces cerevisiae for second-generation ethanol production from xylo-oligosaccharides and acetate. Sci Rep 2023; 13:19182. [PMID: 37932303 PMCID: PMC10628280 DOI: 10.1038/s41598-023-46293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
Simultaneous intracellular depolymerization of xylo-oligosaccharides (XOS) and acetate fermentation by engineered Saccharomyces cerevisiae offers significant potential for more cost-effective second-generation (2G) ethanol production. In the present work, the previously engineered S. cerevisiae strain, SR8A6S3, expressing enzymes for xylose assimilation along with an optimized route for acetate reduction, was used as the host for expressing two β-xylosidases, GH43-2 and GH43-7, and a xylodextrin transporter, CDT-2, from Neurospora crassa, yielding the engineered SR8A6S3-CDT-2-GH34-2/7 strain. Both β-xylosidases and the transporter were introduced by replacing two endogenous genes, GRE3 and SOR1, that encode aldose reductase and sorbitol (xylitol) dehydrogenase, respectively, and catalyse steps in xylitol production. The engineered strain, SR8A6S3-CDT-2-GH34-2/7 (sor1Δ gre3Δ), produced ethanol through simultaneous XOS, xylose, and acetate co-utilization. The mutant strain produced 60% more ethanol and 12% less xylitol than the control strain when a hemicellulosic hydrolysate was used as a mono- and oligosaccharide source. Similarly, the ethanol yield was 84% higher for the engineered strain using hydrolysed xylan, compared with the parental strain. Xylan, a common polysaccharide in lignocellulosic residues, enables recombinant strains to outcompete contaminants in fermentation tanks, as XOS transport and breakdown occur intracellularly. Furthermore, acetic acid is a ubiquitous toxic component in lignocellulosic hydrolysates, deriving from hemicellulose and lignin breakdown. Therefore, the consumption of XOS, xylose, and acetate expands the capabilities of S. cerevisiae for utilization of all of the carbohydrate in lignocellulose, potentially increasing the efficiency of 2G biofuel production.
Collapse
Affiliation(s)
- Dielle Pierotti Procópio
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo (USP), São Paulo, SP, 05508-010, Brazil
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo), São Paulo, SP, 05508-900, Brazil
| | - Jae Won Lee
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
| | - Jonghyeok Shin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
- Environment and Technological Processes Program, University of Sorocaba (UNISO), Sorocaba, SP, 18023-000, Brazil
| | - Patrícia Felix Ávila
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Lívia Beatriz Brenelli
- Interdisciplinary Centre of Energy Planning, University of Campinas (UNICAMP), Campinas, SP, 13083-896, Brazil
| | - Fabio Márcio Squina
- Environment and Technological Processes Program, University of Sorocaba (UNISO), Sorocaba, SP, 18023-000, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Sarita Cândida Rabelo
- Departament of Bioprocesses and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, SP, 18618-687, Brazil
| | - Rosana Goldbeck
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Telma Teixeira Franco
- Interdisciplinary Centre of Energy Planning, University of Campinas (UNICAMP), Campinas, SP, 13083-896, Brazil
- School of Chemical Engineering, University of Campinas (UNICAMP), Campinas, SP, 13083-852, Brazil
| | - David Leak
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABER), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, 61801, USA
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo (USP), São Paulo, SP, 05508-010, Brazil.
| |
Collapse
|
5
|
Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
Collapse
Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| |
Collapse
|
6
|
Wan W, Zhao H, Yu K, Xiang Y, Dai W, Du C, Tian E. Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence in Brassica napus. Int J Mol Sci 2023; 24:12902. [PMID: 37629083 PMCID: PMC10454214 DOI: 10.3390/ijms241612902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Brassica napus is a globally important vegetable and oil crop. The research is meaningful for the yield and plant architecture of B. napus. In this study, one natural mutant line with determinate and capitulum-like inflorescence was chosen for further study. Genetic analysis indicated that the segregation patterns of inflorescences in the F2 populations supported a digenic inheritance model, which was further approved via the BSA-Seq technique. The BSA-Seq method detected two QTL regions on C02 (14.27-18.41 Mb) and C06 (32.98-33.68 Mb) for the genetic control of determinate inflorescences in MT plants. In addition, the expression profile in MT compared with WT was analyzed, and a total of 133 candidate genes for regulating the flower development (75 genes, 56.4%), shoot meristem development (29 genes, 21.8%), and inflorescence meristem development (13 genes, 9.8%) were identified. Then one joint analysis combing BSA-Seq and RNA-Seq identified two candidate genes of BnaTFL1 and BnaAP1 for regulating the MT phenotype. Furthermore, the potential utilization of the MT plants was also discussed.
Collapse
Affiliation(s)
- Wei Wan
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Haifei Zhao
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Kunjiang Yu
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Yang Xiang
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Wendong Dai
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Caifu Du
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Entang Tian
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| |
Collapse
|
7
|
Nalabothu RL, Fisher KJ, LaBella AL, Meyer TA, Opulente DA, Wolters JF, Rokas A, Hittinger CT. Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts. Mol Biol Evol 2023; 40:msad111. [PMID: 37154525 PMCID: PMC10263009 DOI: 10.1093/molbev/msad111] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene-trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.
Collapse
Affiliation(s)
- Rishitha L Nalabothu
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Kaitlin J Fisher
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC
| | - Taylor A Meyer
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
- Department of Biology, Villanova University, Villanova, PA
| | - John F Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
8
|
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
|
9
|
Lagos MAP, Caviativa JAC, Pinzón DCT, Roa DHR, Basso TO, Lozano MEV. Xylose Metabolization by a Saccharomyces cerevisiae Strain Isolated in Colombia. Indian J Microbiol 2023; 63:84-90. [PMID: 37179578 PMCID: PMC10172406 DOI: 10.1007/s12088-023-01054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/03/2023] [Indexed: 02/20/2023] Open
Abstract
Saccharomyces cerevisiae (S. cerevisiae) is the most widely used yeast in biotechnology in the world because its well-known metabolism and physiology as well as its recognized ability to ferment sugars such as hexoses. However, it does not metabolize pentoses such as arabinose and xylose, which are present in lignocellulosic biomass. Lignocellulose is a widely available raw material, with xylose content of approximately 35% of total sugars. This xylose fraction could be used to obtain high added-value chemical products such as xylitol. One of these yeasts isolated from a Colombian locality, designated as 202-3, showed interesting properties. 202-3 was identified through different approaches as a strain of S. cerevisiae, with an interesting consumption of xylose metabolizing into xylitol, in addition with excellent ability as a hexose fermenter with high ethanol yields and shows resistance to inhibitors present in lignocellulosic hydrolysates. The xylose metabolization by the 202-3 strain and their kinetics parameters had not been previously reported for any other natural strain of S. cerevisiae. These results suggest the great potential of natural strains for obtaining high value-added chemical products using sugars available in lignocellulosic biomass. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01054-z.
Collapse
Affiliation(s)
- Margareth Andrea Patiño Lagos
- Facultad de Ciencias, Instituto de Biotecnología, Universidad Nacional de Colombia – Sede Bogotá, Calle 44 # 45-67 Bloque B5, oficina 703, Bogotá, Colombia
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Diana Carolina Tusso Pinzón
- Facultad de Ciencias, Instituto de Biotecnología, Universidad Nacional de Colombia – Sede Bogotá, Calle 44 # 45-67 Bloque B5, oficina 703, Bogotá, Colombia
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diego Hernando Romero Roa
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Thiago Olitta Basso
- Departament of Chemical Engineering, University of Sao Paulo, São Paulo, Brazil
| | - Mario Enrique Velásquez Lozano
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| |
Collapse
|
10
|
Brown AJP. Fungal resilience and host-pathogen interactions: Future perspectives and opportunities. Parasite Immunol 2023; 45:e12946. [PMID: 35962618 PMCID: PMC10078341 DOI: 10.1111/pim.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
We are constantly exposed to the threat of fungal infection. The outcome-clearance, commensalism or infection-depends largely on the ability of our innate immune defences to clear infecting fungal cells versus the success of the fungus in mounting compensatory adaptive responses. As each seeks to gain advantage during these skirmishes, the interactions between host and fungal pathogen are complex and dynamic. Nevertheless, simply compromising the physiological robustness of fungal pathogens reduces their ability to evade antifungal immunity, their virulence, and their tolerance against antifungal therapy. In this article I argue that this physiological robustness is based on a 'Resilience Network' which mechanistically links and controls fungal growth, metabolism, stress resistance and drug tolerance. The elasticity of this network probably underlies the phenotypic variability of fungal isolates and the heterogeneity of individual cells within clonal populations. Consequently, I suggest that the definition of the fungal Resilience Network represents an important goal for the future which offers the clear potential to reveal drug targets that compromise drug tolerance and synergise with current antifungal therapies.
Collapse
Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
| |
Collapse
|
11
|
Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
Collapse
Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
| |
Collapse
|
12
|
Majeed A, Johar P, Raina A, Salgotra RK, Feng X, Bhat JA. Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding. Front Genet 2022; 13:944501. [PMID: 36003337 PMCID: PMC9393495 DOI: 10.3389/fgene.2022.944501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 12/26/2022] Open
Abstract
Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.
Collapse
Affiliation(s)
- Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University (PAU), Ludhiana, India
| | - Prerna Johar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Aamir Raina
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - R. K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Javaid Akhter Bhat
- Zhejiang Lab, Hangzhou, China
- International Genome Center, Jiangsu University, Zhenjiang, China
| |
Collapse
|
13
|
Aggeli D, Marad DA, Liu X, Buskirk SW, Levy SF, Lang GI. Overdominant and partially dominant mutations drive clonal adaptation in diploid Saccharomyces cerevisiae. Genetics 2022; 221:6569837. [PMID: 35435209 PMCID: PMC9157133 DOI: 10.1093/genetics/iyac061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/06/2022] [Indexed: 11/14/2022] Open
Abstract
Identification of adaptive targets in experimental evolution typically relies on extensive replication and genetic reconstruction. An alternative approach is to directly assay all mutations in an evolved clone by generating pools of segregants that contain random combinations of evolved mutations. Here, we apply this method to six Saccharomyces cerevisiae clones isolated from four diploid populations that were clonally evolved for 2,000 generations in rich glucose medium. Each clone contains 17-26 mutations relative to the ancestor. We derived intermediate genotypes between the founder and the evolved clones by bulk mating sporulated cultures of the evolved clones to a barcoded haploid version of the ancestor. We competed the resulting barcoded diploids en masse and quantified fitness in the experimental and alternative environments by barcode sequencing. We estimated average fitness effects of evolved mutations using barcode-based fitness assays and whole genome sequencing for a subset of segregants. In contrast to our previous work with haploid evolved clones, we find that diploids carry fewer beneficial mutations, with modest fitness effects (up to 5.4%) in the environment in which they arose. In agreement with theoretical expectations, reconstruction experiments show that all mutations with a detectable fitness effect manifest some degree of dominance over the ancestral allele, and most are overdominant. Genotypes with lower fitness effects in alternative environments allowed us to identify conditions that drive adaptation in our system.
Collapse
Affiliation(s)
- Dimitra Aggeli
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
| | - Daniel A Marad
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
| | - Xianan Liu
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA94025, USA
| | - Sean W Buskirk
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA.,Department of Biology, West Chester University, West Chester, PA19383, USA
| | - Sasha F Levy
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA94025, USA
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
| |
Collapse
|
14
|
Ashton GD, Sang F, Blythe M, Zadik D, Holmes N, Malla S, Camps SMT, Wright V, Melchers WJG, Verweij PE, Dyer PS. Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus. Front Cell Infect Microbiol 2022; 12:841138. [PMID: 35531335 PMCID: PMC9069965 DOI: 10.3389/fcimb.2022.841138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/03/2022] [Indexed: 12/19/2022] Open
Abstract
A sexual cycle was described in 2009 for the opportunistic fungal pathogen Aspergillus fumigatus, opening up for the first time the possibility of using techniques reliant on sexual crossing for genetic analysis. The present study was undertaken to evaluate whether the technique 'bulk segregant analysis' (BSA), which involves detection of differences between pools of progeny varying in a particular trait, could be applied in conjunction with next-generation sequencing to investigate the underlying basis of monogenic traits in A. fumigatus. Resistance to the azole antifungal itraconazole was chosen as a model, with a dedicated bioinformatic pipeline developed to allow identification of SNPs that differed between the resistant progeny pool and resistant parent compared to the sensitive progeny pool and parent. A clinical isolate exhibiting monogenic resistance to itraconazole of unknown basis was crossed to a sensitive parent and F1 progeny used in BSA. In addition, the use of backcrossing and increasing the number in progeny pools was evaluated as ways to enhance the efficiency of BSA. Use of F1 pools of 40 progeny led to the identification of 123 candidate genes with SNPs distributed over several contigs when aligned to an A1163 reference genome. Successive rounds of backcrossing enhanced the ability to identify specific genes and a genomic region, with BSA of progeny (using 40 per pool) from a third backcross identifying 46 genes with SNPs, and BSA of progeny from a sixth backcross identifying 20 genes with SNPs in a single 292 kb region of the genome. The use of an increased number of 80 progeny per pool also increased the resolution of BSA, with 29 genes demonstrating SNPs between the different sensitive and resistant groupings detected using progeny from just the second backcross with the majority of variants located on the same 292 kb region. Further bioinformatic analysis of the 292 kb region identified the presence of a cyp51A gene variant resulting in a methionine to lysine (M220K) change in the CYP51A protein, which was concluded to be the causal basis of the observed resistance to itraconazole. The future use of BSA in genetic analysis of A. fumigatus is discussed.
Collapse
Affiliation(s)
- George D. Ashton
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Fei Sang
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Martin Blythe
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Daniel Zadik
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Nadine Holmes
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Sunir Malla
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Simone M. T. Camps
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Victoria Wright
- DeepSeq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
15
|
Songdech P, Intasit R, Yingchutrakul Y, Butkinaree C, Ratanakhanokchai K, Soontorngun N. Activation of cryptic xylose metabolism by a transcriptional activator Znf1 boosts up xylitol production in the engineered Saccharomyces cerevisiae lacking xylose suppressor BUD21 gene. Microb Cell Fact 2022; 21:32. [PMID: 35248023 PMCID: PMC8897867 DOI: 10.1186/s12934-022-01757-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Xylitol is a valuable pentose sugar alcohol, used in the food and pharmaceutical industries. Biotechnological xylitol production is currently attractive due to possible conversion from abundant and low-cost industrial wastes or agricultural lignocellulosic biomass. In this study, the transcription factor Znf1 was characterised as being responsible for the activation of cryptic xylose metabolism in a poor xylose-assimilating S. cerevisiae for xylitol production.
Results
The results suggest that the expression of several xylose-utilising enzyme genes, encoding xylose reductases for the reduction of xylose to xylitol was derepressed by xylose. Their expression and those of a pentose phosphate shunt and related pathways required for xylose utilisation were strongly activated by the transcription factor Znf1. Using an engineered S. cerevisiae strain overexpressing ZNF1 in the absence of the xylose suppressor bud21Δ, xylitol production was maximally by approximately 1200% to 12.14 g/L of xylitol, corresponding to 0.23 g/g xylose consumed, during 10% (w/v) xylose fermentation. Proteomic analysis supported the role of Znf1 and Bud21 in modulating levels of proteins associated with carbon metabolism, xylose utilisation, ribosomal protein synthesis, and others. Increased tolerance to lignocellulosic inhibitors and improved cell dry weight were also observed in this engineered bud21∆ + pLJ529-ZNF1 strain. A similar xylitol yield was achieved using fungus-pretreated rice straw hydrolysate as an eco-friendly and low-cost substrate.
Conclusions
Thus, we identified the key modulators of pentose sugar metabolism, namely the transcription factor Znf1 and the suppressor Bud21, for enhanced xylose utilisation, providing a potential application of a generally recognised as safe yeast in supporting the sugar industry and the sustainable lignocellulose-based bioeconomy.
Graphical Abstract
Collapse
|
16
|
Zhang J, Xiong H, Guo H, Li Y, Xie X, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Identification of the Q Gene Playing a Role in Spike Morphology Variation in Wheat Mutants and Its Regulatory Network. FRONTIERS IN PLANT SCIENCE 2022; 12:807731. [PMID: 35087560 PMCID: PMC8787668 DOI: 10.3389/fpls.2021.807731] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/13/2021] [Indexed: 05/27/2023]
Abstract
The wheat AP2 family gene Q controls domestication traits, including spike morphology and threshability, which are critical for the widespread cultivation and yield improvement of wheat. Although many studies have investigated the molecular mechanisms of the Q gene, its direct target genes, especially those controlling spike morphology, are not clear, and its regulatory pathways are not well established. In this study, we conducted gene mapping of a wheat speltoid spike mutant and found that a new allele of the Q gene with protein truncation played a role in spike morphology variation in the mutant. Dynamic expression levels of the Q gene throughout the spike development process suggested that the transcript abundances of the mutant were decreased at the W6 and W7 scales compared to those of the WT. We identified several mutation sites on the Q gene and showed that mutations in different domains resulted in distinct phenotypes. In addition, we found that the Q gene produced three transcripts via alternative splicing and that they exhibited differential expression patterns in nodes, internodes, flag leaves, and spikes. Finally, we identified several target genes directly downstream of Q, including TaGRF1-2D and TaMGD-6B, and proposed a possible regulatory network. This study uncovered the target genes of Q, and the results can help to clarify the mechanism of wheat spike morphology and thereby improve wheat grain yield.
Collapse
|
17
|
Chen DG, Zhou XQ, Chen K, Chen PL, Guo J, Liu CG, Chen YD. Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:6. [PMID: 35103045 PMCID: PMC8792131 DOI: 10.1007/s11032-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/13/2022] [Indexed: 05/16/2023]
Abstract
UNLABELLED Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-022-01275-y.
Collapse
Affiliation(s)
- Da-gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Xin-qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ping-li Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuan-guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - You-ding Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| |
Collapse
|
18
|
Poudel HP, Tilhou NW, Sanciangco MD, Vaillancourt B, Kaeppler SM, Buell CR, Casler MD. Genetic loci associated with winter survivorship in diverse lowland switchgrass populations. THE PLANT GENOME 2021; 14:e20159. [PMID: 34661986 DOI: 10.1002/tpg2.20159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
High winter mortality limits biomass yield of lowland switchgrass (Panicum virgatum L.) planted in the northern latitudes of North America. Breeding of cold tolerant switchgrass cultivars requires many years due to its perennial growth habit and the unpredictable winter selection pressure that is required to identify winter-hardy individuals. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 populations with differential winter survivorship were used for BSA. A maximum of 10% of the individuals (8-20) were bulked to create survivor and nonsurvivor DNA pools from each population and location. The DNA pools were evaluated using exome capture sequencing, and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine quatitative trait loci (QTL) from tetraploid populations and seven QTL from octoploid populations. Many QTL were population-specific, but some were identified in multiple populations that originated across a broad geographic landscape. Four QTL (at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N) were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.
Collapse
Affiliation(s)
- Hari P Poudel
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Neal W Tilhou
- Dep. of Agronomy, Univ. of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - C Robin Buell
- Dep. of Plant Biology, Michigan State Univ., East Lansing, MI, USA
| | | |
Collapse
|
19
|
Li X, Wang Y, Li G, Liu Q, Pereira R, Chen Y, Nielsen J. Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis. Nat Catal 2021. [DOI: 10.1038/s41929-021-00670-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
20
|
He Y, Li H, Chen L, Zheng L, Ye C, Hou J, Bao X, Liu W, Shen Y. Production of xylitol by Saccharomyces cerevisiae using waste xylose mother liquor and corncob residues. Microb Biotechnol 2021; 14:2059-2071. [PMID: 34255428 PMCID: PMC8449662 DOI: 10.1111/1751-7915.13881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 06/01/2021] [Accepted: 06/14/2021] [Indexed: 11/28/2022] Open
Abstract
Exorbitant outputs of waste xylose mother liquor (WXML) and corncob residue from commercial‐scale production of xylitol create environmental problems. To reduce the wastes, a Saccharomyces cerevisiae strain tolerant to WXML was conferred with abilities to express the genes of xylose reductase, a xylose‐specific transporter and enzymes of the pentose phosphate pathway. This strain showed a high capacity to produce xylitol from xylose in WXML with glucose as a co‐substrate. Additionally, a simultaneous saccharification and fermentation (SSF) process was designed to use corncob residues and cellulase instead of directly adding glucose as a co‐substrate. Xylitol titer and the productivity were, respectively, 91.0 g l‐1 and 1.26 ± 0.01 g l‐1 h‐1 using 20% WXML, 55 g DCW l‐1 delignified corncob residues and 11.8 FPU gcellulose‐1 cellulase at 35° during fermentation. This work demonstrates the promising strategy of SSF to exploit waste products to xylitol fermentation process.
Collapse
Affiliation(s)
- Yao He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongxing Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qi Lu University of Technology, Jinan, 250353, China
| | - Liyuan Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Liyuan Zheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chunhui Ye
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.,State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qi Lu University of Technology, Jinan, 250353, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| |
Collapse
|
21
|
Shi XC, Zhang Y, Wang T, Wang XC, Lv HB, Laborda P, Duan TT. Metabolic and transcriptional analysis of recombinant Saccharomyces?cerevisiae for xylose fermentation: a feasible and efficient approach. IEEE J Biomed Health Inform 2021; 26:2425-2434. [PMID: 34077376 DOI: 10.1109/jbhi.2021.3085313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lignocellulose is an abundant xylose-containing biomass found in agricultural wastes, and has arisen as a suitable alternative to fossil fuels for the production of bioethanol. Although Saccharomyces cerevisiae has been thoroughly used for the production of bioethanol, its potential to utilize lignocellulose remains poorly understood. In this work, xylose-metabolic genes of Pichia stipitis and Candida tropicalis, under the control of different promoters, were introduced into S. cerevisiae. RNA-seq analysis was use to examine the response of S. cerevisiae metabolism to the introduction of xylose-metabolic genes. The use of the PGK1 promoter to drive xylitol dehydrogenase (XDH) expression, instead of the TEF1 promoter, improved xylose utilization in ?XR-pXDH? strain by overexpressing xylose reductase (XR) and XDH from C. tropicalis, enhancing the production of xylitol (13.66 ? 0.54 g/L after 6 days fermentation). Overexpression of xylulokinase and XR/XDH from P. stipitis remarkably decreased xylitol accumulation (1.13 ? 0.06 g/L and 0.89 ? 0.04 g/L xylitol, respectively) and increased ethanol production (196.14% and 148.50% increases during the xylose utilization stage, respectively), in comparison with the results of XR-pXDH. This result may be produced due to the enhanced xylose transport, Embden?Meyerhof and pentose phosphate pathways, as well as alleviated oxidative stress. The low xylose consumption rate in these recombinant strains comparing with P. stipitis and C. tropicalis may be explained by the insufficient supplementation of NADPH and NAD+. The results obtained in this work provide new insights on the potential utilization of xylose using bioengineered S. cerevisiae strains.
Collapse
|
22
|
Acosta Morel W, Anta Fernández F, Baroncelli R, Becerra S, Thon MR, van Kan JAL, Díaz-Mínguez JM, Benito EP. A Major Effect Gene Controlling Development and Pathogenicity in Botrytis cinerea Identified Through Genetic Analysis of Natural Mycelial Non-pathogenic Isolates. FRONTIERS IN PLANT SCIENCE 2021; 12:663870. [PMID: 33936154 PMCID: PMC8079791 DOI: 10.3389/fpls.2021.663870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Botrytis cinerea is a necrotrophic plant pathogenic fungus with a wide host range. Its natural populations are phenotypically and genetically very diverse. A survey of B. cinerea isolates causing gray mold in the vineyards of Castilla y León, Spain, was carried out and as a result eight non-pathogenic natural variants were identified. Phenotypically these isolates belong to two groups. The first group consists of seven isolates displaying a characteristic mycelial morphotype, which do not sporulate and is unable to produce sclerotia. The second group includes one isolate, which sporulates profusely and does not produce sclerotia. All of them are unresponsive to light. Crosses between a representative mycelial non-pathogenic isolate and a highly aggressive field isolate revealed that the phenotypic differences regarding pathogenicity, sporulation and production of sclerotia cosegregated in the progeny and are determined by a single genetic locus. By applying a bulked segregant analysis strategy based on the comparison of the two parental genomes the locus was mapped to a 110 kb region in chromosome 4. Subcloning and transformation experiments revealed that the polymorphism is an SNP affecting gene Bcin04g03490 in the reference genome of B. cinerea. Genetic complementation analysis and sequencing of the Bcin04g03490 alleles demonstrated that the mutations in the mycelial isolates are allelic and informed about the nature of the alterations causing the phenotypes observed. Integration of the allele of the pathogenic isolate into the non-pathogenic isolate fully restored the ability to infect, to sporulate and to produce sclerotia. Therefore, it is concluded that a major effect gene controlling differentiation and developmental processes as well as pathogenicity has been identified in B. cinerea. It encodes a protein with a GAL4-like Zn(II)2Cys6 binuclear cluster DNA binding domain and an acetyltransferase domain, suggesting a role in regulation of gene expression through a mechanism involving acetylation of specific substrates.
Collapse
Affiliation(s)
- Wilson Acosta Morel
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Francisco Anta Fernández
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Riccardo Baroncelli
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Sioly Becerra
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Michael R. Thon
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - José María Díaz-Mínguez
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Ernesto Pérez Benito
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| |
Collapse
|
23
|
Vogel G, LaPlant KE, Mazourek M, Gore MA, Smart CD. A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1015-1031. [PMID: 33388885 DOI: 10.1007/s00122-020-03747-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Two QTL mapping approaches were used to identify a total of six QTL associated with Phytophthora root and crown rot resistance in a biparental squash population. Phytophthora root and crown rot, caused by the soilborne oomycete pathogen Phytophthora capsici, leads to severe yield losses in squash (Cucurbita pepo). To identify quantitative trait loci (QTL) involved in resistance to this disease, we crossed a partially resistant squash breeding line with a susceptible zucchini cultivar and evaluated over 13,000 F2 seedlings in a greenhouse screen. Bulked segregant analysis with whole genome resequencing (BSA-Seq) resulted in the identification of five genomic regions-on chromosomes 4, 5, 8, 12, and 16-featuring significant allele frequency differentiation between susceptible and resistant bulks in each of two independent replicates. In addition, we conducted linkage mapping using a population of 176 F3 families derived from individually genotyped F2 individuals. Variation in disease severity among these families was best explained by a four-QTL model, comprising the same loci identified via BSA-Seq on chromosomes 4, 5, and 8 as well as an additional locus on chromosome 19, for a combined total of six QTL identified between both methods. Loci, whether those identified by BSA-Seq or linkage mapping, were of small-to-moderate effect, collectively accounting for 28-35% and individually for 2-10% of the phenotypic variance explained. However, a multiple linear regression model using one marker in each BSA-Seq QTL could predict F2:3 disease severity with only a slight drop in cross-validation accuracy compared to genomic prediction models using genome-wide markers. These results suggest that marker-assisted selection could be a suitable approach for improving Phytophthora crown and root rot resistance in squash.
Collapse
Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - Kyle E LaPlant
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA.
| |
Collapse
|
24
|
Zhang L, Dong C, Chen Z, Gui L, Chen C, Li D, Xie Z, Zhang Q, Zhang X, Xia C, Liu X, Kong X, Wang J. WheatGmap: a comprehensive platform for wheat gene mapping and genomic studies. MOLECULAR PLANT 2021; 14:187-190. [PMID: 33271333 DOI: 10.1016/j.molp.2020.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 05/26/2023]
Affiliation(s)
- Lichao Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunhao Dong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; Department of Life Science, Tcuni, Inc., Chengdu 610041, China
| | - Lixuan Gui
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; Department of Life Science, Tcuni, Inc., Chengdu 610041, China
| | - Cheng Chen
- Department of Life Science, Tcuni, Inc., Chengdu 610041, China
| | - Danping Li
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhencheng Xie
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiang Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueying Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Xia
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
25
|
Yang BX, Xie CY, Xia ZY, Wu YJ, Gou M, Tang YQ. Improving xylitol yield by deletion of endogenous xylitol-assimilating genes: a study of industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. FEMS Yeast Res 2020; 20:5986616. [PMID: 33201998 DOI: 10.1093/femsyr/foaa061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/14/2020] [Indexed: 01/12/2023] Open
Abstract
Engineered Saccharomyces cerevisiae can reduce xylose to xylitol. However, in S.cerevisiae, there are several endogenous enzymes including xylitol dehydrogenase encoded by XYL2, sorbitol dehydrogenases encoded by SOR1/SOR2 and xylulokinase encoded by XKS1 may lead to the assimilation of xylitol. In this study, to increase xylitol accumulation, these genes were separately deleted through CRISPR/Cas9 system. Their effects on xylitol yield of an industrial S. cerevisiae CK17 overexpressing Candida tropicalis XYL1 (encoding xylose reductase) were investigated. Deletion of SOR1/SOR2 or XKS1 increased the xylitol yield in both batch and fed-batch fermentation with different concentrations of glucose and xylose. The analysis of the transcription level of key genes in the mutants during fed-batch fermentation suggests that SOR1/SOR2 are more crucially responsible for xylitol oxidation than XYL2 under the genetic background of S.cerevisiae CK17. The deletion of XKS1 gene could also weaken SOR1/SOR2 expression, thereby increasing the xylitol accumulation. The XKS1-deleted strain CK17ΔXKS1 produced 46.17 g/L of xylitol and reached a xylitol yield of 0.92 g/g during simultaneous saccharification and fermentation (SSF) of pretreated corn stover slurry. Therefore, the deletion of XKS1 gene provides a promising strategy to meet the industrial demands for xylitol production from lignocellulosic biomass.
Collapse
Affiliation(s)
- Bai-Xue Yang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Ya-Jing Wu
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| |
Collapse
|
26
|
Guo Z, Cai L, Chen Z, Wang R, Zhang L, Guan S, Zhang S, Ma W, Liu C, Pan G. Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201081. [PMID: 33391797 PMCID: PMC7735347 DOI: 10.1098/rsos.201081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.
Collapse
Affiliation(s)
- Zhenhua Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Lijun Cai
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154007, People's Republic of China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Ruiying Wang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Lanming Zhang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Shiwu Guan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Shuhua Zhang
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Wendong Ma
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Chuanxue Liu
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| | - Guojun Pan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, People's Republic of China
| |
Collapse
|
27
|
Abstract
The budding yeast, Saccharomyces cerevisiae, has been widely used for genetic studies of fundamental cellular functions. The isolation and analysis of yeast mutants is a commonly used and powerful technique to identify the genes that are involved in a process of interest. Furthermore, natural genetic variation among wild yeast strains has been studied for analysis of polygenic traits by quantitative trait loci mapping. Whole-genome sequencing, often combined with bulk segregant analysis, is a powerful technique that helps determine the identity of mutations causing a phenotype. Here, we describe protocols for the construction of libraries for S. cerevisiae whole-genome sequencing. We also present a bioinformatic pipeline to determine the genetic variants in a yeast strain using whole-genome sequencing data. This pipeline can also be used for analyzing Schizosaccharomyces pombe mutants. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of haploid spores for bulk segregant analysis Basic Protocol 2: Extraction of genomic DNA from yeast cells Basic Protocol 3: Shearing of genomic DNA for library preparation Basic Protocol 4: Construction and amplification of DNA libraries Support Protocol 1: Annealing oligonucleotides for forming Y-adapters Support Protocol 2: Size selection and cleanup using SPRI beads Basic Protocol 5: Identification of genomic variants from sequencing data.
Collapse
Affiliation(s)
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
28
|
Ravishankar A, Pupo A, Gallagher JEG. Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure. G3 (BETHESDA, MD.) 2020; 10:2043-2056. [PMID: 32299824 PMCID: PMC7263678 DOI: 10.1534/g3.120.401183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/13/2020] [Indexed: 12/16/2022]
Abstract
The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell's functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.
Collapse
Affiliation(s)
| | - Amaury Pupo
- Department of Biology, West Virginia University
| | | |
Collapse
|
29
|
Devia J, Bastías C, Kessi-Pérez EI, Villarroel CA, De Chiara M, Cubillos FA, Liti G, Martínez C, Salinas F. Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments. Front Genet 2020; 11:293. [PMID: 32425968 PMCID: PMC7212421 DOI: 10.3389/fgene.2020.00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/11/2020] [Indexed: 12/02/2022] Open
Abstract
In the past decade, the sequencing of large cohorts of Saccharomyces cerevisiae strains has revealed a landscape of genomic regions acquired by Horizontal Gene Transfer (HGT). The genes acquired by HGT play important roles in yeast adaptation to the fermentation process, improving nitrogen and carbon source utilization. However, the functional characterization of these genes at the molecular level has been poorly attended. In this work, we carried out a systematic analysis of the promoter activity and protein level of 30 genes contained in three horizontally acquired regions commonly known as regions A, B, and C. In three strains (one for each region), we used the luciferase reporter gene and the mCherry fluorescent protein to quantify the transcriptional and translational activity of these genes, respectively. We assayed the strains generated in four different culture conditions; all showed low levels of transcriptional and translational activity across these environments. However, we observed an increase in protein levels under low nitrogen culture conditions, suggesting a possible role of the horizontally acquired genes in the adaptation to nitrogen-limited environments. Furthermore, since the strains carrying the luciferase reporter gene are null mutants for the horizontally acquired genes, we assayed growth parameters (latency time, growth rate, and efficiency) and the fermentation kinetics in this set of deletion strains. The results showed that single deletion of 20 horizontally acquired genes modified the growth parameters, whereas the deletion of five of them altered the maximal CO2 production rate (Vmax). Interestingly, we observed a correlation between growth parameters and Vmax for an ORF within region A, encoding an ortholog to a thiamine (vitamin B1) transporter whose deletion decreased the growth rate, growth efficiency, and CO2 production. Altogether, our results provided molecular and phenotypic evidence highlighting the importance of horizontally acquired genes in yeast adaptation to fermentative environments.
Collapse
Affiliation(s)
- Joaquín Devia
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Camila Bastías
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Carlos A Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | | | - Francisco A Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
| |
Collapse
|
30
|
Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
Collapse
|
31
|
Deaner M, Alper HS. Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:foz076. [PMID: 31665284 DOI: 10.1093/femsyr/foz076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Although only 6 years old, the CRISPR system has blossomed into a tool for rapid, on-demand genome engineering and gene regulation in Saccharomyces cerevisiae. In this minireview, we discuss fundamental CRISPR technologies, tools to improve the efficiency and capabilities of gene targeting, and cutting-edge techniques to explore gene editing and transcriptional regulation at genome scale using pooled approaches. The focus is on applications to metabolic engineering with topics including development of techniques to edit the genome in multiplex, tools to enable large numbers of genetic modifications using pooled single-guide RNA libraries and efforts to enable programmable transcriptional regulation using endonuclease-null Cas enzymes.
Collapse
Affiliation(s)
- Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
| |
Collapse
|
32
|
Correlating Genotype and Phenotype in the Asexual Yeast Candida orthopsilosis Implicates ZCF29 in Sensitivity to Caffeine. G3-GENES GENOMES GENETICS 2019; 9:3035-3043. [PMID: 31352406 PMCID: PMC6723125 DOI: 10.1534/g3.119.400348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Candida orthopsilosis is diploid asexual yeast that causes human disease. Most C. orthopsilosis isolates arose from at least four separate hybridizations between related, but not identical, parents. Here, we used population genomics data to correlate genotypic and phenotypic variation in 28 C. orthopsilosis isolates. We used cosine similarity scores to identify 65 variants with potential high-impact (deleterious effects) that correlated with specific phenotypes. Of these, 19 were Single Nucleotide Polymorphisms (SNPs) that changed stop or start codons, or splice sites. One variant resulted in a premature stop codon in both alleles of the gene ZCF29 in C. orthopsilosis isolate 185, which correlated with sensitivity to nystatin and caffeine. We used CRISPR-Cas9 editing to introduce this polymorphism into two resistant C. orthopsilosis isolates. Introducing the stop codon resulted in sensitivity to caffeine and to ketoconazole, but not to nystatin. Our analysis shows that it is possible to associate genomic variants with phenotype in asexual Candida species, but that only a small amount of genomic variation can be easily explored.
Collapse
|
33
|
Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
Collapse
Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
| |
Collapse
|
34
|
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems 2019; 4:mSystems00170-18. [PMID: 30834327 PMCID: PMC6392091 DOI: 10.1128/msystems.00170-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/21/2019] [Indexed: 11/23/2022] Open
Abstract
Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism. Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.
Collapse
|
35
|
Wetzel LA, Levin TC, Hulett RE, Chan D, King GA, Aldayafleh R, Booth DS, Sigg MA, King N. Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta. eLife 2018; 7:e41482. [PMID: 30556809 PMCID: PMC6322860 DOI: 10.7554/elife.41482] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
In a previous study we established forward genetics in the choanoflagellate Salpingoeca rosetta and found that a C-type lectin gene is required for rosette development (Levin et al., 2014). Here we report on critical improvements to genetic screens in S. rosetta while also investigating the genetic basis for rosette defect mutants in which single cells fail to develop into orderly rosettes and instead aggregate promiscuously into amorphous clumps of cells. Two of the mutants, Jumble and Couscous, mapped to lesions in genes encoding two different predicted glycosyltransferases and displayed aberrant glycosylation patterns in the basal extracellular matrix (ECM). In animals, glycosyltransferases sculpt the polysaccharide-rich ECM, regulate integrin and cadherin activity, and, when disrupted, contribute to tumorigenesis. The finding that predicted glycosyltransferases promote proper rosette development and prevent cell aggregation in S. rosetta suggests a pre-metazoan role for glycosyltransferases in regulating development and preventing abnormal tumor-like multicellularity.
Collapse
Affiliation(s)
- Laura A Wetzel
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Tera C Levin
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Ryan E Hulett
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Daniel Chan
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Grant A King
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Reef Aldayafleh
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - David S Booth
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Monika Abedin Sigg
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Nicole King
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| |
Collapse
|
36
|
Whole Genome Resequencing from Bulked Populations as a Rapid QTL and Gene Identification Method in Rice. Int J Mol Sci 2018; 19:ijms19124000. [PMID: 30545055 PMCID: PMC6321147 DOI: 10.3390/ijms19124000] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 11/16/2022] Open
Abstract
Most Quantitative Trait Loci (QTL) and gene isolation approaches, such as positional- or map-based cloning, are time-consuming and low-throughput methods. Understanding and detecting the genetic material that controls a phenotype is a key means to functionally analyzing genes as well as to enhance crop agronomic traits. In this regard, high-throughput technologies have great prospects for changing the paradigms of DNA marker revealing, genotyping, and for discovering crop genetics and genomic study. Bulk segregant analysis, based on whole genome resequencing approaches, permits the rapid isolation of the genes or QTL responsible for the causative mutation of the phenotypes. MutMap, MutMap Gap, MutMap+, modified MutMap, and QTL-seq methods are among those approaches that have been confirmed to be fruitful gene mapping approaches for crop plants, such as rice, irrespective of whether the characters are determined by polygenes. As a result, in the present study we reviewed the progress made by all these methods to identify QTL or genes in rice.
Collapse
|
37
|
Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C. Model organism data evolving in support of translational medicine. Lab Anim (NY) 2018; 47:277-289. [PMID: 30224793 PMCID: PMC6322546 DOI: 10.1038/s41684-018-0150-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Model organism databases (MODs) have been collecting and integrating biomedical research data for 30 years and were designed to meet specific needs of each model organism research community. The contributions of model organism research to understanding biological systems would be hard to overstate. Modern molecular biology methods and cost reductions in nucleotide sequencing have opened avenues for direct application of model organism research to elucidating mechanisms of human diseases. Thus, the mandate for model organism research and databases has now grown to include facilitating use of these data in translational applications. Challenges in meeting this opportunity include the distribution of research data across many databases and websites, a lack of data format standards for some data types, and sustainability of scale and cost for genomic database resources like MODs. The issues of widely distributed data and application of data standards are some of the challenges addressed by FAIR (Findable, Accessible, Interoperable, and Re-usable) data principles. The Alliance of Genome Resources is now moving to address these challenges by bringing together expertly curated research data from fly, mouse, rat, worm, yeast, zebrafish, and the Gene Ontology consortium. Centralized multi-species data access, integration, and format standardization will lower the data utilization barrier in comparative genomics and translational applications and will provide a framework in which sustainable scale and cost can be addressed. This article presents a brief historical perspective on how the Alliance model organisms are complementary and how they have already contributed to understanding the etiology of human diseases. In addition, we discuss four challenges for using data from MODs in translational applications and how the Alliance is working to address them, in part by applying FAIR data principles. Ultimately, combined data from these animal models are more powerful than the sum of the parts.
Collapse
Affiliation(s)
- Douglas G Howe
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
| | | | - Yvonne M Bradford
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | | | | | - Ranjana Kishore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stanley J F Laulederkind
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sierra A T Moxon
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | | |
Collapse
|
38
|
Zhang K, Wang X, Zhu W, Qin X, Xu J, Cheng C, Lou Q, Li J, Chen J. Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2229-2243. [PMID: 30078164 DOI: 10.1007/s00122-018-3150-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/23/2018] [Indexed: 05/16/2023]
Abstract
Key message A single recessive gene for complete resistance to powdery mildew and a major-effect QTL for partial resistance to downy mildew were co-localized in a Cucumis hystrix introgression line of cucumber. Downy mildew (DM) and powdery mildew (PM) are two major foliar diseases in cucumber. DM resistance (DMR) and PM resistance (PMR) may share common components; however, the genetic relationship between them remains unclear. IL52, a Cucumis hystrix introgression line of cucumber which has been reported to possess DMR, was recently identified to exhibit PMR as well. In this study, a single recessive gene pm for PMR was mapped to an approximately 468-kb region on chromosome 5 with 155 recombinant inbred lines (RILs) and 193 F2 plants derived from the cross between a susceptible line 'changchunmici' and IL52. Interestingly, pm was co-localized with the major-effect DMR QTL dm5.2 confirmed by combining linkage analysis and BSA-seq, which was consistent with the observed linkage of DMR and PMR in IL52. Further, phenotype-genotype correlation analysis of DMR and PMR in the RILs indicated that the co-localized locus pm/dm5.2 confers complete resistance to PM and partial resistance to DM. Seven candidate genes for DMR were identified within dm5.2 by BSA-seq analysis, of which Csa5M622800.1, Csa5M622830.1 and Csa5M623490.1 were also the same candidate genes for PMR. A single nucleotide polymorphism that is present in the 3' untranslated region (3'UTR) of Csa5M622830.1 co-segregated perfectly with PMR. The GATA transcriptional factor gene Csa5M622830.1 may be a likely candidate gene for DMR and PMR. This study has provided a clear evidence for the relationship between DMR and PMR in IL52 and sheds new light on the potential value of IL52 for cucumber DMR and PMR breeding program.
Collapse
Affiliation(s)
- Kaijing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Wenwei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China.
| |
Collapse
|
39
|
Sharma S, Varghese E, Arora A, Singh KN, Singh S, Nain L, Paul D. Augmenting Pentose Utilization and Ethanol Production of Native Saccharomyces cerevisiae LN Using Medium Engineering and Response Surface Methodology. Front Bioeng Biotechnol 2018; 6:132. [PMID: 30320081 PMCID: PMC6166573 DOI: 10.3389/fbioe.2018.00132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022] Open
Abstract
Economics of ethanol production from lignocellulosic biomass depends on complete utilization of constituent carbohydrates and efficient fermentation of mixed sugars present in biomass hydrolysates. Saccharomyces cerevisiae, the commercial strain for ethanol production uses only glucose while pentoses remain unused. Recombinant strains capable of utilizing pentoses have been engineered but with limited success. Recently, presence of endogenous pentose assimilation pathway in S. cerevisiae was reported. On the contrary, evolutionary engineering of native xylose assimilating strains is promising approach. In this study, a native strain S. cerevisiae LN, isolated from fruit juice, was found to be capable of xylose assimilation and mixed sugar fermentation. Upon supplementation with yeast extract and peptone, glucose (10%) fermentation efficiency was 78% with ~90% sugar consumption. Medium engineering augmented mixed sugars (5% glucose + 5% xylose) fermentation efficiency to ~50 and 1.6% ethanol yield was obtained with concomitant sugar consumption ~60%. Statistical optimization of input variables Glucose (5.36%), Xylose (3.30%), YE (0.36%), and peptone (0.25%) with Response surface methodology led to improved sugar consumption (74.33%) and 2.36% ethanol within 84 h. Specific activities of Xylose Reductase and Xylitol Dehydrogenase exhibited by S. cerevisiae LN were relatively low. Their ratio indicated metabolism diverted toward ethanol than xylitol and other byproducts. Strain was tolerant to concentrations of HMF, furfural and acetic acid commonly encountered in biomass hydrolysates. Thus, genetic setup for xylose assimilation in S. cerevisiae LN is not merely artifact of xylose metabolizing pathway and can be augmented by adaptive evolution. This strain showed potential for commercial exploitation.
Collapse
Affiliation(s)
- Shalley Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Eldho Varghese
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anju Arora
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K N Singh
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida, India
| |
Collapse
|
40
|
Abstract
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.
Collapse
|
41
|
Sardi M, Gasch AP. Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering. FEMS Yeast Res 2018. [PMID: 28637316 DOI: 10.1093/femsyr/fox042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
Collapse
Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
42
|
Sun J, Yang L, Wang J, Liu H, Zheng H, Xie D, Zhang M, Feng M, Jia Y, Zhao H, Zou D. Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. RICE (NEW YORK, N.Y.) 2018; 11:24. [PMID: 29671148 PMCID: PMC5906412 DOI: 10.1186/s12284-018-0218-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 04/04/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice. RESULTS A novel major QTL, qPSST6, controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of qPSST6. Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as "response to cold" by gene ontology (GO) analysis. qRT-PCR analysis revealed that LOC_Os06g39750 was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of LOC_Os06g39750 in regulating the PSST of rice, suggesting that it was the candidate gene of qPSST6. CONCLUSIONS The information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).
Collapse
Affiliation(s)
- Jian Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Dongwei Xie
- The Institute of Industrial Crops of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 China
| | - Mingfang Feng
- College of Life Science, Northeast Agricultural University, Harbin, 150030 China
| | - Yan Jia
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hongwei Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| |
Collapse
|
43
|
Sardi M, Paithane V, Place M, Robinson DE, Hose J, Wohlbach DJ, Gasch AP. Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PLoS Genet 2018; 14:e1007217. [PMID: 29474395 PMCID: PMC5849340 DOI: 10.1371/journal.pgen.1007217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/13/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cellulosic plant biomass is a promising sustainable resource for generating alternative biofuels and biochemicals with microbial factories. But a remaining bottleneck is engineering microbes that are tolerant of toxins generated during biomass processing, because mechanisms of toxin defense are only beginning to emerge. Here, we exploited natural diversity in 165 Saccharomyces cerevisiae strains isolated from diverse geographical and ecological niches, to identify mechanisms of hydrolysate-toxin tolerance. We performed genome-wide association (GWA) analysis to identify genetic variants underlying toxin tolerance, and gene knockouts and allele-swap experiments to validate the involvement of implicated genes. In the process of this work, we uncovered a surprising difference in genetic architecture depending on strain background: in all but one case, knockout of implicated genes had a significant effect on toxin tolerance in one strain, but no significant effect in another strain. In fact, whether or not the gene was involved in tolerance in each strain background had a bigger contribution to strain-specific variation than allelic differences. Our results suggest a major difference in the underlying network of causal genes in different strains, suggesting that mechanisms of hydrolysate tolerance are very dependent on the genetic background. These results could have significant implications for interpreting GWA results and raise important considerations for engineering strategies for industrial strain improvement. Understanding the genetic architecture of complex traits is important for elucidating the genotype-phenotype relationship. Many studies have sought genetic variants that underlie phenotypic variation across individuals, both to implicate causal variants and to inform on architecture. Here we used genome-wide association analysis to identify genes and processes involved in tolerance of toxins found in plant-biomass hydrolysate, an important substrate for sustainable biofuel production. We found substantial variation in whether or not individual genes were important for tolerance across genetic backgrounds. Whether or not a gene was important in a given strain background explained more variation than the alleleic differences in the gene. These results suggest substantial variation in gene contributions, and perhaps underlying mechanisms, of toxin tolerance.
Collapse
Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Vaishnavi Paithane
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - De Elegant Robinson
- Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dana J Wohlbach
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
44
|
Cheng C, Tang RQ, Xiong L, Hector RE, Bai FW, Zhao XQ. Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:28. [PMID: 29441126 PMCID: PMC5798184 DOI: 10.1186/s13068-018-1018-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae wild strains generally have poor xylose-utilization capability, which is a major barrier for efficient bioconversion of lignocellulosic biomass. Laboratory adaption is commonly used to enhance xylose utilization of recombinant S. cerevisiae. Apparently, yeast cells could remodel the metabolic network for xylose metabolism. However, it still remains unclear why natural isolates of S. cerevisiae poorly utilize xylose. Here, we analyzed a unique S. cerevisiae natural isolate YB-2625 which has superior xylose metabolism capability in the presence of mixed-sugar. Comparative transcriptomic analysis was performed using S. cerevisiae YB-2625 grown in a mixture of glucose and xylose, and the model yeast strain S288C served as a control. Global gene transcription was compared at both the early mixed-sugar utilization stage and the latter xylose-utilization stage. RESULTS Genes involved in endogenous xylose-assimilation (XYL2 and XKS1), gluconeogenesis, and TCA cycle showed higher transcription levels in S. cerevisiae YB-2625 at the xylose-utilization stage, when compared to the reference strain. On the other hand, transcription factor encoding genes involved in regulation of glucose repression (MIG1, MIG2, and MIG3) as well as HXK2 displayed decreased transcriptional levels in YB-2625, suggesting the alleviation of glucose repression of S. cerevisiae YB-2625. Notably, genes encoding antioxidant enzymes (CTT1, CTA1, SOD2, and PRX1) showed higher transcription levels in S. cerevisiae YB-2625 in the xylose-utilization stage than that of the reference strain. Consistently, catalase activity of YB-2625 was 1.9-fold higher than that of S. cerevisiae S288C during the xylose-utilization stage. As a result, intracellular reactive oxygen species levels of S. cerevisiae YB-2625 were 43.3 and 58.6% lower than that of S288C at both sugar utilization stages. Overexpression of CTT1 and PRX1 in the recombinant strain S. cerevisiae YRH396 deriving from S. cerevisiae YB-2625 increased cell growth when xylose was used as the sole carbon source, leading to 13.5 and 18.1%, respectively, more xylose consumption. CONCLUSIONS Enhanced oxidative stress tolerance and relief of glucose repression are proposed to be two major mechanisms for superior xylose utilization by S. cerevisiae YB-2625. The present study provides insights into the innate regulatory mechanisms underlying xylose utilization in wild-type S. cerevisiae, which benefits the rapid development of robust yeast strains for lignocellulosic biorefineries.
Collapse
Affiliation(s)
- Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL USA
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| |
Collapse
|
45
|
Rong-Mullins X, Ravishankar A, McNeal KA, Lonergan ZR, Biega AC, Creamer JP, Gallagher JEG. Genetic variation in Dip5, an amino acid permease, and Pdr5, a multiple drug transporter, regulates glyphosate resistance in S. cerevisiae. PLoS One 2017; 12:e0187522. [PMID: 29155836 PMCID: PMC5695762 DOI: 10.1371/journal.pone.0187522] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/20/2017] [Indexed: 11/22/2022] Open
Abstract
S. cerevisiae from different environments are subject to a wide range of selective pressures, whether intentional or by happenstance. Chemicals classified by their application, such as herbicides, fungicides and antibiotics, can affect non-target organisms. First marketed as RoundUp™, glyphosate is the most widely used herbicide. In plants, glyphosate inhibits EPSPS, of the shikimate pathway, which is present in many organisms but lacking in mammals. The shikimate pathway produces chorismate which is the precursor to all the aromatic amino acids, para-aminobenzoic acid, and Coenzyme Q10. Crops engineered to be resistant to glyphosate contain a homolog of EPSPS that is not bound by glyphosate. Here, we show that S. cerevisiae has a wide-range of glyphosate resistance. Sequence comparison between the target proteins, i.e., the plant EPSPS and the yeast orthologous protein Aro1, predicted that yeast would be resistant to glyphosate. However, the growth variation seen in the subset of yeast tested was not due to polymorphisms within Aro1, instead, it was caused by genetic variation in an ABC multiple drug transporter, Pdr5, and an amino acid permease, Dip5. Using genetic variation as a probe into glyphosate response, we uncovered mechanisms that contribute to the transportation of glyphosate in and out of the cell. Taking advantage of the natural genetic variation within yeast and measuring growth under different conditions that would change the use of the shikimate pathway, we uncovered a general transport mechanism of glyphosate into eukaryotic cells.
Collapse
Affiliation(s)
- Xiaoqing Rong-Mullins
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Apoorva Ravishankar
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Kirsten A. McNeal
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Zachery R. Lonergan
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Audrey C. Biega
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - J. Philip Creamer
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Jennifer E. G. Gallagher
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
| |
Collapse
|
46
|
Smukowski Heil CS, DeSevo CG, Pai DA, Tucker CM, Hoang ML, Dunham MJ. Loss of Heterozygosity Drives Adaptation in Hybrid Yeast. Mol Biol Evol 2017; 34:1596-1612. [PMID: 28369610 PMCID: PMC5455960 DOI: 10.1093/molbev/msx098] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we examine hybrid genome evolution using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae × Saccharomyces uvarum and their parentals. We evolved these strains in nutrient-limited conditions for hundreds of generations and sequenced the resulting cultures identifying numerous point mutations, copy number changes, and loss of heterozygosity (LOH) events, including species-biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated LOH at the high-affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the LOH is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
Collapse
Affiliation(s)
| | - Christopher G DeSevo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Dave A Pai
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Cheryl M Tucker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Margaret L Hoang
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution, Baltimore, MD.,Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA
| |
Collapse
|
47
|
Rong-Mullins X, Winans MJ, Lee JB, Lonergan ZR, Pilolli VA, Weatherly LM, Carmenzind TW, Jiang L, Cumming JR, Oporto GS, Gallagher JEG. Proteomic and genetic analysis of the response of S. cerevisiae to soluble copper leads to improvement of the antimicrobial function of cellulosic copper nanoparticles. Metallomics 2017; 9:1304-1315. [PMID: 28869270 PMCID: PMC5741080 DOI: 10.1039/c7mt00147a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Copper (Cu) was used in antiquity to prevent waterborne and food diseases because, as a broad-spectrum antimicrobial agent, it generates reactive oxygen species, ROS. New technologies incorporating Cu into low-cost biodegradable nanomaterials built on cellulose, known as cellulosic cupric nanoparticles or c-CuNPs, present novel approaches to deliver Cu in a controlled manner to control microbial growth. We challenged strains of Saccharomyces cerevisiae with soluble Cu and c-CuNPs to evaluate the potential of c-CuNPs as antifungal agents. Cells exposed to c-CuNPs demonstrated greater sensitivity to Cu than cells exposed to soluble Cu, although Cu-resistant strains were more tolerant than Cu-sensitive strains of c-CuNP exposure. At the same level of growth inhibition, 157 μM c-CuNPs led to the same internal Cu levels as did 400 μM CuSO4, offering evidence for alternative mechanisms of toxicity, perhaps through β-arrestin dependent endocytosis, which was supported by flow cytometry and fluorescence microscopy of c-CuNPs distributed both on the cell surface and within the cytoplasm. Genes responsible for genetic variation in response to copper were mapped to the ZRT2 and the CUP1 loci. Through proteomic analyses, we found that the expression of other zinc (Zn) transporters increased in Cu-tolerant yeast compared to Cu-sensitive strains. Further, the addition of Zn at low levels increased the potency of c-CuNPs to inhibit even the most Cu-tolerant yeast. Through unbiased systems biological approaches, we identified Zn as a critical component of the yeast response to Cu and the addition of Zn increased the potency of the c-CuNPs.
Collapse
Affiliation(s)
| | - Matthew J Winans
- Department of Biology, West Virginia University, Morgantown, WV, USA.
| | - Justin B Lee
- Department of Biology, West Virginia University, Morgantown, WV, USA.
| | | | - Vincent A Pilolli
- Department of Biology, West Virginia University, Morgantown, WV, USA.
| | | | | | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford University, Stanford, CA, USA
| | | | - Gloria S Oporto
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | | |
Collapse
|
48
|
Liti G, Warringer J, Blomberg A. Budding Yeast Strains and Genotype-Phenotype Mapping. Cold Spring Harb Protoc 2017; 2017:pdb.top077735. [PMID: 28765302 DOI: 10.1101/pdb.top077735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A small number of well-studied laboratory strains of Saccharomyces cerevisiae, mostly derived from S288C, are used in yeast research. Although powerful, studies for understanding S288C do not always capture the phenotypic essence or the genetic complexity of S. cerevisiae biology. This is particularly problematic for multilocus phenotypes identified in laboratory strains because these loci have never been jointly exposed to natural selection and the corresponding phenotypes do not represent optimization for any particular purpose or environment. Isolation and sequencing of new natural yeast strains also reveal that the total sequence diversity of the S. cerevisiae global population is poorly sampled in common laboratory strains. Here we discuss methodologies required for using the natural genetic variation in yeast to complete a genotype-phenotype map.
Collapse
Affiliation(s)
- Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, 06107 Nice, France
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), 1432 Ås, Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden;
| |
Collapse
|
49
|
Abkallo HM, Martinelli A, Inoue M, Ramaprasad A, Xangsayarath P, Gitaka J, Tang J, Yahata K, Zoungrana A, Mitaka H, Acharjee A, Datta PP, Hunt P, Carter R, Kaneko O, Mustonen V, Illingworth CJR, Pain A, Culleton R. Rapid identification of genes controlling virulence and immunity in malaria parasites. PLoS Pathog 2017; 13:e1006447. [PMID: 28704525 PMCID: PMC5507557 DOI: 10.1371/journal.ppat.1006447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/05/2017] [Indexed: 11/20/2022] Open
Abstract
Identifying the genetic determinants of phenotypes that impact disease severity is of fundamental importance for the design of new interventions against malaria. Here we present a rapid genome-wide approach capable of identifying multiple genetic drivers of medically relevant phenotypes within malaria parasites via a single experiment at single gene or allele resolution. In a proof of principle study, we found that a previously undescribed single nucleotide polymorphism in the binding domain of the erythrocyte binding like protein (EBL) conferred a dramatic change in red blood cell invasion in mutant rodent malaria parasites Plasmodium yoelii. In the same experiment, we implicated merozoite surface protein 1 (MSP1) and other polymorphic proteins, as the major targets of strain-specific immunity. Using allelic replacement, we provide functional validation of the substitution in the EBL gene controlling the growth rate in the blood stages of the parasites. Developing a greater understanding of malaria genetics is a key step in combating the threat posed by the disease. Here we use a novel approach to study two important properties of the parasite; the rate at which parasites grow within a single host, and the means by which parasites are affected by the host immune system. Two malaria strains with different biological properties were crossed in mosquitoes to produce a hybrid population, which was then grown in naïve and vaccinated mice. Parasites with genes conveying increased growth or immune evasion are favoured under natural selection, leaving a signature on the genetic composition of the cross population. We describe a novel mathematical approach to interpret this signature, identifying selected genes within the parasite population. We discover new genetic variants conveying increased within-host growth and resistance to host immunity in a mouse malaria strain. Experimental validation highlights the ability of this rapid experimental process for generating insights into malaria biology.
Collapse
Affiliation(s)
- Hussein M. Abkallo
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Axel Martinelli
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Megumi Inoue
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Abhinay Ramaprasad
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Phonepadith Xangsayarath
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Protozooolgy, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Jesse Gitaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Protozooolgy, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Centre for Malaria Elimination, School of Medicine, Mount Kenya University, Thika, Kenya
| | - Jianxia Tang
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Jiangsu, China
| | - Kazuhide Yahata
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Protozooolgy, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Augustin Zoungrana
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hayato Mitaka
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Arita Acharjee
- Indian Institute of Science Education and Research Kolkata, Mohanpur - 741 246, West Bengal, India
| | - Partha P. Datta
- Indian Institute of Science Education and Research Kolkata, Mohanpur - 741 246, West Bengal, India
| | - Paul Hunt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard Carter
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Osamu Kaneko
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Protozooolgy, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Christopher J. R. Illingworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CJRI); (AP); (RC)
| | - Arnab Pain
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- * E-mail: (CJRI); (AP); (RC)
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail: (CJRI); (AP); (RC)
| |
Collapse
|
50
|
Mezzetti F, Fay JC, Giudici P, De Vero L. Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae. PLoS One 2017; 12:e0180814. [PMID: 28683117 PMCID: PMC5500363 DOI: 10.1371/journal.pone.0180814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/21/2017] [Indexed: 12/30/2022] Open
Abstract
Glutathione (GSH) production during wine fermentation is a desirable trait as it can limit must and wine oxidation and protect various aromatic compounds. UMCC 2581 is a Saccharomyces cerevisiae wine strain with enhanced GSH content at the end of wine fermentation. This strain was previously derived by selection for molybdate resistance following a sexual cycle of UMCC 855 using an evolution-based strategy. In this study, we examined genetic and gene expression changes associated with the derivation of UMCC 2581. For genetic analysis we sporulated the diploid UMCC 855 parental strain and found four phenotype classes of segregants related to molybdate resistance, demonstrating the presence of segregating variation from the parental strain. Using bulk segregant analysis we mapped molybdate traits to two loci. By sequencing both the parental and evolved strain genomes we identified candidate mutations within the two regions as well as an extra copy of chromosome 1 in UMCC 2581. Combining the mapped loci with gene expression profiles of the evolved and parental strains we identified a number of candidate genes with genetic and/or gene expression changes that could underlie molybdate resistance and increased GSH levels. Our results provide insight into the genetic basis of GSH production relevant to winemaking and highlight the value of enhancing wine strains using existing variation present in wine strains.
Collapse
Affiliation(s)
- Francesco Mezzetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Justin C. Fay
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St. Louis, Missouri, United States of America
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Luciana De Vero
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| |
Collapse
|