1
|
Liang J, Xiao K, Wang X, Hou T, Zeng C, Gao X, Wang B, Zhong C. Revisiting Solar Energy Flow in Nanomaterial-Microorganism Hybrid Systems. Chem Rev 2024. [PMID: 38900019 DOI: 10.1021/acs.chemrev.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Nanomaterial-microorganism hybrid systems (NMHSs), integrating semiconductor nanomaterials with microorganisms, present a promising platform for broadband solar energy harvesting, high-efficiency carbon reduction, and sustainable chemical production. While studies underscore its potential in diverse solar-to-chemical energy conversions, prevailing NMHSs grapple with suboptimal energy conversion efficiency. Such limitations stem predominantly from an insufficient systematic exploration of the mechanisms dictating solar energy flow. This review provides a systematic overview of the notable advancements in this nascent field, with a particular focus on the discussion of three pivotal steps of energy flow: solar energy capture, cross-membrane energy transport, and energy conversion into chemicals. While key challenges faced in each stage are independently identified and discussed, viable solutions are correspondingly postulated. In view of the interplay of the three steps in affecting the overall efficiency of solar-to-chemical energy conversion, subsequent discussions thus take an integrative and systematic viewpoint to comprehend, analyze and improve the solar energy flow in the current NMHSs of different configurations, and highlighting the contemporary techniques that can be employed to investigate various aspects of energy flow within NMHSs. Finally, a concluding section summarizes opportunities for future research, providing a roadmap for the continued development and optimization of NMHSs.
Collapse
Affiliation(s)
- Jun Liang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kemeng Xiao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianfeng Hou
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Cuiping Zeng
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiang Gao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bo Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
2
|
Zhang S, Song L, Zheng R, Zhang F, Wang Q, Mao X, Fan JX, Liu B, Zhao YD, Chen W. Quantification of MicroRNA in a Single Living Cell via Ionic Current Rectification-Based Nanopore for Triple Negative Breast Cancer Diagnosis. Anal Chem 2024; 96:7411-7420. [PMID: 38652893 DOI: 10.1021/acs.analchem.3c05027] [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: 04/25/2024]
Abstract
Accurate analysis of microRNAs (miRNAs) at the single-cell level is extremely important for deeply understanding their multiple and intricate biological functions. Despite some advancements in analyzing single-cell miRNAs, challenges such as intracellular interferences and insufficient detection limits still remain. In this work, an ultrasensitive nanopore sensor for quantitative single-cell miRNA-155 detection is constructed based on ionic current rectification (ICR) coupled with enzyme-free catalytic hairpin assembly (CHA). Benefiting from the enzyme-free CHA amplification strategy, the detection limit of the nanopore sensor for miRNA-155 reaches 10 fM and the nanopore sensor is more adaptable to complex intracellular environments. With the nanopore sensor, the concentration of miRNA-155 in living single cells is quantified to realize the early diagnosis of triple-negative breast cancer (TNBC). Furthermore, the nanopore sensor can be applied in screening anticancer drugs by tracking the expression level of miRNA-155. This work provides an adaptive and universal method for quantitatively analyzing intracellular miRNAs, which will greatly improve our understanding of cell heterogeneity and provide a more reliable scientific basis for exploring major diseases at the single-cell level.
Collapse
Affiliation(s)
- Shujie Zhang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Laibo Song
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Ruina Zheng
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Fang Zhang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Qimeng Wang
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Xiaosui Mao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Jin-Xuan Fan
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Bo Liu
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Yuan-Di Zhao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
- Key Laboratory of Biomedical Photonics (HUST), Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Wei Chen
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| |
Collapse
|
3
|
Yu Y, Lu L, Xu J, Wang L, Guo S. Microbial lipid synthesis based on visible light-driven oxygen doped-graphitic carbon nitride /oleaginous yeast hybrid system. BIORESOURCE TECHNOLOGY 2024; 397:130476. [PMID: 38387842 DOI: 10.1016/j.biortech.2024.130476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
The use of solar energy and heterotrophic microbes to synthesize microbial lipids is a promising strategy to solve energy crisis and reduce CO2 emissions. In this study, a photocatalyst, oxygen-doped graphitic carbon nitride (O-g-C3N4), was synthesized and combined with an oleaginous yeast strain, Cutaneotrichosporon dermatis ZZ-46, to construct a photocatalyst-microbe hybrid (PMH) system. Under illumination, the lipid yield of the PMH system reached 1.61 g/L after 96 h (87 % higher than that of control). NADPH/NADP+ ratio of ZZ-46 cells in the PMH system increased. Metabolomics results revealed that glutathione generation was increased, and the fatty acid decomposition pathway in ZZ-46 cells was inhibited in the PMH system. This study provides a new approach for the synthesis of microbial lipids based on solar energy and heterotrophic microbes.
Collapse
Affiliation(s)
- Yadong Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, Jiangsu, PR China.
| | - Lingxia Lu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, Jiangsu, PR China
| | - Jie Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, Jiangsu, PR China
| | - Laiyou Wang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang 473004, PR China
| | - Shuxian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang 473004, PR China
| |
Collapse
|
4
|
Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [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: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
Collapse
Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| |
Collapse
|
5
|
Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
Collapse
Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| |
Collapse
|
6
|
Ramírez Martínez C, Gómez-Pérez LS, Ordaz A, Torres-Huerta AL, Antonio-Perez A. Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications. Int J Mol Sci 2023; 24:14741. [PMID: 37834188 PMCID: PMC10572898 DOI: 10.3390/ijms241914741] [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: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.
Collapse
Affiliation(s)
| | | | | | | | - Aurora Antonio-Perez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Ciudad López Mateos, Atizapán de Zaragoza 52926, Estado de México, Mexico; (C.R.M.); (L.S.G.-P.); (A.O.); (A.L.T.-H.)
| |
Collapse
|
7
|
Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metab Eng 2023; 79:97-107. [PMID: 37422133 DOI: 10.1016/j.ymben.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Dynamic metabolic engineering is a strategy to switch key metabolic pathways in microbial cell factories from biomass generation to accumulation of target products. Here, we demonstrate that optogenetic intervention in the cell cycle of budding yeast can be used to increase production of valuable chemicals, such as the terpenoid β-carotene or the nucleoside analog cordycepin. We achieved optogenetic cell-cycle arrest in the G2/M phase by controlling activity of the ubiquitin-proteasome system hub Cdc48. To analyze the metabolic capacities in the cell cycle arrested yeast strain, we studied their proteomes by timsTOF mass spectrometry. This revealed widespread, but highly distinct abundance changes of metabolic key enzymes. Integration of the proteomics data in protein-constrained metabolic models demonstrated modulation of fluxes directly associated with terpenoid production as well as metabolic subsystems involved in protein biosynthesis, cell wall synthesis, and cofactor biosynthesis. These results demonstrate that optogenetically triggered cell cycle intervention is an option to increase the yields of compounds synthesized in a cellular factory by reallocation of metabolic resources.
Collapse
Affiliation(s)
- Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Johannes Scheffer
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Zahra Razaghi-Moghadam
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Bastian Pook
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Hagen Nußhär
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Sophia Hasenjäger
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany.
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35032, Marburg, Germany; School of Science and Technology, University Siegen, 57076, Siegen, Germany.
| |
Collapse
|
8
|
Harmer ZP, McClean MN. High-Throughput Optogenetics Experiments in Yeast Using the Automated Platform Lustro. J Vis Exp 2023:10.3791/65686. [PMID: 37590537 PMCID: PMC11085938 DOI: 10.3791/65686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
Optogenetics offers precise control over cellular behavior by utilizing genetically encoded light-sensitive proteins. However, optimizing these systems to achieve the desired functionality often requires multiple design-build-test cycles, which can be time-consuming and labor-intensive. To address this challenge, we have developed Lustro, a platform that combines light stimulation with laboratory automation, enabling efficient high-throughput screening and characterization of optogenetic systems. Lustro utilizes an automation workstation equipped with an illumination device, a shaking device, and a plate reader. By employing a robotic arm, Lustro automates the movement of a microwell plate between these devices, allowing for the stimulation of optogenetic strains and the measurement of their response. This protocol provides a step-by-step guide on using Lustro to characterize optogenetic systems for gene expression control in the budding yeast Saccharomyces cerevisiae. The protocol covers the setup of Lustro's components, including the integration of the illumination device with the automation workstation. It also provides detailed instructions for programming the illumination device, plate reader, and robot, ensuring smooth operation and data acquisition throughout the experimental process.
Collapse
Affiliation(s)
- Zachary P Harmer
- Department of Biomedical Engineering, University of Wisconsin-Madison
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health;
| |
Collapse
|
9
|
Tang Y, Tang Y, Ren D, Wang C, Qu Y, Huang L, Xue Y, Jiang Y, Wang Y, Xu L, Zhu P. White Collar 1 Modulates Oxidative Sensitivity and Virulence by Regulating the HOG1 Pathway in Fusarium asiaticum. Microbiol Spectr 2023; 11:e0520622. [PMID: 37195224 PMCID: PMC10269464 DOI: 10.1128/spectrum.05206-22] [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: 12/18/2022] [Accepted: 04/21/2023] [Indexed: 05/18/2023] Open
Abstract
Fusarium asiaticum is an epidemiologically important pathogen of cereal crops in east Asia, accounting for both yield losses and mycotoxin contamination problems in food and feed products. FaWC1, a component of the blue-light receptor White Collar complex (WCC), relies on its transcriptional regulatory zinc finger domain rather than the light-oxygen-voltage domain to regulate pathogenicity of F. asiaticum, although the downstream mechanisms remain obscure. In this study, the pathogenicity factors regulated by FaWC1 were analyzed. It was found that loss of FaWC1 resulted in higher sensitivity to reactive oxygen species (ROS) than in the wild type, while exogenous application of the ROS quencher ascorbic acid restored the pathogenicity of the ΔFawc1 strain to the level of the wild type, indicating that the reduced pathogenicity of the ΔFawc1 strain is due to a defect in ROS tolerance. Moreover, the expression levels of the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway genes and their downstream genes encoding ROS scavenging enzymes were downregulated in the ΔFawc1 mutant. Upon ROS stimulation, the FaHOG1-green fluorescent protein (GFP)-expressing signal driven by the native promoter was inducible in the wild type but negligible in the ΔFawc1 strain. Overexpressing Fahog1 in the ΔFawc1 strain could recover the ROS tolerance and pathogenicity of the ΔFawc1 mutant, but it remained defective in light responsiveness. In summary, this study dissected the roles of the blue-light receptor component FaWC1 in regulating expression levels of the intracellular HOG-MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. IMPORTANCE The well-conserved fungal blue-light receptor White Collar complex (WCC) is known to regulate virulence of several pathogenic species for either plant or human hosts, but how WCC determines fungal pathogenicity remains largely unknown. The WCC component FaWC1 in the cereal pathogen Fusarium asiaticum was previously found to be required for full virulence. The present study dissected the roles of FaWC1 in regulating the intracellular HOG MAPK signaling pathway to affect ROS sensitivity and pathogenicity in F. asiaticum. This work thus extends knowledge of the association between fungal light receptors and the intracellular stress signaling pathway to regulate oxidative stress tolerance and pathogenicity in an epidemiologically important fungal pathogen of cereal crops.
Collapse
Affiliation(s)
- Ying Tang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yan Tang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Dandan Ren
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Congcong Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yao Qu
- School of Life Sciences, East China Normal University, Shanghai, China
- No. 2 High School of East China Normal University, Shanghai, China
| | - Li Huang
- School of Life Sciences, East China Normal University, Shanghai, China
- Suzhou Industrial Park Xingyang School, Suzhou, China
| | - Yongjun Xue
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yina Jiang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Yiwen Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Ling Xu
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Pinkuan Zhu
- School of Life Sciences, East China Normal University, Shanghai, China
| |
Collapse
|
10
|
Camponeschi I, Montanari A, Mazzoni C, Bianchi MM. Light Stress in Yeasts: Signaling and Responses in Creatures of the Night. Int J Mol Sci 2023; 24:ijms24086929. [PMID: 37108091 PMCID: PMC10139380 DOI: 10.3390/ijms24086929] [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: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Living organisms on the surface biosphere are periodically yet consistently exposed to light. The adaptive or protective evolution caused by this source of energy has led to the biological systems present in a large variety of organisms, including fungi. Among fungi, yeasts have developed essential protective responses against the deleterious effects of light. Stress generated by light exposure is propagated through the synthesis of hydrogen peroxide and mediated by regulatory factors that are also involved in the response to other stressors. These have included Msn2/4, Crz1, Yap1, and Mga2, thus suggesting that light stress is a common factor in the yeast environmental response.
Collapse
Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michele Maria Bianchi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
11
|
Li W, Wang Z, Cao J, Dong Y, Chen Y. Perfecting the Life Clock: The Journey from PTO to TTFL. Int J Mol Sci 2023; 24:ijms24032402. [PMID: 36768725 PMCID: PMC9916482 DOI: 10.3390/ijms24032402] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The ubiquity of biological rhythms in life implies that it results from selection in the evolutionary process. The origin of the biological clock has two possible hypotheses: the selective pressure hypothesis of the oxidative stress cycle and the light evasion hypothesis. Moreover, the biological clock gives life higher adaptability. Two biological clock mechanisms have been discovered: the negative feedback loop of transcription-translation (TTFL) and the post-translational oscillation mechanism (PTO). The TTFL mechanism is the most classic and relatively conservative circadian clock oscillation mechanism, commonly found in eukaryotes. We have introduced the TTFL mechanism of the classical model organisms. However, the biological clock of prokaryotes is based on the PTO mechanism. The Peroxiredoxin (PRX or PRDX) protein-based PTO mechanism circadian clock widely existing in eukaryotic and prokaryotic life is considered a more conservative oscillation mechanism. The coexistence of the PTO and TTFL mechanisms in eukaryotes prompted us to explain the relationship between the two. Finally, we speculated that there might be a driving force for the evolution of the biological clock. The biological clock may have an evolutionary trend from the PTO mechanism to the TTFL mechanism, resulting from the evolution of organisms adapting to the environment.
Collapse
Affiliation(s)
- Weitian Li
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Zixu Wang
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Jing Cao
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Yulan Dong
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Yaoxing Chen
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
- Department of Nutrition and Health, China Agricultural University, Haidian, Beijing 100193, China
- Correspondence: ; Tel.: +86-10-62733778
| |
Collapse
|
12
|
Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
|
13
|
Goines S, Dick JE. Investigating the cytotoxic redox mechanism of PFOS within Hep G2 by hyperspectral-assisted scanning electrochemical microscopy. Analyst 2022; 147:4356-4364. [PMID: 36043461 PMCID: PMC10308698 DOI: 10.1039/d2an00904h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Perfluorooctane sulfonate (PFOS) is one of the most lethal per- and poly-fluoroalkyl substances (PFAS). Generally, exposure effects are studied through case-controlled studies, cohort studies, or cell assays. Unfortunately, most studies involving two-dimensional cell cultures require cell lysis or fixation. For in vitro studies, fluorescence microscopy has been useful, but methods to simultaneously discern phototoxic effects during an experiment are limited. Here, we use hepatocarcinoma (Hep G2) cells to examine the redox mechanism of PFOS cytotoxicity in vitro, while using hyperspectral-assisted scanning electrochemical microscopy (SECM) to differentiate between PFOS and redox mediator induced stress. Specifically, we correlate an increase in the electrochemical response of ferrocenemethanol oxidation with an increase in intracellular reactive oxygen species. Corresponding hyperspectral images of redox indicative-fluorophores implicate superoxide in the cytotoxic redox mechanism.
Collapse
Affiliation(s)
- Sondrica Goines
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey E Dick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
14
|
Mahrou B, Pirhanov A, Alijanvand MH, Cho YK, Shin YJ. Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae. Biosystems 2022; 219:104717. [PMID: 35690291 DOI: 10.1016/j.biosystems.2022.104717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/02/2022]
Abstract
Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 min-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.
Collapse
Affiliation(s)
- Bahareh Mahrou
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Electrical Engineering Department, University of Connecticut, Storrs, CT, 06069, USA.
| | - Azady Pirhanov
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Moluk Hadi Alijanvand
- Department of Epidemiology and Biostatistics, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yong Ku Cho
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Chemical and Biomolecular Engineering Department, University of Connecticut, Storrs, CT, 06269, USA.
| | - Yong-Jun Shin
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| |
Collapse
|
15
|
Abstract
Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb3-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.
Collapse
|
16
|
Goines S, Deng M, Glasscott MW, Leung JWC, Dick JE. Enhancing scanning electrochemical microscopy's potential to probe dynamic co-culture systems via hyperspectral assisted-imaging. Analyst 2022; 147:2396-2404. [PMID: 35579029 PMCID: PMC9287841 DOI: 10.1039/d2an00319h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Precise determination of boundaries in co-culture systems is difficult to achieve with scanning electrochemical microscopy alone. Thus, biological scanning electrochemical microscope platforms generally consist of a scanning electrochemical microscope positioner mounted on the stage of an inverted microscope for correlated electrochemical and optical imaging. Use of a fluorescence microscope allows for site-specific fluorescence labeling to obtain more clearly resolved spatial and electrochemical data. Here, we construct a unique hyperspectral assisted-biological scanning electrochemical microscope platform to widen the scope of biological imaging. Specifically, we incorporate a variable fluorescence bandpass source into a biological scanning electrochemical microscope platform for simultaneous optical, spectral, and electrochemical imaging. Not only does this platform serve as a cost-effective alternative to white light laser imaging, but additionally it provides multi-functional analysis of biological samples. Here, we demonstrate the efficacy of our platform to discern the electrochemical contribution of site-specific cells by optically and spectroscopically resolving boundaries as well as cell types within a complex biological system.
Collapse
Affiliation(s)
- Sondrica Goines
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Mingchu Deng
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Matthew W Glasscott
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jeffrey E Dick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
17
|
Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
Collapse
Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| |
Collapse
|
18
|
Flores-Cotera LB, Chávez-Cabrera C, Martínez-Cárdenas A, Sánchez S, García-Flores OU. Deciphering the mechanism by which the yeast Phaffia rhodozyma responds adaptively to environmental, nutritional, and genetic cues. J Ind Microbiol Biotechnol 2021; 48:kuab048. [PMID: 34302341 PMCID: PMC8788774 DOI: 10.1093/jimb/kuab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Phaffia rhodozyma is a basidiomycetous yeast that synthesizes astaxanthin (ASX), which is a powerful and highly valuable antioxidant carotenoid pigment. P. rhodozyma cells accrue ASX and gain an intense red-pink coloration when faced with stressful conditions such as nutrient limitations (e.g., nitrogen or copper), the presence of toxic substances (e.g., antimycin A), or are affected by mutations in the genes that are involved in nitrogen metabolism or respiration. Since cellular accrual of ASX occurs under a wide variety of conditions, this yeast represents a valuable model for studying the growth conditions that entail oxidative stress for yeast cells. Recently, we proposed that ASX synthesis can be largely induced by conditions that lead to reduction-oxidation (redox) imbalances, particularly the state of the NADH/NAD+ couple together with an oxidative environment. In this work, we review the multiple known conditions that elicit ASX synthesis expanding on the data that we formerly examined. When considered alongside the Mitchell's chemiosmotic hypothesis, the study served to rationalize the induction of ASX synthesis and other adaptive cellular processes under a much broader set of conditions. Our aim was to propose an underlying mechanism that explains how a broad range of divergent conditions converge to induce ASX synthesis in P. rhodozyma. The mechanism that links the induction of ASX synthesis with the occurrence of NADH/NAD+ imbalances may help in understanding how other organisms detect any of a broad array of stimuli or gene mutations, and then adaptively respond to activate numerous compensatory cellular processes.
Collapse
Affiliation(s)
- Luis B Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Anahi Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México city 04510, México
| | - Oscar Ulises García-Flores
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| |
Collapse
|
19
|
Kim S, McMahon DG. Light sets the brain's daily clock by regional quickening and slowing of the molecular clockworks at dawn and dusk. eLife 2021; 10:70137. [PMID: 34927581 PMCID: PMC8687663 DOI: 10.7554/elife.70137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 12/15/2022] Open
Abstract
How daily clocks in the brain are set by light to local environmental time and encode the seasons is not fully understood. The suprachiasmatic nucleus (SCN) is a central circadian clock in mammals that orchestrates physiology and behavior in tune with daily and seasonal light cycles. Here, we have found that optogenetically simulated light input to explanted mouse SCN changes the waveform of the molecular clockworks from sinusoids in free-running conditions to highly asymmetrical shapes with accelerated synthetic (rising) phases and extended degradative (falling) phases marking clock advances and delays at simulated dawn and dusk. Daily waveform changes arise under ex vivo entrainment to simulated winter and summer photoperiods, and to non-24 hr periods. Ex vivo SCN imaging further suggests that acute waveform shifts are greatest in the ventrolateral SCN, while period effects are greatest in the dorsomedial SCN. Thus, circadian entrainment is encoded by SCN clock gene waveform changes that arise from spatiotemporally distinct intrinsic responses within the SCN neural network.
Collapse
Affiliation(s)
- Suil Kim
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, United States
| | - Douglas G McMahon
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, United States.,Department of Biological Sciences, Vanderbilt University, Nashville, United States
| |
Collapse
|
20
|
Catrileo D, Moreira S, Ganga MA, Godoy L. Effect of Light and p-Coumaric Acid on the Growth and Expression of Genes Related to Oxidative Stress in Brettanomyces bruxellensis LAMAP2480. Front Microbiol 2021; 12:747868. [PMID: 34899635 PMCID: PMC8656254 DOI: 10.3389/fmicb.2021.747868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022] Open
Abstract
Brettanomyces bruxellensis is considered the most significant contaminant yeast in the wine industry since it causes a deterioration in the organoleptic properties of the wine and significant economic losses. This deterioration is due to the production of volatile phenols from hydroxycinnamic acids. These compounds possess antimicrobial properties; however, B. bruxellensis can resist this effect because it metabolizes them into less toxic ones. Recent studies have reported that B. bruxellensis grows under different stress conditions, including p-coumaric acid (pCA) but effective methods for its control have not been found yet. Since that in other yeasts, such as Saccharomyces cerevisiae, it has been described that light affects its growth, and we evaluated whether the light would have a similar effect on B. bruxellensis. The results show that at light intensities of 2,500 and 4,000 lux in the absence of pCA, B. bruxellensis LAMAP2480 does not grow in the culture medium; however, when the medium contains this acid, the yeast adapts to both factors of stress managing to grow. The expression of genes related to oxidative stress in B. bruxellensis LAMAP2480, such as SOD1, GCN4, and ESBP6, showed a higher relative expression when the yeast was exposed to 2,500 lux compared to 4,000 lux, agreeing with the growth curves. This suggests that a higher expression of the genes studied would be related to stress-protective effects by pCA.
Collapse
Affiliation(s)
- Daniela Catrileo
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sandra Moreira
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago, Chile
| | - María Angélica Ganga
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago, Chile
| | - Liliana Godoy
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
21
|
Yang J, Johnson CH. Bioluminescent Sensors for Ca ++ Flux Imaging and the Introduction of a New Intensity-Based Ca ++ Sensor. Front Bioeng Biotechnol 2021; 9:773353. [PMID: 34778237 PMCID: PMC8578923 DOI: 10.3389/fbioe.2021.773353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Sensitive detection of biological events is a goal for the design and characterization of sensors that can be used in vitro and in vivo. One important second messenger is Ca++ which has been a focus of using genetically encoded Ca++ indicators (GECIs) within living cells or intact organisms in vivo. An ideal GECI would exhibit high signal intensity, excellent signal-to-noise ratio (SNR), rapid kinetics, a large dynamic range within relevant physiological conditions, and red-shifted emission. Most available GECIs are based on fluorescence, but bioluminescent GECIs have potential advantages in terms of avoiding tissue autofluorescence, phototoxicity, photobleaching, and spectral overlap, as well as enhancing SNR. Here, we summarize current progress in the development of bioluminescent GECIs and introduce a new and previously unpublished biosensor. Because these biosensors require a substrate, we also describe the pros and cons of various substrates used with these sensors. The novel GECI that is introduced here is called CalBiT, and it is a Ca++ indicator based on the functional complementation of NanoBiT which shows a high dynamic change in response to Ca++ fluxes. Here, we use CalBiT for the detection of Ca++ fluctuations in cultured cells, including its ability for real-time imaging in living cells.
Collapse
Affiliation(s)
- Jie Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
22
|
Organic light emitting diode for in vitro antimicrobial photodynamic therapy of Candida strains. Photodiagnosis Photodyn Ther 2021; 36:102567. [PMID: 34614427 DOI: 10.1016/j.pdpdt.2021.102567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/10/2021] [Accepted: 09/30/2021] [Indexed: 11/20/2022]
Abstract
Organic light emitting diodes (OLEDs) are very attractive light sources because they are large area emitters, and can in principle be deposited on flexible substrates. These features make them suitable for ambulatory photodynamic therapy (PDT). A few reports of in vitro or in vivo OLED based PDT studies for cancer or microbial inhibition are published but to our best knowledge, none against yeasts. Yeast infections are a significant health risk, especially in low income countries with limited medical facilities. In this work, OLED-based antimicrobial PDT (aPDT), using methylene blue (MB) as photosensitizer (PS), is studied to inactivate opportunistic yeast of four Candida strains of two species: Candida albicans and Candida tropicalis. Before aPDT experiments, fluconazole-resistance was evaluated for all strains, showing that both strains of C. tropicalis were resistant and both strains of C. albicans were sensitive to it. We found that 3 repetitive irradiations work better than a single dose while keeping the total fluence constant, and that this result applies whether or not the strains are resistant to fluconazole.
Collapse
|
23
|
Brych A, Haas FB, Parzefall K, Panzer S, Schermuly J, Altmüller J, Engelsdorf T, Terpitz U, Rensing SA, Kiontke S, Batschauer A. Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis. Fungal Genet Biol 2021; 152:103570. [PMID: 34004340 DOI: 10.1016/j.fgb.2021.103570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Ustilago maydis encodes ten predicted light-sensing proteins. The biological functions of only a few of them are elucidated. Among the characterized ones are two DNA-photolyases and two rhodopsins that act as DNA-repair enzymes or green light-driven proton pumps, respectively. Here we report on the role of two other photoreceptors in U. maydis, namely White collar 1 (Wco1) and Phytochrome 1 (Phy1). We show that they bind flavins or biliverdin as chromophores, respectively. Both photoreceptors undergo a photocycle in vitro. Wco1 is the dominant blue light receptor in the saprophytic phase, controlling all of the 324 differentially expressed genes in blue light. U. maydis also responds to red and far-red light. However, the number of red or far-red light-controlled genes is less compared to blue light-regulated ones. Moreover, most of the red and far-red light-controlled genes not only depend on Phy1 but also on Wco1, indicating partial coregulation of gene expression by both photoreceptors. GFP-fused Wco1 is preferentially located in the nucleus, Phy1 in the cytosol, thus providing no hint that these photoreceptors directly interact or operate within the same complex. This is the first report on a functional characterization and coaction of White collar 1 and phytochrome orthologs in basidiomycetes.
Collapse
Affiliation(s)
- Annika Brych
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Fabian B Haas
- University of Marburg, Department of Biology, Plant Cell Biology, Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Germany
| | - Katharina Parzefall
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Sabine Panzer
- Theodor-Boveri-Institute, Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Jeanette Schermuly
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Timo Engelsdorf
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Ulrich Terpitz
- Theodor-Boveri-Institute, Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilian-University, Würzburg, Germany
| | - Stefan A Rensing
- University of Marburg, Department of Biology, Plant Cell Biology, Marburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Germany
| | - Stephan Kiontke
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany
| | - Alfred Batschauer
- University of Marburg, Department of Biology, Plant Physiology and Photobiology, Marburg, Germany.
| |
Collapse
|
24
|
de Paula GS, Oliveira MC, Sales LS, Boriollo M, Rodrigues LKA, Nobre-Dos-Santos M, Steiner-Oliveira C. Antimicrobial photodynamic therapy mediated by methylene blue coupled to β-cyclodextrin reduces early colonizing microorganisms from the oral biofilm. Photodiagnosis Photodyn Ther 2021; 34:102283. [PMID: 33813017 DOI: 10.1016/j.pdpdt.2021.102283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/20/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To test the effect of antimicrobial photodynamic therapy (A-PDT) on the oral biofilm formed with early colonizing microorganisms, using the photosensitizer methylene blue coupled with β-cyclodextrin nanoparticles and red light sources laser or LED (λ =660 nm). METHODS The groups were divided into (n = 3, in triplicate): C (negative control, 0.9 % NaCl), CX (positive control, 0.2 % chlorhexidine), P (Photosensitizer/Nanoparticle), L (Laser), LED (light-emitting diode), LP (Laser + Photosensitizer/Nanoparticle) and LEDP (LED + Photosensitizer/Nanoparticle). A multispecies biofilm composed ofS. gordonii, S. oralis, S. mitis, and S. sanguinis was grown in microplates containing BHI supplemented with 1% sucrose (w/v) for 24 h. Light irradiations were applied with a laser at 9 J for 90 s (320 J/cm2), or with LED, at 8.1 J for 90 s (8.1 J/cm2). The microbial reduction was assessed by counting viable biofilm microorganisms in selective culture media, before and after the treatments. Data normality was assessed by the Shapiro-Wilk test, and the results were submitted to Kruskal-Wallis analysis, followed by Dunn's test, with a significance level of 5%. RESULTS The groups LP and LEDP were able to significantly reduce the biofilm microorganism counts by as much as 4 log10 times compared to the negative control group (p < 0.05) and did not statistically differ from the positive control group (CX) (p > 0.05). CONCLUSION The A-PDT mediated by encapsulated β-cyclodextrin methylene blue irradiated by Laser or LED was effective in the microbial reduction of multispecies biofilm composed of early colonizing microorganisms.
Collapse
Affiliation(s)
- Gabriela Santana de Paula
- Department of Health Sciences and Pediatric Dentistry, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| | - Mateus Cardoso Oliveira
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| | - Luciana Solera Sales
- Department of Health Sciences and Pediatric Dentistry, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| | - Marcelo Boriollo
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| | - Lidiany Karla Azevedo Rodrigues
- Department of Operative Dentistry, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, CE, Zip Code: 60430-170, Brazil.
| | - Marinês Nobre-Dos-Santos
- Department of Health Sciences and Pediatric Dentistry, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| | - Carolina Steiner-Oliveira
- Department of Health Sciences and Pediatric Dentistry, Piracicaba Dental School, University of Campinas, UNICAMP, Av. Limeira, 901 - Areião, Piracicaba, SP, 13414-903, Brazil.
| |
Collapse
|
25
|
Figueroa D, Rojas V, Romero A, Larrondo LF, Salinas F. The rise and shine of yeast optogenetics. Yeast 2020; 38:131-146. [PMID: 33119964 DOI: 10.1002/yea.3529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.
Collapse
Affiliation(s)
- David Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Vicente Rojas
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andres Romero
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| |
Collapse
|
26
|
Molin M, Logg K, Bodvard K, Peeters K, Forsmark A, Roger F, Jörhov A, Mishra N, Billod JM, Amir S, Andersson M, Eriksson LA, Warringer J, Käll M, Blomberg A. Protein kinase A controls yeast growth in visible light. BMC Biol 2020; 18:168. [PMID: 33198745 PMCID: PMC7667738 DOI: 10.1186/s12915-020-00867-4] [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: 07/28/2020] [Accepted: 09/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background A wide variety of photosynthetic and non-photosynthetic species sense and respond to light, having developed protective mechanisms to adapt to damaging effects on DNA and proteins. While the biology of UV light-induced damage has been well studied, cellular responses to stress from visible light (400–700 nm) remain poorly understood despite being a regular part of the life cycle of many organisms. Here, we developed a high-throughput method for measuring growth under visible light stress and used it to screen for light sensitivity in the yeast gene deletion collection. Results We found genes involved in HOG pathway signaling, RNA polymerase II transcription, translation, diphthamide modifications of the translational elongation factor eEF2, and the oxidative stress response to be required for light resistance. Reduced nuclear localization of the transcription factor Msn2 and lower glycogen accumulation indicated higher protein kinase A (cAMP-dependent protein kinase, PKA) activity in many light-sensitive gene deletion strains. We therefore used an ectopic fluorescent PKA reporter and mutants with constitutively altered PKA activity to show that repression of PKA is essential for resistance to visible light. Conclusion We conclude that yeast photobiology is multifaceted and that protein kinase A plays a key role in the ability of cells to grow upon visible light exposure. We propose that visible light impacts on the biology and evolution of many non-photosynthetic organisms and have practical implications for how organisms are studied in the laboratory, with or without illumination.
Collapse
Affiliation(s)
- Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. .,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Katarina Logg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristofer Bodvard
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Ken Peeters
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Annabelle Forsmark
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Friederike Roger
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Jörhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Neha Mishra
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Horizon Discovery, Cambridge, CB25 9TL, UK
| | - Jean-Marc Billod
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Bio-Me A/S, Oslo Science Park, Gaustadalléen, 210349, Oslo, Norway
| | - Sabiha Amir
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Käll
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
27
|
O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
Collapse
Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
| |
Collapse
|
28
|
McCormick HK, Dick JE. Nanoelectrochemical quantification of single-cell metabolism. Anal Bioanal Chem 2020; 413:17-24. [PMID: 32915282 DOI: 10.1007/s00216-020-02899-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022]
Abstract
At the most fundamental level, the behavior of tissue is governed by the activity of its single cells. A detailed examination of single-cell biology is necessary in order to gain a deeper understanding of disease progression. While single-cell genomics and transcriptomics are mature due to robust amplification strategies, the metabolome is difficult to quantify. Nanoelectrochemical techniques stand poised to quantify single-cell metabolism as a result of the fabrication of nanoelectrodes, which allow one to make intracellular electrochemical measurements. This article is concerned with intracellular nanoelectrochemistry, focusing on the sensitive and selective quantification of various metabolites within a single, living cell. We will review the strong literature behind this field, discuss the potential deleterious effects of passing charge inside cells, and provide future outlooks for this promising avenue of inquiry. We also present a mathematical relationship based on Faraday's Law and bulk electrolysis theory to examine the consumption of analyte within a cell due to passing charge at the nanotip.Graphical abstract.
Collapse
Affiliation(s)
- Hadley K McCormick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeffrey E Dick
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
29
|
Rodríguez-González V, Obregón S, Patrón-Soberano OA, Terashima C, Fujishima A. An approach to the photocatalytic mechanism in the TiO 2-nanomaterials microorganism interface for the control of infectious processes. APPLIED CATALYSIS. B, ENVIRONMENTAL 2020; 270:118853. [PMID: 32292243 DOI: 10.1016/j.apcatb.2020.118857] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 05/21/2023]
Abstract
The approach of this timely review considers the current literature that is focused on the interface nanostructure/cell-wall microorganism to understand the annihilation mechanism. Morphological studies use optical and electronic microscopes to determine the physical damage on the cell-wall and the possible cell lysis that confirms the viability and microorganism death. The key parameters of the tailoring the surface of the photoactive nanostructures such as the metal functionalization with bacteriostatic properties, hydrophilicity, textural porosity, morphology and the formation of heterojunction systems, can achieve the effective eradication of the microorganisms under natural conditions, ranging from practical to applications in environment, agriculture, and so on. However, to our knowledge, a comprehensive review of the microorganism/nanomaterial interface approach has rarely been conducted. The final remarks point the ideal photocatalytic way for the effective prevention/eradication of microorganisms, considering the resistance that the microorganism could develop without the appropriate regulatory aspects for human and ecosystem safety.
Collapse
Affiliation(s)
- Vicente Rodríguez-González
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Materiales Avanzados, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Sergio Obregón
- Universidad Autónoma de Nuevo León, UANL, CICFIM-Facultad de Ciencias Físico Matemáticas, Av. Universidad S/N, San Nicolás de los Garza, 66455, Nuevo León, Mexico
| | - Olga A Patrón-Soberano
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Biología Molecular, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Chiaki Terashima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akira Fujishima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| |
Collapse
|
30
|
Rodríguez-González V, Obregón S, Patrón-Soberano OA, Terashima C, Fujishima A. An approach to the photocatalytic mechanism in the TiO 2-nanomaterials microorganism interface for the control of infectious processes. APPLIED CATALYSIS. B, ENVIRONMENTAL 2020; 270:118853. [PMID: 32292243 PMCID: PMC7111711 DOI: 10.1016/j.apcatb.2020.118853] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 05/08/2023]
Abstract
The approach of this timely review considers the current literature that is focused on the interface nanostructure/cell-wall microorganism to understand the annihilation mechanism. Morphological studies use optical and electronic microscopes to determine the physical damage on the cell-wall and the possible cell lysis that confirms the viability and microorganism death. The key parameters of the tailoring the surface of the photoactive nanostructures such as the metal functionalization with bacteriostatic properties, hydrophilicity, textural porosity, morphology and the formation of heterojunction systems, can achieve the effective eradication of the microorganisms under natural conditions, ranging from practical to applications in environment, agriculture, and so on. However, to our knowledge, a comprehensive review of the microorganism/nanomaterial interface approach has rarely been conducted. The final remarks point the ideal photocatalytic way for the effective prevention/eradication of microorganisms, considering the resistance that the microorganism could develop without the appropriate regulatory aspects for human and ecosystem safety.
Collapse
Affiliation(s)
- Vicente Rodríguez-González
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Materiales Avanzados, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Sergio Obregón
- Universidad Autónoma de Nuevo León, UANL, CICFIM-Facultad de Ciencias Físico Matemáticas, Av. Universidad S/N, San Nicolás de los Garza, 66455, Nuevo León, Mexico
| | - Olga A. Patrón-Soberano
- Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), División de Biología Molecular, Camino a la Presa San José 2055, Lomas 4a, Sección, 78216, San Luis Potosí, Mexico
| | - Chiaki Terashima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Akira Fujishima
- Photocatalysis International Research Center, Research Institute for Science & Technology, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| |
Collapse
|
31
|
Camponeschi I, Damasco A, Uversky VN, Giuliani A, Bianchi MM. Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators. J Biomol Struct Dyn 2020; 39:2490-2501. [PMID: 32223547 DOI: 10.1080/07391102.2020.1749133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mutual interaction between environment and life is a main topic of biological sciences. An interesting aspect of this interaction is the existence of biological rhythms spanning all the levels of organisms from bacteria to humans. On the other hand, the existence of a coupling between external oscillatory stimuli and adaptation and evolution rate of biological systems is a still unexplored issue. Here we give the demonstration of a substantial increase of heritable phenotypic changes in yeast, an organism lacking a photoreception system, when growing at 12 h light/dark cycles, with respect to both stable dark (or light) or non-12 + 12 h cycling. The model system was a yeast strain lacking a gene whose product is at the crossroad of many different physiological regulations, so ruling out any simple explanation in terms of increase in reverse gene mutations. The abundance of intrinsically disordered protein regions (IDPRs) in both deleted gene product and in its vast ensemble of interactors supports the hypothesis that resonance with the environmental cycle might be mediated by intrinsic disorder-driven interactions of protein molecules. This result opens to the speculation of the effect of environment/biological resonance phenomena in evolution and of the role of protein intrinsically disordered regions as internal mediators.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| | - Achille Damasco
- Department of Physics 'Ettore Pancini', Università di Napoli Federico II, Napoli, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Michele M Bianchi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| |
Collapse
|
32
|
Agricultural waste materials enhance protease production by Bacillus subtilis B22 in submerged fermentation under blue light-emitting diodes. Bioprocess Biosyst Eng 2020; 43:821-830. [DOI: 10.1007/s00449-019-02277-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/25/2019] [Indexed: 12/18/2022]
|
33
|
Li Q, Tian M, Teng J, Gao P, Tang BQ, Wu H. Radio frequency-induced superoxide accumulation affected the growth and viability of Saccharomyces cerevisiae. Int Microbiol 2020; 23:391-396. [PMID: 31898034 DOI: 10.1007/s10123-019-00111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/24/2019] [Accepted: 11/29/2019] [Indexed: 12/26/2022]
Abstract
With the development of the electric technologies, the biological effects of electromagnetic fields (EMF) were widely studied. However, the results remain controversial and the biophysical mechanisms are still unknown. To our knowledge, little studies pay attention to the radio frequency (RF) of 2.6-5 MHz. In the present study, we investigated the effect of these radio frequencies on the growth and cell viability of Saccharomyces cerevisiae at very low power density below 0.1 mT. The result appeared to be time-dependent. The growth of the yeast cells was obviously affected by the RF-EMF with a 43.5% increase when exposed for 30 h, and the growth-promoting effect decreased along with the radiation time and eventually turned to an inhibiting effect retarding growth by 20.7% at 89 h. The cell viability was improved to 70.1% at 8 h and reduced by 33.5% at 28 h. The superoxide accumulated in exposed cells as radiation time increased which may lead to the inhibition of viability and growth of the cells. However, the efficient frequency, power density, and exposure dosage await further investigation. Nevertheless, the wave band studied in this research is effective to produce biological effect, and therefore, it may provide an optional new radio frequency which is valuable for the development and utilization in therapy technique and medical use.
Collapse
Affiliation(s)
- Qing Li
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Miao Tian
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Jie Teng
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Peng Gao
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Bruce Qing Tang
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China
| | - Hong Wu
- Institute of Life Science & Technology, ENN Group, South District of ENN Industrial Park, Langfang, 065001, Hebei, China.
| |
Collapse
|
34
|
Live cell imaging of signaling and metabolic activities. Pharmacol Ther 2019; 202:98-119. [DOI: 10.1016/j.pharmthera.2019.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
|
35
|
Vasconcelos MEOC, Cardoso AA, da Silva JN, Alexandrino FJR, Stipp RN, Nobre-dos-Santos M, Rodrigues LKA, Steiner-Oliveira C. Combined Effectiveness of β-Cyclodextrin Nanoparticles in Photodynamic Antimicrobial Chemotherapy on In Vitro Oral Biofilms. PHOTOBIOMODULATION PHOTOMEDICINE AND LASER SURGERY 2019; 37:567-573. [DOI: 10.1089/photob.2019.4669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Andréia Alves Cardoso
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas—UNICAMP, Piracicaba, São Paulo, Brazil
| | - Josianne Neres da Silva
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas—UNICAMP, Piracicaba, São Paulo, Brazil
| | - Francisca Jamila Ricarte Alexandrino
- Postgraduate Program of Medical Microbiology, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Paulo Picanço School of Dentistry, Fortaleza, Ceará, Brazil
| | - Rafael Nobrega Stipp
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas—UNICAMP, Piracicaba, São Paulo, Brazil
| | - Marinês Nobre-dos-Santos
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas—UNICAMP, Piracicaba, São Paulo, Brazil
| | - Lidiany Karla Azevedo Rodrigues
- Postgraduate Program of Dentistry, Faculty of Pharmacy, Dentistry and Nursing, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Carolina Steiner-Oliveira
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas—UNICAMP, Piracicaba, São Paulo, Brazil
| |
Collapse
|
36
|
Bruder S, Moldenhauer EJ, Lemke RD, Ledesma-Amaro R, Kabisch J. Drop-in biofuel production using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:202. [PMID: 31462926 PMCID: PMC6708191 DOI: 10.1186/s13068-019-1542-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/10/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Oleaginous yeasts are potent hosts for the renewable production of lipids and harbor great potential for derived products, such as biofuels. Several promising processes have been described that produce hydrocarbon drop-in biofuels based on fatty acid decarboxylation and fatty aldehyde decarbonylation. Unfortunately, besides fatty aldehyde toxicity and high reactivity, the most investigated enzyme, aldehyde-deformylating oxygenase, shows unfavorable catalytic properties which hindered high yields in previous metabolic engineering approaches. RESULTS To demonstrate an alternative alkane production pathway for oleaginous yeasts, we describe the production of diesel-like, odd-chain alkanes and alkenes, by heterologously expressing a recently discovered light-driven oxidase from Chlorella variabilis (CvFAP) in Yarrowia lipolytica. Initial experiments showed that only strains engineered to have an increased pool of free fatty acids were susceptible to sufficient decarboxylation. Providing these strains with glucose and light in a synthetic medium resulted in titers of 10.9 mg/L of hydrocarbons. Using custom 3D printed labware for lighting bioreactors, and an automated pulsed glycerol fed-batch strategy, intracellular titers of 58.7 mg/L were achieved. The production of odd-numbered alkanes and alkenes with a length of 17 and 15 carbons shown in previous studies could be confirmed. CONCLUSIONS Oleaginous yeasts such as Yarrowia lipolytica can transform renewable resources such as glycerol into fatty acids and lipids. By heterologously expressing a fatty acid photodecarboxylase from the algae Chlorella variabilis hydrocarbons were produced in several scales from microwell plate to 400 mL bioreactors. The lighting turned out to be a crucial factor in terms of growth and hydrocarbon production, therefore, the evaluation of different conditions was an important step towards a tailor-made process. In general, the developed bioprocess shows a route to the renewable production of hydrocarbons for a variety of applications ranging from being substrates for further enzymatic or chemical modification or as a drop-in biofuel blend.
Collapse
Affiliation(s)
- Stefan Bruder
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Eva Johanna Moldenhauer
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Robert Denis Lemke
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Johannes Kabisch
- Computer-Aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 12, 64287 Darmstadt, Germany
| |
Collapse
|
37
|
Lu H, Mazumder M, Jaikaran ASI, Kumar A, Leis EK, Xu X, Altmann M, Cochrane A, Woolley GA. A Yeast System for Discovering Optogenetic Inhibitors of Eukaryotic Translation Initiation. ACS Synth Biol 2019; 8:744-757. [PMID: 30901519 DOI: 10.1021/acssynbio.8b00386] [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] [Indexed: 01/08/2023]
Abstract
The precise spatiotemporal regulation of protein synthesis is essential for many complex biological processes such as memory formation, embryonic development, and tumor formation. Current methods used to study protein synthesis offer only a limited degree of spatiotemporal control. Optogenetic methods, in contrast, offer the prospect of controlling protein synthesis noninvasively within minutes and with a spatial scale as small as a single synapse. Here, we present a hybrid yeast system where growth depends on the activity of human eukaryotic initiation factor 4E (eIF4E) that is suitable for screening optogenetic designs for the down-regulation of protein synthesis. We used this system to screen a diverse initial panel of 15 constructs designed to couple a light switchable domain (PYP, RsLOV, AsLOV, Dronpa) to 4EBP2 (eukaryotic initiation factor 4E binding protein 2), a native inhibitor of translation initiation. We identified cLIPS1 (circularly permuted LOV inhibitor of protein synthesis 1), a fusion of a segment of 4EBP2 and a circularly permuted version of the LOV2 domain from Avena sativa, as a photoactivated inhibitor of translation. Adapting the screen for higher throughput, we tested small libraries of cLIPS1 variants and found cLIPS2, a construct with an improved degree of optical control. We show that these constructs can both inhibit translation in yeast harboring a human eIF4E in vivo, and bind human eIF4E in vitro in a light-dependent manner. This hybrid yeast system thus provides a convenient way for discovering optogenetic constructs that can regulate human eIF4E-dependent translation initiation in a mechanistically defined manner.
Collapse
Affiliation(s)
- Huixin Lu
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Mostafizur Mazumder
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anna S. I. Jaikaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anil Kumar
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Eric K. Leis
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Xiuling Xu
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Michael Altmann
- Institut für Biochemie und Molekulare Medizin, Universität Bern, Bühlstr. 28, CH-3012 Bern, Switzerland
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| |
Collapse
|
38
|
Guo J, Suástegui M, Sakimoto KK, Moody VM, Xiao G, Nocera DG, Joshi NS. Light-driven fine chemical production in yeast biohybrids. Science 2019; 362:813-816. [PMID: 30442806 DOI: 10.1126/science.aat9777] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Inorganic-biological hybrid systems have potential to be sustainable, efficient, and versatile chemical synthesis platforms by integrating the light-harvesting properties of semiconductors with the synthetic potential of biological cells. We have developed a modular bioinorganic hybrid platform that consists of highly efficient light-harvesting indium phosphide nanoparticles and genetically engineered Saccharomyces cerevisiae, a workhorse microorganism in biomanufacturing. The yeast harvests photogenerated electrons from the illuminated nanoparticles and uses them for the cytosolic regeneration of redox cofactors. This process enables the decoupling of biosynthesis and cofactor regeneration, facilitating a carbon- and energy-efficient production of the metabolite shikimic acid, a common precursor for several drugs and fine chemicals. Our work provides a platform for the rational design of biohybrids for efficient biomanufacturing processes with higher complexity and functionality.
Collapse
Affiliation(s)
- Junling Guo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Miguel Suástegui
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| | - Kelsey K Sakimoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vanessa M Moody
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, PA 19104, USA
| | - Gao Xiao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. .,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
39
|
Pawlik A, Ruminowicz-Stefaniuk M, Frąc M, Mazur A, Wielbo J, Janusz G. The wood decay fungus Cerrena unicolor adjusts its metabolism to grow on various types of wood and light conditions. PLoS One 2019; 14:e0211744. [PMID: 30721259 PMCID: PMC6363171 DOI: 10.1371/journal.pone.0211744] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/18/2019] [Indexed: 12/20/2022] Open
Abstract
Cerrena unicolor is a wood-degrading basidiomycete with ecological and biotechnological importance. Comprehensive Biolog-based analysis was performed to assess the metabolic capabilities and sensitivity to chemicals of C. unicolor FCL139 growing in various sawdust substrates and light conditions. The metabolic preferences of the fungus towards utilization of specific substrates were shown to be correlated with the sawdust medium applied for fungus growth and the light conditions. The highest catabolic activity of C. unicolor was observed after fungus precultivation on birch and ash sawdust media. The fungus growing in the dark showed the highest metabolic activity which was indicated by capacity to utilize a broad spectrum of compounds and the decomposition of 74/95 of the carbon sources. In all the culture light conditions, p-hydroxyphenylacetic acid was the most readily metabolized compound. The greatest tolerance to chemicals was also observed during C. unicolor growth in darkness. The fungus was the most sensitive to nitrogen compounds and antibiotics, but more resistant to chelators. Comparative analysis of C. unicolor and selected wood-decay fungi from different taxonomic and ecological groups revealed average catabolic activity of the fungus. However, C. unicolor showed outstanding capabilities to catabolize salicin and arbutin. The obtained picture of C. unicolor metabolism showed that the fungus abilities to decompose woody plant material are influenced by various environmental factors.
Collapse
Affiliation(s)
- Anna Pawlik
- Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland
| | | | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Skłodowska University, Lublin, Poland
| |
Collapse
|
40
|
Causton HC. Metabolic rhythms: A framework for coordinating cellular function. Eur J Neurosci 2018; 51:1-12. [PMID: 30548718 DOI: 10.1111/ejn.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.
Collapse
Affiliation(s)
- Helen C Causton
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, New York
| |
Collapse
|
41
|
Cusicanqui Méndez DA, Gutierres E, José Dionisio E, Afonso Rabelo Buzalaf M, Cardoso Oliveira R, Andrade Moreira Machado MA, Cruvinel T. Curcumin-mediated antimicrobial photodynamic therapy reduces the viability and vitality of infected dentin caries microcosms. Photodiagnosis Photodyn Ther 2018; 24:102-108. [PMID: 30240927 DOI: 10.1016/j.pdpdt.2018.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/26/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND To our knowledge, there is a lack of evidence on the effect of Antimicrobial Photodynamic Therapy (aPDT) by the application of curcumin against complex biofilms of dental caries lesions. This study aimed to evaluate the viability, vitality, and acid metabolism of infected dentin caries microcosms treated with curcumin-mediated aPDT. METHODS After microcosm biofilms growing anaerobically on bovine dentin disks immersed in McBain medium with 1% sucrose at 37 °C for 5 days, the biofilms were treated by the association of DMSO water solution or 600 μmol L-1 curcumin with 0, 37.5 or 75 J cm-2 blue LED (455 nm). Then, the colony-forming units (CFU) counts of total microorganisms, total streptococci, mutans streptococci, and total lactobacilli were determined by plating. The lactic acid concentration was analyzed by enzymatic spectrophotometry method, while the vitality of intact biofilms was evaluated by confocal laser scanning microscope (CLSM). Statistical analysis was performed by Kruskal Wallis and post-hoc Dunn's tests (P < 0.05). RESULTS Curcumin alone did not affect the viability of microorganisms and the vitality of intact biofilms. However, 75 J cm-2 LED alone decreased the total microorganisms and total lactobacilli counts. The combination of curcumin and LED reduced significantly the counts of all microorganism groups and the vitality of intact biofilms. Differences were not observed between the lactic acid concentrations of distinct groups. CONCLUSIONS Therefore, curcumin-mediated aPDT was effective in reducing the viability and the vitality of infected dentin caries microcosms, without interfering in their acidogenicity.
Collapse
Affiliation(s)
| | - Eliézer Gutierres
- Department of Pediatric Dentistry, Orthodontics and Public Health, Bauru School of Dentistry, University of São Paulo, Brazil
| | - Evandro José Dionisio
- Department of Pediatric Dentistry, Orthodontics and Public Health, Bauru School of Dentistry, University of São Paulo, Brazil
| | | | | | | | - Thiago Cruvinel
- Department of Pediatric Dentistry, Orthodontics and Public Health, Bauru School of Dentistry, University of São Paulo, Brazil.
| |
Collapse
|
42
|
Fungal Light-Oxygen-Voltage Domains for Optogenetic Control of Gene Expression and Flocculation in Yeast. mBio 2018; 9:mBio.00626-18. [PMID: 30065085 PMCID: PMC6069114 DOI: 10.1128/mbio.00626-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Optogenetic switches permit accurate control of gene expression upon light stimulation. These synthetic switches have become a powerful tool for gene regulation, allowing modulation of customized phenotypes, overcoming the obstacles of chemical inducers, and replacing their use by an inexpensive resource: light. In this work, we implemented FUN-LOV, an optogenetic switch based on the photon-regulated interaction of WC-1 and VVD, two LOV (light-oxygen-voltage) blue-light photoreceptors from the fungus Neurospora crassa. When tested in yeast, FUN-LOV yields light-controlled gene expression with exquisite temporal resolution and a broad dynamic range of over 1,300-fold, as measured by a luciferase reporter. We also tested the FUN-LOV switch for heterologous protein expression in Saccharomyces cerevisiae, where Western blot analysis confirmed strong induction upon light stimulation, surpassing by 2.5 times the levels achieved with a classic GAL4/galactose chemical-inducible system. Additionally, we utilized FUN-LOV to control the ability of yeast cells to flocculate. Light-controlled expression of the flocculin-encoding gene FLO1, by the FUN-LOV switch, yielded flocculation in light (FIL), whereas the light-controlled expression of the corepressor TUP1 provided flocculation in darkness (FID). Altogether, the results reveal the potential of the FUN-LOV optogenetic switch to control two biotechnologically relevant phenotypes such as heterologous protein expression and flocculation, paving the road for the engineering of new yeast strains for industrial applications. Importantly, FUN-LOV’s ability to accurately manipulate gene expression, with a high temporal dynamic range, can be exploited in the analysis of diverse biological processes in various organisms. Optogenetic switches are molecular devices which allow the control of different cellular processes by light, such as gene expression, providing a versatile alternative to chemical inducers. Here, we report a novel optogenetic switch (FUN-LOV) based on the LOV domain interaction of two blue-light photoreceptors (WC-1 and VVD) from the fungus N. crassa. In yeast cells, FUN-LOV allowed tight regulation of gene expression, with low background in darkness and a highly dynamic and potent control by light. We used FUN-LOV to optogenetically manipulate, in yeast, two biotechnologically relevant phenotypes, heterologous protein expression and flocculation, resulting in strains with potential industrial applications. Importantly, FUN-LOV can be implemented in diverse biological platforms to orthogonally control a multitude of cellular processes.
Collapse
|
43
|
Jeong SY, Velmurugan P, Lim JM, Oh BT, Jeong DY. Photobiological (LED light)-mediated fermentation of blueberry (Vaccinium corymbosum L.) fruit with probiotic bacteria to yield bioactive compounds. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
44
|
L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast. Nat Commun 2018; 9:1931. [PMID: 29789561 PMCID: PMC5964156 DOI: 10.1038/s41467-017-02208-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/13/2017] [Indexed: 11/24/2022] Open
Abstract
The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a light-controlled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light. The extent of recombination depends on induction time and concentration of the chromophore phycocyanobilin (PCB), which can be easily adjusted. The tool presented here provides improved recombination control over the previously reported estradiol-dependent SCRaMbLE induction system, mediating a larger variety of possible recombination events in SCRaMbLE-ing a reporter plasmid. Thereby, L-SCRaMbLE boosts the potential for further customization and provides a facile application for use in the S. cerevisiae genome re-engineering project Sc2.0 or in other recombination-based systems. The International Synthetic Yeast Sc2.0 project has built Cre recombinase sites into synthetic chromosomes, enabling rapid genome evolution. Here the authors demonstrate L-SCRaMbLE, a light-controlled recombinase tool with improved control over recombination events.
Collapse
|
45
|
Fuller KK, Dunlap JC, Loros JJ. Light-regulated promoters for tunable, temporal, and affordable control of fungal gene expression. Appl Microbiol Biotechnol 2018; 102:3849-3863. [PMID: 29569180 DOI: 10.1007/s00253-018-8887-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/08/2023]
Abstract
Regulatable promoters are important genetic tools, particularly for assigning function to essential and redundant genes. They can also be used to control the expression of enzymes that influence metabolic flux or protein secretion, thereby optimizing product yield in bioindustry. This review will focus on regulatable systems for use in filamentous fungi, an important group of organisms whose members include key research models, devastating pathogens of plants and animals, and exploitable cell factories. Though we will begin by cataloging those promoters that are controlled by nutritional or chemical means, our primary focus will rest on those who can be controlled by a literal flip-of-the-switch: promoters of light-regulated genes. The vvd promoter of Neurospora will first serve as a paradigm for how light-driven systems can provide tight, robust, tunable, and temporal control of either autologous or heterologous fungal proteins. We will then discuss a theoretical approach to, and practical considerations for, the development of such promoters in other species. To this end, we have compiled genes from six previously published light-regulated transcriptomic studies to guide the search for suitable photoregulatable promoters in your fungus of interest.
Collapse
Affiliation(s)
- Kevin K Fuller
- Department of Molecular and Systems Biology, Geisel School of Medicine, Hanover, NH, USA.
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine, Hanover, NH, USA
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine, Hanover, NH, USA. .,Department of Biochemistry and Cell Biology, Geisel School of Medicine, Hanover, NH, USA.
| |
Collapse
|
46
|
Effect of methylene blue-mediated antimicrobial photodynamic therapy on dentin caries microcosms. Lasers Med Sci 2017; 33:479-487. [DOI: 10.1007/s10103-017-2379-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/26/2017] [Indexed: 01/10/2023]
|
47
|
Dodd BJT, Kralj JM. Live Cell Imaging Reveals pH Oscillations in Saccharomyces cerevisiae During Metabolic Transitions. Sci Rep 2017; 7:13922. [PMID: 29066766 PMCID: PMC5654966 DOI: 10.1038/s41598-017-14382-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022] Open
Abstract
Addition of glucose to starved Saccharomyces cerevisiae initiates collective NADH dynamics termed glycolytic oscillations. Numerous questions remain about the extent to which single cells can oscillate, if oscillations occur in natural conditions, and potential physiological consequences of oscillations. In this paper, we report sustained glycolytic oscillations in single cells without the need for cyanide. Glucose addition to immobilized cells induced pH oscillations that could be imaged with fluorescent sensors. A population of cells had oscillations that were heterogeneous in frequency, start time, stop time, duration and amplitude. These changes in cytoplasmic pH were necessary and sufficient to drive changes in NADH. Oscillators had lower mitochondrial membrane potentials and budded more slowly than non-oscillators. We also uncovered a new type of oscillation during recovery from H2O2 challenge. Our data show that pH in S. cerevisiae changes over several time scales, and that imaging pH offers a new way to measure glycolytic oscillations on individual cells.
Collapse
Affiliation(s)
| | - Joel M Kralj
- BioFrontiers Institute, University of Colorado, Boulder, 80303, USA. .,Molecular Cellular and Developmental Biology Department, University of Colorado, Boulder, 80303, USA.
| |
Collapse
|
48
|
Hochrein L, Machens F, Messerschmidt K, Mueller-Roeber B. PhiReX: a programmable and red light-regulated protein expression switch for yeast. Nucleic Acids Res 2017; 45:9193-9205. [PMID: 28911120 PMCID: PMC5587811 DOI: 10.1093/nar/gkx610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiReX is based on the combination of a customizable synTALE DNA-binding domain, the VP64 activation domain and the light-sensitive dimerization of the photoreceptor PhyB and its interacting partner PIF3 from Arabidopsis thaliana. Robust gene expression and high protein levels are achieved by combining genome integrated red light-sensing components with an episomal high-copy reporter construct. The gene of interest as well as the synTALE DNA-binding domain can be easily exchanged, allowing the flexible regulation of any desired gene by targeting endogenous or heterologous promoter regions. To allow low-cost induction of gene expression for industrial fermentation processes, we engineered yeast to endogenously produce the chromophore required for the effective dimerization of PhyB and PIF3. Time course experiments demonstrate high-level induction over a period of at least 48 h.
Collapse
Affiliation(s)
- Lena Hochrein
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Katrin Messerschmidt
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Department of Molecular Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.,Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| |
Collapse
|
49
|
Lucia U, Grisolia G, Ponzetto A, Silvagno F. An engineering thermodynamic approach to select the electromagnetic wave effective on cell growth. J Theor Biol 2017; 429:181-189. [DOI: 10.1016/j.jtbi.2017.06.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 12/19/2022]
|
50
|
Bodvard K, Peeters K, Roger F, Romanov N, Igbaria A, Welkenhuysen N, Palais G, Reiter W, Toledano MB, Käll M, Molin M. Light-sensing via hydrogen peroxide and a peroxiredoxin. Nat Commun 2017; 8:14791. [PMID: 28337980 PMCID: PMC5376668 DOI: 10.1038/ncomms14791] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 01/27/2017] [Indexed: 02/08/2023] Open
Abstract
Yeast lacks dedicated photoreceptors; however, blue light still causes pronounced oscillations of the transcription factor Msn2 into and out of the nucleus. Here we show that this poorly understood phenomenon is initiated by a peroxisomal oxidase, which converts light into a hydrogen peroxide (H2O2) signal that is sensed by the peroxiredoxin Tsa1 and transduced to thioredoxin, to counteract PKA-dependent Msn2 phosphorylation. Upon H2O2, the nuclear retention of PKA catalytic subunits, which contributes to delayed Msn2 nuclear concentration, is antagonized in a Tsa1-dependent manner. Conversely, peroxiredoxin hyperoxidation interrupts the H2O2 signal and drives Msn2 oscillations by superimposing on PKA feedback regulation. Our data identify a mechanism by which light could be sensed in all cells lacking dedicated photoreceptors. In particular, the use of H2O2 as a second messenger in signalling is common to Msn2 oscillations and to light-induced entrainment of circadian rhythms and suggests conserved roles for peroxiredoxins in endogenous rhythms. While yeasts lack dedicated photoreceptors, they nonetheless possess metabolic rhythms responsive to light. Here the authors find that light signalling in budding yeast involves the production of H2O2, which in turn regulates protein kinase A through a peroxiredoxin-thioredoxin redox relay.
Collapse
Affiliation(s)
- Kristofer Bodvard
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden.,Department of Physics, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Ken Peeters
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
| | - Friederike Roger
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
| | - Natalie Romanov
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, A-1030 Vienna, Austria
| | - Aeid Igbaria
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Niek Welkenhuysen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden.,Hohmann Lab, Department of Biology and Biological Engineering, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Gaël Palais
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Wolfgang Reiter
- Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr Bohrgasse 9, A-1030 Vienna, Austria
| | - Michel B Toledano
- Oxidative Stress and Cancer, SBIGEM, iBiTec-S, FRE3377 CEA-CNRS-Université Paris-Sud, CEA-Saclay, bat 142 F-91191 Gif Sur Yvette, France
| | - Mikael Käll
- Department of Physics, Chalmers University of Technology, S-412 96 Göteborg, Sweden
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-413 90 Göteborg, Sweden
| |
Collapse
|