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Tan LR, Liu JJ, Deewan A, Lee JW, Xia PF, Rao CV, Jin YS, Wang SG. Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide. FEMS Yeast Res 2022; 22:6595876. [PMID: 35640892 DOI: 10.1093/femsyr/foac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/30/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO2 under both aerobic and anaerobic conditions. High solubility of CO2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO2 as compared to N2 and O2 limited conditions. While both CO2 and N2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO2. Interestingly, signal transduction was uniquely regulated under CO2 condition, where up-regulated genes (STE3, MSB2, WSC3, STE12 and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO2 sensing and CO2-induced metabolisms in yeast. Our study identifies CO2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.
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Affiliation(s)
- Lin-Rui Tan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jae Won Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Christopher V Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, P. R. China.,Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, P. R. China
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Clinger JA, Moreau DW, McLeod MJ, Holyoak T, Thorne RE. Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection. IUCRJ 2021; 8:784-792. [PMID: 34584739 PMCID: PMC8420759 DOI: 10.1107/s2052252521007053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/08/2021] [Indexed: 05/28/2023]
Abstract
Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy-kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.
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Affiliation(s)
- Jonathan A. Clinger
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - David W. Moreau
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
| | - Matthew J. McLeod
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert E. Thorne
- Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA
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