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Ziegelhoffer T, Verma AK, Delewski W, Schilke BA, Hill PM, Pitek M, Marszalek J, Craig EA. NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo. Nucleic Acids Res 2024; 52:3346-3357. [PMID: 38224454 PMCID: PMC11014269 DOI: 10.1093/nar/gkae005] [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: 11/14/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
The area surrounding the tunnel exit of the 60S ribosomal subunit is a hub for proteins involved in maturation and folding of emerging nascent polypeptide chains. How different factors vie for positioning at the tunnel exit in the complex cellular environment is not well understood. We used in vivo site-specific cross-linking to approach this question, focusing on two abundant factors-the nascent chain-associated complex (NAC) and the Hsp70 chaperone system that includes the J-domain protein co-chaperone Zuotin. We found that NAC and Zuotin can cross-link to each other at the ribosome, even when translation initiation is inhibited. Positions yielding NAC-Zuotin cross-links indicate that when both are present the central globular domain of NAC is modestly shifted from the mutually exclusive position observed in cryogenic electron microscopy analysis. Cross-linking results also suggest that, even in NAC's presence, Hsp70 can situate in a manner conducive for productive nascent chain interaction-with the peptide binding site at the tunnel exit and the J-domain of Zuotin appropriately positioned to drive stabilization of nascent chain binding. Overall, our results are consistent with the idea that, in vivo, the NAC and Hsp70 systems can productively position on the ribosome simultaneously.
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Affiliation(s)
- Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Amit K Verma
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Brenda A Schilke
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Paige M Hill
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Jaroslaw Marszalek
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80-307, Poland
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI 53726, USA
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2
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Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK, Hittinger CT. Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:20. [PMID: 38321504 PMCID: PMC10848558 DOI: 10.1186/s13068-024-02467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/28/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Cost-effective production of biofuels from lignocellulose requires the fermentation of D-xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD+ to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. RESULTS We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae. Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis. CONCLUSION Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.
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Affiliation(s)
- Katharina O Barros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Megan Mader
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Computer Science, San Jose State University, One Washington Square, San Jose, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Department, University of California Berkeley, Berkeley, CA, USA
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
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3
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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.
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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;
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4
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Liu L, Ansari RU, Vang-Smith M, Hittinger CT, Sato TK. A role for ion homeostasis in yeast ionic liquid tolerance. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000718. [PMID: 36820393 PMCID: PMC9938406 DOI: 10.17912/micropub.biology.000718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
The model yeast Saccharomyces cerevisiae is being developed as a biocatalyst for the conversion of renewable lignocellulosic biomass into biofuels. The ionic liquid 1-ethyl-3-methylimidazolium chloride (EMIMCl) solubilizes lignocellulose for deconstruction into fermentable sugars, but it inhibits yeast fermentation. EMIMCl tolerance is mediated by the efflux pump Sge1p and uncharacterized protein Ilt1p. Through genetic investigation, we found that disruption of ion homeostasis through mutations in genes encoding the Trk1p potassium transporter and its protein kinase regulators, Sat4p and Hal5p, causes EMIMCl sensitivity. These results suggest that maintenance of ion homeostasis is important for tolerance to EMIMCl.
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Affiliation(s)
- Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI
| | - Rahim U. Ansari
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
,
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI
,
J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI
,
Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
,
Correspondence to: Chris Todd Hittinger (
)
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
,
Correspondence to: Trey K. Sato (
)
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5
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Grewal J, Khare SK, Drewniak L, Pranaw K. Recent perspectives on microbial and ionic liquid interactions with implications for biorefineries. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 2022; 21:6650360. [PMID: 35883225 PMCID: PMC9508847 DOI: 10.1093/femsyr/foac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.
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Affiliation(s)
- Elena Vanacloig-Pedros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Kaitlin J Fisher
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Megan K M Young
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Trey K Sato
- Corresponding author: Trey K. Sato, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 4117 Wisconsin Energy Institute, 1552 University Ave, Madison, WI 53726. Tel: (608) 890-2546; E-mail:
| | - Audrey P Gasch
- Corresponding author: Audrey P. Gasch, Center for Genomic Science Innovation, University of Wisconsin-Madison, 3422 Genetics-Biotechnology Center, 425 Henry Mall, Madison, WI 53704, United States. Tel: (608)265-0859; E-mail:
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7
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Gene Coexpression Connectivity Predicts Gene Targets Underlying High Ionic-Liquid Tolerance in Yarrowia lipolytica. mSystems 2022; 7:e0034822. [PMID: 35862814 PMCID: PMC9426553 DOI: 10.1128/msystems.00348-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Microbial tolerance to organic solvents such as ionic liquids (ILs) is a robust phenotype beneficial for novel biotransformation. While most microbes become inhibited in 1% to 5% (vol/vol) IL (e.g., 1-ethyl-3-methylimidazolium acetate), we engineered a robust Yarrowia lipolytica strain (YlCW001) that tolerates a record high of 18% (vol/vol) IL via adaptive laboratory evolution. Yet, genotypes conferring high IL tolerance in YlCW001 remain to be discovered. In this study, we shed light on the underlying cellular processes that enable robust Y. lipolytica to thrive in inhibitory ILs. By using dynamic transcriptome sequencing (RNA-Seq) data, we introduced Gene Coexpression Connectivity (GeCCo) as a metric to discover genotypes conferring desirable phenotypes that might not be found by the conventional differential expression (DE) approaches. GeCCo selects genes based on their number of coexpressed genes in a subnetwork of upregulated genes by the target phenotype. We experimentally validated GeCCo by reverse engineering a high-IL-tolerance phenotype in wild-type Y. lipolytica. We found that gene targets selected by both DE and GeCCo exhibited the best statistical chance at increasing IL tolerance when individually overexpressed. Remarkably, the best combination of dual-overexpression genes was genes selected by GeCCo alone. This nonintuitive combination of genes, BRN1 and OYE2, is involved in guiding/regulating mitotic cell division, chromatin segregation/condensation, microtubule and cytoskeletal organization, and Golgi vesicle transport. IMPORTANCE Cellular robustness to cope with stressors is an important phenotype. Y. lipolytica is an industrial robust oleaginous yeast that has recently been discovered to tolerate record high concentrations of ILs, beneficial for novel biotransformation in organic solvents. However, genotypes that link to IL tolerance in Y. lipolytica are largely unknown. Due to the complex IL-tolerant phenotype, conventional gene discovery and validation based on differential gene expression approaches are time-consuming due to a large search space and might encounter a high false-discovery rate. Here, using the developed Gene Coexpression Connectivity (GeCCo) method, we identified and validated a subset of most promising gene targets conferring the IL-tolerant phenotypes and shed light on their potential mechanisms. We anticipate GeCCo being a useful method to discover the genotype-to-phenotype link.
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8
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Gambacorta FV, Wagner ER, Jacobson TB, Tremaine M, Muehlbauer LK, McGee MA, Baerwald JJ, Wrobel RL, Wolters JF, Place M, Dietrich JJ, Xie D, Serate J, Gajbhiye S, Liu L, Vang-Smith M, Coon JJ, Zhang Y, Gasch AP, Amador-Noguez D, Hittinger CT, Sato TK, Pfleger BF. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 2022; 7:738-749. [PMID: 35387233 PMCID: PMC8938195 DOI: 10.1016/j.synbio.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketol-acid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.
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Affiliation(s)
- Francesca V. Gambacorta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ellen R. Wagner
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin J. Baerwald
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Russell L. Wrobel
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Mike Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Dietrich
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose Serate
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Shabda Gajbhiye
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F. Pfleger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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9
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Schilke BA, Craig EA. Essentiality of Sis1, a J-domain protein Hsp70 cochaperone, can be overcome by Tti1, a specialized PIKK chaperone. Mol Biol Cell 2021; 33:br3. [PMID: 34935410 PMCID: PMC9250385 DOI: 10.1091/mbc.e21-10-0493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
J-domain protein cochaperones drive much of the functional diversity of Hsp70-based chaperone systems. Sis1 is the only essential J-domain protein of the cytosol/nucleus of Saccharomyces cerevisiae. Why it is required for cell growth is not understood, nor how critical its role is in regulation of heat shock transcription factor 1 (Hsf1). We report that single-residue substitutions in Tti1, a component of the heterotrimeric TTT complex, a specialized chaperone system for phosphatidylinositol 3-kinase-related kinase (PIKK) proteins, allow growth of cells lacking Sis1. Upon depletion of Sis1, cells become hypersensitive to rapamycin, a specific inhibitor of TORC1 kinase. In addition, levels of the three essential PIKKs (Mec1, Tra1, and Tor2), as well as Tor1, decrease upon Sis1 depletion. Overexpression of Tti1 allows growth without an increase in the other subunits of the TTT complex, Tel2 and Tti2, suggesting that it can function independent of the complex. Cells lacking Sis1, with viability supported by Tti1 suppressor, substantially up-regulate some, but not all, heat shock elements activated by Hsf1. Together, our results suggest that Sis1 is required as a cochaperone of Hsp70 for the folding/maintenance of PIKKs, making Sis1 an essential gene, and its requirement for Hsf1 regulation is more nuanced than generally appreciated.
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Affiliation(s)
- Brenda A Schilke
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin - Madison, Madison, Wisconsin 53706
| | - Elizabeth A Craig
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin - Madison, Madison, Wisconsin 53706
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10
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Lee SB, Tremaine M, Place M, Liu L, Pier A, Krause DJ, Xie D, Zhang Y, Landick R, Gasch AP, Hittinger CT, Sato TK. Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae. Metab Eng 2021; 68:119-130. [PMID: 34592433 DOI: 10.1016/j.ymben.2021.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/29/2022]
Abstract
Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.
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Affiliation(s)
- Sae-Byuk Lee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA; Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA; Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA
| | - Austin Pier
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA; Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA; Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA; Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA; Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI, USA.
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11
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Cho CW, Pham TPT, Zhao Y, Stolte S, Yun YS. Review of the toxic effects of ionic liquids. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147309. [PMID: 33975102 DOI: 10.1016/j.scitotenv.2021.147309] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 05/11/2023]
Abstract
Interest in ionic liquids (ILs), called green or designer solvents, has been increasing because of their excellent properties such as thermal stability and low vapor pressure; thus, they can replace harmful organic chemicals and help several industrial fields e.g., energy-storage materials production and biomaterial pretreatment. However, the claim that ILs are green solvents should be carefully considered from an environmental perspective. ILs, given their minimal vapor pressure, may not directly cause atmospheric pollution. However, they have the potential to cause adverse effects if leaked into the environment, for instance if they are spilled due to human mistakes or technical errors. To estimate the risks of ILs, numerous ILs have had their toxicity assessed toward several micro- and macro-organisms over the past few decades. Since the toxic effects of ILs depend on the method of estimating toxicity, it is necessary to briefly summarize and comprehensively discuss the biological effects of ILs according to their structure and toxicity testing levels. This can help simplify our understanding of the toxicity of ILs. Therefore, in this review, we discuss the key findings of toxicological information of ILs, collect some toxicity data of ILs to different species, and explain the influence of IL structure on their toxic properties. In the discussion, we estimated two different sensitivity values of toxicity testing levels depending on the experiment condition, which are theoretical magnitudes of the inherent sensitivity of toxicity testing levels in various conditions and their changes in biological response according to the change in IL structure. Finally, some perspectives, future research directions, and limitations to toxicological research of ILs, presented so far, are discussed.
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Affiliation(s)
- Chul-Woong Cho
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea.
| | - Thi Phuong Thuy Pham
- Faculty of Biotechnology, HoChiMihn University of Food Industry, Ho Chi Minh City, Viet Nam
| | - Yufeng Zhao
- College of Resource and Environmental Science, South-Central University for Nationalities, Wuhan 430074, Hubei Province, China
| | - Stefan Stolte
- Technische Universität Dresden, Faculty of Environmental Sciences, Department of Hydrosciences, Institute of Water Chemistry, Bergstraße 66, 01062 Dresden, Germany
| | - Yeoung-Sang Yun
- School of Chemical Engineering, Chonbuk National University, 567 Beakje-dearo, Deokjin-gu, Jeonju, Jeonbuk 561-756, South Korea.
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12
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Stoneman HR, Wrobel RL, Place M, Graham M, Krause DJ, De Chiara M, Liti G, Schacherer J, Landick R, Gasch AP, Sato TK, Hittinger CT. CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. G3 (BETHESDA, MD.) 2020; 10:4287-4294. [PMID: 32963084 PMCID: PMC7642938 DOI: 10.1534/g3.120.401498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023]
Abstract
CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of guide RNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.
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Affiliation(s)
- Hayley R Stoneman
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
| | - Russell L Wrobel
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
| | - Michael Graham
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Audrey P Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, WI 53726
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison WI 53726
- Wisconsin Energy Institute, University of Wisconsin-Madison, WI 53726
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726
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13
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Ahmadi F, Quach ABV, Shih SCC. Is microfluidics the "assembly line" for CRISPR-Cas9 gene-editing? BIOMICROFLUIDICS 2020; 14:061301. [PMID: 33262863 PMCID: PMC7688342 DOI: 10.1063/5.0029846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Acclaimed as one of the biggest scientific breakthroughs, the technology of CRISPR has brought significant improvement in the biotechnological spectrum-from editing genetic defects in diseases for gene therapy to modifying organisms for the production of biofuels. Since its inception, the CRISPR-Cas9 system has become easier and more versatile to use. Many variants have been found, giving the CRISPR toolkit a great range that includes the activation and repression of genes aside from the previously known knockout and knockin of genes. Here, in this Perspective, we describe efforts on automating the gene-editing workflow, with particular emphasis given on the use of microfluidic technology. We discuss how automation can address the limitations of gene-editing and how the marriage between microfluidics and gene-editing will expand the application space of CRISPR.
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Affiliation(s)
| | | | - Steve C. C. Shih
- Author to whom correspondence should be addressed:. Tel.: +1-(514) 848-2424 x7579
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14
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Fletcher E, Baetz K. Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:539902. [PMID: 33154962 PMCID: PMC7591714 DOI: 10.3389/fbioe.2020.539902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.
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Affiliation(s)
- Eugene Fletcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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15
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Sitepu I, Enriquez L, Nguyen V, Fry R, Simmons B, Singer S, Simmons C, Boundy-Mills KL. Ionic Liquid Tolerance of Yeasts in Family Dipodascaceae and Genus Wickerhamomyces. Appl Biochem Biotechnol 2020; 191:1580-1593. [PMID: 32185613 DOI: 10.1007/s12010-020-03293-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 11/26/2022]
Abstract
In previous studies of ionic liquid (IL) tolerance of numerous species of ascomycetous yeasts, two strains of Wickerhamomyces ciferrii and Galactomyces candidus had unusually high tolerance in media containing up to 5% (w/v) of the 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]). The study aimed at investigating whether additional strains of these species, and additional species in the Dipodascaceae family, also possess IL tolerance, and to compare sensitivity to the acetate and chloride versions of the ionic liquid. Fifty five yeast strains in the family Dipodascaceae, which encompasses genera Galactomyces, Geotrichum, and Dipodascus, and seven yeast strains of species Wickerhamomyces ciferrii were tested for ability to grow in laboratory medium containing no IL, 242 mM [C2C1Im][OAc], or 242 mM [C2C1Im]Cl, and in IL-pretreated switchgrass hydrolysate. Many yeasts exhibited tolerance of one or both ILs, with higher tolerance of the chloride anion than of the acetate anion. Different strains of the same species exhibited varying degrees of IL tolerance. Galactomyces candidus, UCDFSTs 52-260, and 50-64, had exceptionally robust growth in [C2C1Im][OAc], and also grew well in the switchgrass hydrolysate. Identification of IL tolerant and IL resistant yeast strains will facilitate studies of the mechanism of IL tolerance, which could include superior efflux, metabolism or exclusion.
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Affiliation(s)
- Irnayuli Sitepu
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Lauren Enriquez
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Valerie Nguyen
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Russell Fry
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Blake Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Steve Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Christopher Simmons
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Kyria L Boundy-Mills
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA.
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Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
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Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica. ACTA ACUST UNITED AC 2019; 46:1715-1724. [DOI: 10.1007/s10295-019-02228-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/10/2019] [Indexed: 01/25/2023]
Abstract
Abstract
Ionic liquids show promise for deconstruction of lignocellulosic biomass prior to fermentation. Yet, imidazolium ionic liquids (IILs) can be toxic to microbes even at concentrations present after recovery. Here, we show that dominant overexpression of an Ilt1p homolog (encoded by YlILT1/YALI0C04884) from the IIL-tolerant yeast Yarrowia lipolytica confers an improvement in 1-ethyl-3-methylimidazolium acetate tolerance in Saccharomyces cerevisiae compared to the endogenous Ilt1p (ScILT1/YDR090C). We subsequently enhance tolerance in S. cerevisiae through directed evolution of YlILT1 using growth-based selection, leading to identification of mutants that grow in up to 3.5% v/v ionic liquid. Lastly, we demonstrate that strains expressing YlILT1 variants demonstrate improved growth rate and ethanol production in the presence of residual IIL. This shows that dominant overexpression of a heterologous protein (wild type or evolved) from an IIL-tolerant yeast can increase tolerance in S. cerevisiae at concentrations relevant to bioethanol production from IIL-treated biomass.
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18
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Walker C, Ryu S, Trinh CT. Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols. Metab Eng 2019; 54:83-95. [DOI: 10.1016/j.ymben.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/24/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
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Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity. J Bacteriol 2019; 201:JB.00069-19. [PMID: 30988034 DOI: 10.1128/jb.00069-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 11/20/2022] Open
Abstract
Plant cell walls contain a renewable, nearly limitless supply of sugar that could be used to support microbial production of commodity chemicals and biofuels. Imidazolium ionic liquid (IIL) solvents are among the best reagents for gaining access to the sugars in this otherwise recalcitrant biomass. However, the sugars from IIL-treated biomass are inevitably contaminated with residual IILs that inhibit growth in bacteria and yeast, blocking biochemical production by these organisms. IIL toxicity is, therefore, a critical roadblock in many industrial biosynthetic pathways. Although several IIL-tolerant (IILT) bacterial and yeast isolates have been identified in nature, few genetic mechanisms have been identified. In this study, we identified two IILT Bacillus isolates as well as a spontaneous IILT Escherichia coli lab strain that are tolerant to high levels of two widely used IILs. We demonstrate that all three IILT strains contain one or more pumps of the small multidrug resistance (SMR) family, and two of these strains contain mutations that affect an adjacent regulatory guanidine riboswitch. Furthermore, we show that the regulation of E. coli sugE by the guanidine II riboswitch can be exploited to promote IIL tolerance by the simple addition of guanidine to the medium. Our results demonstrate the critical role that transporter genes play in IIL tolerance in their native bacterial hosts. The study presented here is another step in engineering IIL tolerance into industrial strains toward overcoming this key gap in biofuels and industrial biochemical production processes.IMPORTANCE This study identifies bacteria that are tolerant to ionic liquid solvents used in the production of biofuels and industrial biochemicals. For industrial microbiology, it is essential to find less-harmful reagents and microbes that are resistant to their cytotoxic effects. We identified a family of small multidrug resistance efflux transporters, which are responsible for the tolerance of these strains. We also found that this resistance can be caused by mutations in the sequences of guanidine-specific riboswitches that regulate these efflux pumps. Extending this knowledge, we demonstrated that guanidine itself can promote ionic liquid tolerance. Our findings will inform genetic engineering strategies that improve conversion of cellulosic sugars into biofuels and biochemicals in processes where low concentrations of ionic liquids surpass bacterial tolerance.
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Physiological Genomics of Multistress Resistance in the Yeast Cell Model and Factory: Focus on MDR/MXR Transporters. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:1-35. [PMID: 30911887 DOI: 10.1007/978-3-030-13035-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The contemporary approach of physiological genomics is vital in providing the indispensable holistic understanding of the complexity of the molecular targets, signalling pathways and molecular mechanisms underlying the responses and tolerance to stress, a topic of paramount importance in biology and biotechnology. This chapter focuses on the toxicity and tolerance to relevant stresses in the cell factory and eukaryotic model yeast Saccharomyces cerevisiae. Emphasis is given to the function and regulation of multidrug/multixenobiotic resistance (MDR/MXR) transporters. Although these transporters have been considered drug/xenobiotic efflux pumps, the exact mechanism of their involvement in multistress resistance is still open to debate, as highlighted in this chapter. Given the conservation of transport mechanisms from S. cerevisiae to less accessible eukaryotes such as plants, this chapter also provides a proof of concept that validates the relevance of the exploitation of the experimental yeast model to uncover the function of novel MDR/MXR transporters in the plant model Arabidopsis thaliana. This knowledge can be explored for guiding the rational design of more robust yeast strains with improved performance for industrial biotechnology, for overcoming and controlling the deleterious activities of spoiling yeasts in the food industry, for developing efficient strategies to improve crop productivity in agricultural biotechnology.
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Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez A, Gladden J, Simmons BA, Petzold CJ, Mukhopadhyay A. Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:41. [PMID: 30858878 PMCID: PMC6391826 DOI: 10.1186/s13068-019-1381-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/18/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Many microbes used for the rapid discovery and development of metabolic pathways have sensitivities to final products and process reagents. Isopentenol (3-methyl-3-buten-1-ol), a biogasoline candidate, has an established heterologous gene pathway but is toxic to several microbial hosts. Reagents used in the pretreatment of plant biomass, such as ionic liquids, also inhibit growth of many host strains. We explored the use of Corynebacterium glutamicum as an alternative host to address these constraints. RESULTS We found C. glutamicum ATCC 13032 to be tolerant to both the final product, isopentenol, as well to three classes of ionic liquids. A heterologous mevalonate-based isopentenol pathway was engineered in C. glutamicum. Targeted proteomics for the heterologous pathway proteins indicated that the 3-hydroxy-3-methylglutaryl-coenzyme A reductase protein, HmgR, is a potential rate-limiting enzyme in this synthetic pathway. Isopentenol titers were improved from undetectable to 1.25 g/L by combining three approaches: media optimization; substitution of an NADH-dependent HmgR homolog from Silicibacter pomeroyi; and development of a C. glutamicum ∆poxB ∆ldhA host chassis. CONCLUSIONS We describe the successful expression of a heterologous mevalonate-based pathway in the Gram-positive industrial microorganism, C. glutamicum, for the production of the biogasoline candidate, isopentenol. We identified critical genetic factors to harness the isopentenol pathway in C. glutamicum. Further media and cultivation optimization enabled isopentenol production from sorghum biomass hydrolysates.
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Affiliation(s)
- Yusuke Sasaki
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Thomas Eng
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Robin A. Herbert
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jessica Trinh
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Alberto Rodriguez
- Joint BioEnergy Institute, Emeryville, CA USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94550 USA
| | - John Gladden
- Joint BioEnergy Institute, Emeryville, CA USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94550 USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A. Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC. Microb Cell Fact 2018; 17:159. [PMID: 30296937 PMCID: PMC6174563 DOI: 10.1186/s12934-018-1006-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Microbial production of chemicals from renewable carbon sources enables a sustainable route to many bioproducts. Sugar streams, such as those derived from biomass pretreated with ionic liquids (IL), provide efficiently derived and cost-competitive starting materials. A limitation to this approach is that residual ILs in the pretreated sugar source can be inhibitory to microbial growth and impair expression of the desired biosynthetic pathway. RESULTS We utilized laboratory evolution to select Escherichia coli strains capable of robust growth in the presence of the IL, 1-ethyl-3-methyl-imidizolium acetate ([EMIM]OAc). Whole genome sequencing of the evolved strain identified a point mutation in an essential gene, cydC, which confers tolerance to two different classes of ILs at concentrations that are otherwise growth inhibitory. This mutation, cydC-D86G, fully restores the specific production of the bio-jet fuel candidate D-limonene, as well as the biogasoline and platform chemical isopentenol, in growth medium containing ILs. Similar amino acids at this position in cydC, such as cydC-D86V, also confer tolerance to [EMIM]OAc. We show that this [EMIM]OAc tolerance phenotype of cydC-D86G strains is independent of its wild-type function in activating the cytochrome bd-I respiratory complex. Using shotgun proteomics, we characterized the underlying differential cellular responses altered in this mutant. While wild-type E. coli cannot produce detectable amounts of either product in the presence of ILs at levels expected to be residual in sugars from pretreated biomass, the engineered cydC-D86G strains produce over 200 mg/L D-limonene and 350 mg/L isopentenol, which are among the highest reported titers in the presence of [EMIM]OAc. CONCLUSIONS The optimized strains in this study produce high titers of two candidate biofuels and bioproducts under IL stress. Both sets of production strains surpass production titers from other IL tolerant mutants in the literature. Our application of laboratory evolution identified a gain of function mutation in an essential gene, which is unusual in comparison to other published IL tolerant mutants.
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Affiliation(s)
- Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Philipp Demling
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Robin A. Herbert
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Veronica Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Joel Martin
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, 94598 USA
| | - Edward E. K. Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, 52074 Aachen, Germany
| | - Christopher J. Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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