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Arunachalam E, Keber FC, Law RC, Kumar CK, Shen Y, Park JO, Wühr M, Needleman DJ. Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.601975. [PMID: 39005310 PMCID: PMC11245115 DOI: 10.1101/2024.07.04.601975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
A long-standing observation is that in fast-growing cells, respiration rate declines with increasing growth rate and is compensated by an increase in fermentation, despite respiration being more efficient than fermentation. This apparent preference for fermentation even in the presence of oxygen is known as aerobic glycolysis, and occurs in bacteria, yeast, and cancer cells. Considerable work has focused on understanding the potential benefits that might justify this seemingly wasteful metabolic strategy, but its mechanistic basis remains unclear. Here we show that aerobic glycolysis results from the saturation of mitochondrial respiration and the decoupling of mitochondrial biogenesis from the production of other cellular components. Respiration rate is insensitive to acute perturbations of cellular energetic demands or nutrient supplies, and is explained simply by the amount of mitochondria per cell. Mitochondria accumulate at a nearly constant rate across different growth conditions, resulting in mitochondrial amount being largely determined by cell division time. In contrast, glucose uptake rate is not saturated, and is accurately predicted by the abundances and affinities of glucose transporters. Combining these models of glucose uptake and respiration provides a quantitative, mechanistic explanation for aerobic glycolysis. The robustness of specific respiration rate and mitochondrial biogenesis, paired with the flexibility of other bioenergetic and biosynthetic fluxes, may play a broad role in shaping eukaryotic cell metabolism.
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2
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Mendes LFS, Gimenes CO, da Silva MDO, Rout SK, Riek R, Costa‐Filho AJ. The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion. Protein Sci 2024; 33:e5085. [PMID: 38923199 PMCID: PMC11201811 DOI: 10.1002/pro.5085] [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: 02/27/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Eukaryotic cells have developed intricate mechanisms for biomolecule transport, particularly in stressful conditions. This interdisciplinary study delves into unconventional protein secretion (UPS) pathways activated during starvation, facilitating the export of proteins bypassing most of the components of the classical secretory machinery. Specifically, we focus on the underexplored mechanisms of the GRASP's role in UPS, particularly in biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results show that liquid-liquid phase separation (LLPS) plays a key role in the coacervation of Grh1, the GRASP yeast homologue, under starvation-like conditions. This association seems a precursor to the Compartment for Unconventional Protein Secretion (CUPS) biogenesis. Grh1's self-association is regulated by electrostatic, hydrophobic, and hydrogen-bonding interactions. Importantly, our study demonstrates that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations. Additionally, we explore how the coacervate liquid-to-solid transition could impact cells' ability to return to normal post-stress states. Our findings offer insights into intracellular protein dynamics and cell adaptive responses to stress.
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Affiliation(s)
- Luis Felipe S. Mendes
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Carolina O. Gimenes
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
| | - Marília D. O. da Silva
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
| | - Saroj K. Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Antonio J. Costa‐Filho
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
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3
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Ren C, Zhang S, Li Q, Jiang Q, Li Y, Gao Z, Cao W, Guo L. Pilot composite tubular bioreactor for outdoor photo-fermentation hydrogen production: From batch to continuous operation. BIORESOURCE TECHNOLOGY 2024; 401:130705. [PMID: 38631655 DOI: 10.1016/j.biortech.2024.130705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
A novel 70 L composite tubular photo-bioreactor was constructed, and its photo-fermentation hydrogen production characteristics of batch and continuous modes were investigated with glucose as the substrate in an outdoor environment. In the batch fermentation stage, the hydrogen production rate peaked at 37.6 mL H2/(L·h) accompanied by a high hydrogen yield of 7 mol H2/mol glucose. The daytime light conversion efficiency is 4 %, with 37 % of light energy from the sun. An optimal hydraulic retention time of 5 d was identified during continuous photo-fermentation. Under this condition, the stability of the cell concentration is maintained and more electrons can be driven to the hydrogen generation pathway while attaining a hydrogen production rate of 20.7 ± 0.9 mL H2/(L·h). The changes of biomass, volatile fatty acids concentration and ion concentration during fermentation were analyzed. Continuous hydrogen production by composite tubular photo-bioreactor offers new ideas for the large-scale deployment of photobiological hydrogen production.
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Affiliation(s)
- Changpeng Ren
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Sihu Zhang
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Qing Li
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Qiushi Jiang
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Yongbing Li
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Zixuan Gao
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
| | - Wen Cao
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China.
| | - Liejin Guo
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, China
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4
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Zhou H, Huo Y, Yang N, Wei T. Phosphatidic acid: from biophysical properties to diverse functions. FEBS J 2024; 291:1870-1885. [PMID: 37103336 DOI: 10.1111/febs.16809] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 04/28/2023]
Abstract
Phosphatidic acid (PA), the simplest phospholipid, acts as a key metabolic intermediate and second messenger that impacts diverse cellular and physiological processes across species ranging from microbes to plants and mammals. The cellular levels of PA dynamically change in response to stimuli, and multiple enzymatic reactions can mediate its production and degradation. PA acts as a signalling molecule and regulates various cellular processes via its effects on membrane tethering, enzymatic activities of target proteins, and vesicular trafficking. Because of its unique physicochemical properties compared to other phospholipids, PA has emerged as a class of new lipid mediators influencing membrane structure, dynamics, and protein interactions. This review summarizes the biosynthesis, dynamics, and cellular functions and properties of PA.
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Affiliation(s)
- Hejiang Zhou
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanwu Huo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Na Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Laboratory of Genetic and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Taotao Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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5
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Botman D, Kanagasabapathi S, Rep MI, van Rossum K, Tutucci E, Teusink B. cAMP in budding yeast: Also a messenger for sucrose metabolism? BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119706. [PMID: 38521467 DOI: 10.1016/j.bbamcr.2024.119706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024]
Abstract
S. cerevisiae (or budding yeast) is an important micro-organism for sucrose-based fermentation in biotechnology. Yet, it is largely unknown how budding yeast adapts to sucrose transitions. Sucrose can only be metabolized when the invertase or the maltose machinery are expressed and we propose that the Gpr1p receptor signals extracellular sucrose availability via the cAMP peak to adapt cells accordingly. A transition to sucrose or glucose gave a transient cAMP peak which was maximally induced for sucrose. When transitioned to sucrose, cAMP signalling mutants showed an impaired cAMP peak together with a lower growth rate, a longer lag phase and a higher final OD600 compared to a glucose transition. These effects were not caused by altered activity or expression of enzymes involved in sucrose metabolism and imply a more general metabolic adaptation defect. Basal cAMP levels were comparable among the mutant strains, suggesting that the transient cAMP peak is required to adapt cells correctly to sucrose. We propose that the short-term dynamics of the cAMP signalling cascade detects long-term extracellular sucrose availability and speculate that its function is to maintain a fermentative phenotype at continuously low glucose and fructose concentrations.
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Affiliation(s)
- Dennis Botman
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Sineka Kanagasabapathi
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Mila I Rep
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Kelly van Rossum
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, AIMMS/ALIFE, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
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6
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Laporte D, Massoni-Laporte A, Lefranc C, Dompierre J, Mauboules D, Nsamba ET, Royou A, Gal L, Schuldiner M, Gupta ML, Sagot I. A stable microtubule bundle formed through an orchestrated multistep process controls quiescence exit. eLife 2024; 12:RP89958. [PMID: 38527106 PMCID: PMC10963028 DOI: 10.7554/elife.89958] [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] [Indexed: 03/27/2024] Open
Abstract
Cells fine-tune microtubule assembly in both space and time to give rise to distinct edifices with specific cellular functions. In proliferating cells, microtubules are highly dynamics, and proliferation cessation often leads to their stabilization. One of the most stable microtubule structures identified to date is the nuclear bundle assembled in quiescent yeast. In this article, we characterize the original multistep process driving the assembly of this structure. This Aurora B-dependent mechanism follows a precise temporality that relies on the sequential actions of kinesin-14, kinesin-5, and involves both microtubule-kinetochore and kinetochore-kinetochore interactions. Upon quiescence exit, the microtubule bundle is disassembled via a cooperative process involving kinesin-8 and its full disassembly is required prior to cells re-entry into proliferation. Overall, our study provides the first description, at the molecular scale, of the entire life cycle of a stable microtubule structure in vivo and sheds light on its physiological function.
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Affiliation(s)
| | | | | | | | | | - Emmanuel T Nsamba
- Genetics, Development, and Cell Biology, Iowa State UniversityAmesUnited States
| | - Anne Royou
- Univ. Bordeaux, CNRS, IBGC, UMR 5095BordeauxFrance
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Mohan L Gupta
- Genetics, Development, and Cell Biology, Iowa State UniversityAmesUnited States
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7
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Heinrich S, Hondele M, Marchand D, Derrer CP, Zedan M, Oswald A, Malinovska L, Uliana F, Khawaja S, Mancini R, Grunwald D, Weis K. Glucose stress causes mRNA retention in nuclear Nab2 condensates. Cell Rep 2024; 43:113593. [PMID: 38113140 DOI: 10.1016/j.celrep.2023.113593] [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: 03/10/2022] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that, upon glucose withdrawal, the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and control gene expression during stress.
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Affiliation(s)
- Stephanie Heinrich
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| | - Maria Hondele
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland; Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Désirée Marchand
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Carina Patrizia Derrer
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Mostafa Zedan
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Alexandra Oswald
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Liliana Malinovska
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Sarah Khawaja
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Roberta Mancini
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - David Grunwald
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA 01605, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
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8
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Rix G, Williams RL, Spinner H, Hu VJ, Marks DS, Liu CC. Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566922. [PMID: 38014077 PMCID: PMC10680746 DOI: 10.1101/2023.11.13.566922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
When nature maintains or evolves a gene's function over millions of years at scale, it produces a diversity of homologous sequences whose patterns of conservation and change contain rich structural, functional, and historical information about the gene. However, natural gene diversity likely excludes vast regions of functional sequence space and includes phylogenetic and evolutionary eccentricities, limiting what information we can extract. We introduce an accessible experimental approach for compressing long-term gene evolution to laboratory timescales, allowing for the direct observation of extensive adaptation and divergence followed by inference of structural, functional, and environmental constraints for any selectable gene. To enable this approach, we developed a new orthogonal DNA replication (OrthoRep) system that durably hypermutates chosen genes at a rate of >10 -4 substitutions per base in vivo . When OrthoRep was used to evolve a conditionally essential maladapted enzyme, we obtained thousands of unique multi-mutation sequences with many pairs >60 amino acids apart (>15% divergence), revealing known and new factors influencing enzyme adaptation. The fitness of evolved sequences was not predictable by advanced machine learning models trained on natural variation. We suggest that OrthoRep supports the prospective and systematic discovery of constraints shaping gene evolution, uncovering of new regions in fitness landscapes, and general applications in biomolecular engineering.
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9
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Harvey HJ, Hendry AC, Chirico M, Archer DB, Avery SV. Adaptation to sorbic acid in low sugar promotes resistance of yeast to the preservative. Heliyon 2023; 9:e22057. [PMID: 38034742 PMCID: PMC10682675 DOI: 10.1016/j.heliyon.2023.e22057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
The weak acid sorbic acid is a common preservative used in soft drink beverages to control microbial spoilage. Consumers and industry are increasingly transitioning to low-sugar food formulations, but potential impacts of reduced sugar on sorbic acid efficacy are barely characterised. In this study, we report enhanced sorbic acid resistance of yeast in low-glucose conditions. We had anticipated that low glucose would induce respiratory metabolism, which was shown previously to be targeted by sorbic acid. However, a shift from respiratory to fermentative metabolism upon sorbic acid exposure of Saccharomyces cerevisiae was correlated with relative resistance to sorbic acid in low glucose. Fermentation-negative yeast species did not show the low-glucose resistance phenotype. Phenotypes observed for certain yeast deletion strains suggested roles for glucose signalling and repression pathways in the sorbic acid resistance at low glucose. This low-glucose induced sorbic acid resistance was reversed by supplementing yeast cultures with succinic acid, a metabolic intermediate of respiratory metabolism (and a food-safe additive) that promoted respiration. The results indicate that metabolic adaptation of yeast can promote sorbic acid resistance at low glucose, a consideration for the preservation of foodstuffs as both food producers and consumers move towards a reduced sugar landscape.
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Affiliation(s)
- Harry J. Harvey
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alex C. Hendry
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marcella Chirico
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David B. Archer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Simon V. Avery
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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10
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Irfan, Soleja N, Mohsin M. FRET-based probe for ratiometric detection and imaging of folic acid in real-time. Anal Biochem 2023; 679:115285. [PMID: 37586674 DOI: 10.1016/j.ab.2023.115285] [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: 07/10/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Inadequate folic acid intake is linked to diseases such as megaloblastic anemia, neural tube defects, and hyperhomocysteinemia, increasing the risk of vascular disease and thrombosis. Folic acid, a cofactor in various enzymes, can be produced by plants and bacteria, but not by humans and other animals. L-5-methyl-tetrahydrofolate (L-5-methyl-THF) is the primary dietary folate form, transported in circulation for cellular metabolism. Traditional methods of determining folic acid levels are unreliable and time-consuming. SenFol (Sensor for folic acid) is a fluorescence resonance energy transfer (FRET)-based nanosensor that we have developed by inserting folic acid-binding protein (FolT) as the folate detecting domain between the pair of enhanced cyan fluorescent protein (ECFP) and Venus. The developed sensor is highly specific, produces a quick signal, which is pH stable, and delivers precise, ratiometric readings in cell-based experiments. The projected affinity score of folic acid with FolT was -7.4 kcal/mol. The apparent affinity (Kd) of SenFol for folic acid is 28.49 × 10-9 M, with a detection range of 5 × 10-9 M to 5 × 10-7 M, and a maximum FRET ratio change of 0.45. WT SenFol, a highly efficient folic acid nanosensor, can dynamically detect intracellular folic acid content in E. coli, yeast, and HEK-293 T cells, confirming its potential.
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Affiliation(s)
- Irfan
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India.
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11
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Laurel M, Mojzita D, Seppänen-Laakso T, Oksman-Caldentey KM, Rischer H. Raspberry Ketone Accumulation in Nicotiana benthamiana and Saccharomyces cerevisiae by Expression of Fused Pathway Genes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13391-13400. [PMID: 37656963 PMCID: PMC10510385 DOI: 10.1021/acs.jafc.3c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023]
Abstract
Raspberry ketone has generated interest in recent years both as a flavor agent and as a health promoting supplement. Raspberry ketone can be synthesized chemically, but the value of a natural nonsynthetic product is among the most valuable flavor compounds on the market. Coumaroyl-coenzyme A (CoA) is the direct precursor for raspberry ketone but also an essential precursor for flavonoid and lignin biosynthesis in plants and therefore highly regulated. The synthetic fusion of 4-coumaric acid ligase (4CL) and benzalacetone synthase (BAS) enables the channeling of coumaroyl-CoA from the ligase to the synthase, proving to be a powerful tool in the production of raspberry ketone in both N. benthamiana and S. cerevisiae. To the best of our knowledge, the key pathway genes for raspberry ketone formation are transiently expressed in N. benthamiana for the first time in this study, producing over 30 μg/g of the compound. Our raspberry ketone producing yeast strains yielded up to 60 mg/L, which is the highest ever reported in yeast.
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Affiliation(s)
- Markus Laurel
- VTT Technical Research Centre
of Finland Ltd., P.O. Box 1000, FI-02044 Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre
of Finland Ltd., P.O. Box 1000, FI-02044 Espoo, Finland
| | | | | | - Heiko Rischer
- VTT Technical Research Centre
of Finland Ltd., P.O. Box 1000, FI-02044 Espoo, Finland
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12
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Grimes B, Jacob W, Liberman AR, Kim N, Zhao X, Masison DC, Greene LE. The Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo. Biomolecules 2023; 13:1370. [PMID: 37759770 PMCID: PMC10526957 DOI: 10.3390/biom13091370] [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: 08/01/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The Sup35 prion protein of budding yeast has been reported to undergo phase separation to form liquid droplets both at low pH in vitro and when energy depletion decreases the intracellular pH in vivo. It also has been shown using purified proteins that this phase separation is driven by the prion domain of Sup35 and does not re-quire its C-terminal domain. In contrast, we now find that a Sup35 fragment consisting of only the N-terminal prion domain and the M-domain does not phase separate in vivo; this phase separation of Sup35 requires the C-terminal domain, which binds Sup45 to form the translation termination complex. The phase-separated Sup35 not only colocalizes with Sup45 but also with Pub1, a stress granule marker protein. In addition, like stress granules, phase separation of Sup35 appears to require mRNA since cycloheximide treatment, which inhibits mRNA release from ribosomes, prevents phase separation of Sup35. Finally, unlike Sup35 in vitro, Sup35 condensates do not disassemble in vivo when the intracellular pH is increased. These results suggest that, in energy-depleted cells, Sup35 forms supramolecular assemblies that differ from the Sup35 liquid droplets that form in vitro.
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Affiliation(s)
- Bryan Grimes
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walter Jacob
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda R. Liberman
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Kim
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong Zhao
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lois E. Greene
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Simpson-Lavy K, Kupiec M. Glucose Inhibits Yeast AMPK (Snf1) by Three Independent Mechanisms. BIOLOGY 2023; 12:1007. [PMID: 37508436 PMCID: PMC10376661 DOI: 10.3390/biology12071007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Snf1, the fungal homologue of mammalian AMP-dependent kinase (AMPK), is a key protein kinase coordinating the response of cells to a shortage of glucose. In fungi, the response is to activate respiratory gene expression and metabolism. The major regulation of Snf1 activity has been extensively investigated: In the absence of glucose, it becomes activated by phosphorylation of its threonine at position 210. This modification can be erased by phosphatases when glucose is restored. In the past decade, two additional independent mechanisms of Snf1 regulation have been elucidated. In response to glucose (or, surprisingly, also to DNA damage), Snf1 is SUMOylated by Mms21 at lysine 549. This inactivates Snf1 and leads to Snf1 degradation. More recently, glucose-induced proton export has been found to result in Snf1 inhibition via a polyhistidine tract (13 consecutive histidine residues) at the N-terminus of the Snf1 protein. Interestingly, the polyhistidine tract plays also a central role in the response to iron scarcity. This review will present some of the glucose-sensing mechanisms of S. cerevisiae, how they interact, and how their interplay results in Snf1 inhibition by three different, and independent, mechanisms.
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Affiliation(s)
- Kobi Simpson-Lavy
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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14
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Zhang C, Liu Y, An H, Wang X, Xu L, Deng H, Wu S, Zhang JR, Liu X. Amino Acid Starvation-Induced Glutamine Accumulation Enhances Pneumococcal Survival. mSphere 2023; 8:e0062522. [PMID: 37017541 PMCID: PMC10286718 DOI: 10.1128/msphere.00625-22] [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: 12/06/2022] [Accepted: 02/19/2023] [Indexed: 04/06/2023] Open
Abstract
Bacteria are known to cope with amino acid starvation by the stringent response signaling system, which is mediated by the accumulation of the (p)ppGpp alarmones when uncharged tRNAs stall at the ribosomal A site. While a number of metabolic processes have been shown to be regulatory targets of the stringent response in many bacteria, the global impact of amino acid starvation on bacterial metabolism remains obscure. This work reports the metabolomic profiling of the human pathogen Streptococcus pneumoniae under methionine starvation. Methionine limitation led to the massive overhaul of the pneumococcal metabolome. In particular, methionine-starved pneumococci showed a massive accumulation of many metabolites such as glutamine, glutamic acid, lactate, and cyclic AMP (cAMP). In the meantime, methionine-starved pneumococci showed a lower intracellular pH and prolonged survival. Isotope tracing revealed that pneumococci depend predominantly on amino acid uptake to replenish intracellular glutamine but cannot convert glutamine to methionine. Further genetic and biochemical analyses strongly suggested that glutamine is involved in the formation of a "prosurvival" metabolic state by maintaining an appropriate intracellular pH, which is accomplished by the enzymatic release of ammonia from glutamine. Methionine starvation-induced intracellular pH reduction and glutamine accumulation also occurred to various extents under the limitation of other amino acids. These findings have uncovered a new metabolic mechanism of bacterial adaptation to amino acid limitation and perhaps other stresses, which may be used as a potential therapeutic target for infection control. IMPORTANCE Bacteria are known to cope with amino acid starvation by halting growth and prolonging survival via the stringent response signaling system. Previous investigations have allowed us to understand how the stringent response regulates many aspects of macromolecule synthesis and catabolism, but how amino acid starvation promotes bacterial survival at the metabolic level remains largely unclear. This paper reports our systematic profiling of the methionine starvation-induced metabolome in S. pneumoniae. To the best of our knowledge, this represents the first reported bacterial metabolome under amino acid starvation. These data have revealed that the significant accumulation of glutamine and lactate enables S. pneumoniae to form a "prosurvival" metabolic state with a lower intracellular pH, which inhibits bacterial growth for prolonged survival. Our findings have provided insightful information on the metabolic mechanisms of pneumococcal adaptation to nutrient limitation during the colonization of the human upper airway.
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Affiliation(s)
- Chengwang Zhang
- Department of Basic Medical Science, School of Medicine, Lishui University, Lishui, Zhejiang, China
| | - Yanhong Liu
- Center for Infectious Disease Research, Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China
| | - Haoran An
- Center for Infectious Disease Research, Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xueying Wang
- National Protein Science Facility, Tsinghua University, Beijing, China
| | - Lina Xu
- National Protein Science Facility, Tsinghua University, Beijing, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Songquan Wu
- Department of Basic Medical Science, School of Medicine, Lishui University, Lishui, Zhejiang, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Liu
- National Protein Science Facility, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
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15
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Wilson HB, Lorenz MC. Candida albicans Hyphal Morphogenesis within Macrophages Does Not Require Carbon Dioxide or pH-Sensing Pathways. Infect Immun 2023; 91:e0008723. [PMID: 37078861 PMCID: PMC10187119 DOI: 10.1128/iai.00087-23] [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: 03/01/2023] [Accepted: 03/29/2023] [Indexed: 04/21/2023] Open
Abstract
The opportunistic fungal pathogen Candida albicans has evolved a variety of mechanisms for surviving inside and escaping macrophages, including the initiation of filamentous growth. Although several distinct models have been proposed to explain this process at the molecular level, the signals driving hyphal morphogenesis in this context have yet to be clarified. Here, we evaluate the following three molecular signals as potential hyphal inducers within macrophage phagosomes: CO2, intracellular pH, and extracellular pH. Additionally, we revisit previous work suggesting that the intracellular pH of C. albicans fluctuates in tandem with morphological changes in vitro. Using time-lapse microscopy, we observed that C. albicans mutants lacking components of the CO2-sensing pathway were able to undergo hyphal morphogenesis within macrophages. Similarly, a rim101Δ strain was competent in hyphal induction, suggesting that neutral/alkaline pH sensing is not necessary for the initiation of morphogenesis within phagosomes either. Contrary to previous findings, single-cell pH-tracking experiments revealed that the cytosolic pH of C. albicans remains tightly regulated both within macrophage phagosomes and under a variety of in vitro conditions throughout the process of morphogenesis. This finding suggests that intracellular pH is not a signal contributing to morphological changes.
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Affiliation(s)
- Hannah B. Wilson
- Graduate School for Biomedical Sciences, University of Texas Science Center at Houston, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Michael C. Lorenz
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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16
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Salas-Navarrete PC, Rosas-Santiago P, Suárez-Rodríguez R, Martínez A, Caspeta L. Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12556-7. [PMID: 37178307 DOI: 10.1007/s00253-023-12556-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Ethanol fermentations can be prematurely halted as Saccharomyces cerevisiae faces adverse conditions, such as acidic pH, presence of acetic acid, and supraoptimal temperatures. The knowledge on yeast responses to these conditions is essential to endowing a tolerant phenotype to another strain by targeted genetic manipulation. In this study, physiological and whole-genome analyses were conducted to obtain insights on molecular responses which potentially render yeast tolerant towards thermoacidic conditions. To this end, we used thermotolerant TTY23, acid tolerant AT22, and thermo-acid tolerant TAT12 strains previously generated by adaptive laboratory evolution (ALE) experiments. The results showed an increase in thermoacidic profiles in the tolerant strains. The whole-genome sequence revealed the importance of genes related to: H+, iron, and glycerol transport (i.e., PMA1, FRE1/2, JEN1, VMA2, VCX1, KHA1, AQY3, and ATO2); transcriptional regulation of stress responses to drugs, reactive oxygen species and heat-shock (i.e., HSF1, SKN7, BAS1, HFI1, and WAR1); and adjustments of fermentative growth and stress responses by glucose signaling pathways (i.e., ACS1, GPA1/2, RAS2, IRA2, and REG1). At 30 °C and pH 5.5, more than a thousand differentially expressed genes (DEGs) were identified in each strain. The integration of results revealed that evolved strains adjust their intracellular pH by H+ and acetic acid transport, modify their metabolism and stress responses via glucose signaling pathways, control of cellular ATP pools by regulating translation and de novo synthesis of nucleotides, and direct the synthesis, folding and rescue of proteins throughout the heat-shock stress response. Moreover, the motifs analysis in mutated transcription factors suggested a significant association of SFP1, YRR1, BAS1, HFI1, HSF1, and SKN7 TFs with DEGs found in thermoacidic tolerant yeast strains. KEY POINTS: • All the evolved strains overexpressed the plasma membrane H+ -ATPase PMA1 at optimal conditions • Tolerant strain TAT12 mutated genes encoding weak acid and heat response TFs HSF1, SKN7, and WAR1 • TFs HSF1 and SKN7 likely controlled the transcription of metabolic genes associated to heat and acid tolerance.
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Affiliation(s)
- Prisciluis Caheri Salas-Navarrete
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Paul Rosas-Santiago
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Ramón Suárez-Rodríguez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Alfredo Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Luis Caspeta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México.
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17
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Liu C, Hao D, Sun R, Zhang Y, Peng Y, Yuan Y, Jiang K, Li W, Wen X, Guo H. Arabidopsis NPF2.13 functions as a critical transporter of bacterial natural compound tunicamycin in plant-microbe interaction. THE NEW PHYTOLOGIST 2023; 238:765-780. [PMID: 36653958 DOI: 10.1111/nph.18752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Metabolites including antibiotics, enzymes, and volatiles produced by plant-associated bacteria are key factors in plant-microbiota interaction that regulates various plant biological processes. There should be crucial mediators responsible for their entry into host plants. However, less is known about the identities of these plant transporters. We report that the Arabidopsis Nitrate Transporter1 (NRT1)/NPF protein NPF2.13 functions in plant uptake of tunicamycin (TM), a natural antibiotic produced by several Streptomyces spp., which inhibits protein N-glycosylation. Loss of NPF2.13 function resulted in enhanced TM tolerance, whereas NPF2.13 overexpression led to TM hypersensitivity. Transport assays confirmed that NPF2.13 is a H+ /TM symporter and the transport is not affected by other substrates like nitrate. NPF2.13 exclusively showed TM transport activity among tested NPFs. Tunicamycin uptake from TM-producing Streptomyces upregulated the expression of nitrate-related genes including NPF2.13. Moreover, nitrate allocation to younger leaves was promoted by TM in host plants. Tunicamycin could also benefit plant defense against the pathogen. Notably, the TM effects were significantly repressed in npf2.13 mutant. Overall, this study identifies NPF2.13 protein as an important TM transporter in plant-microbe interaction and provides insights into multiple facets of NPF proteins in modulating plant nutrition and defense by transporting exterior bacterial metabolites.
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Affiliation(s)
- Chuanfa Liu
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Dongdong Hao
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Ruixue Sun
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yi Zhang
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yang Peng
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yang Yuan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Centre and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kai Jiang
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
- SUSTech Academy for Advanced and Interdisciplinary Studies, SUSTech, 518055, Shenzhen, China
| | - Wenyang Li
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Xing Wen
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Hongwei Guo
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
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18
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Staples MI, Frazer C, Fawzi NL, Bennett RJ. Phase separation in fungi. Nat Microbiol 2023; 8:375-386. [PMID: 36782025 PMCID: PMC10081517 DOI: 10.1038/s41564-022-01314-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
Phase separation, in which macromolecules partition into a concentrated phase that is immiscible with a dilute phase, is involved with fundamental cellular processes across the tree of life. We review the principles of phase separation and highlight how it impacts diverse processes in the fungal kingdom. These include the regulation of autophagy, cell signalling pathways, transcriptional circuits and the establishment of asymmetry in fungal cells. We describe examples of stable, phase-separated assemblies including membraneless organelles such as the nucleolus as well as transient condensates that also arise through phase separation and enable cells to rapidly and reversibly respond to important environmental cues. We showcase how research into phase separation in model yeasts, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe, in conjunction with that in plant and human fungal pathogens, such as Ashbya gossypii and Candida albicans, is continuing to enrich our understanding of fundamental molecular processes.
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Affiliation(s)
- Mae I Staples
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Corey Frazer
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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19
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Yukawa T, Bamba T, Matsuda M, Yoshida T, Inokuma K, Kim J, Won Lee J, Jin YS, Kondo A, Hasunuma T. Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnol Bioeng 2023; 120:511-523. [PMID: 36321324 DOI: 10.1002/bit.28278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
To realize lignocellulose-based bioeconomy, efficient conversion of xylose into valuable chemicals by microbes is necessary. Xylose oxidative pathways that oxidize xylose into xylonate can be more advantageous than conventional xylose assimilation pathways because of fewer reaction steps without loss of carbon and ATP. Moreover, commodity chemicals like 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone can be produced from the intermediates of xylose oxidative pathway. However, successful implementations of xylose oxidative pathway in yeast have been hindered because of the secretion and accumulation of xylonate which is a key intermediate of the pathway, leading to low yield of target product. Here, high-yield production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. Specifically, 3,4-dihydroxybutyrate biosynthetic pathway was established in yeast through deletion of ADH6 and overexpression of yneI. Also, inspired by the mismatch of pH between host strain and key enzyme of XylD, alkaline fermentations (pH ≥ 7.0) were performed to minimize xylonate accumulation. Under the alkaline conditions, xylonate was re-assimilated by engineered yeast and combined product yields of 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone resulted in 0.791 mol/mol-xylose, which is highest compared with previous study. These results shed light on the utility of the xylose oxidative pathway in yeast.
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Affiliation(s)
- Takahiro Yukawa
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Jungyeon Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jae Won Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Engineering Biology Research Center, Kobe University, Kobe, Japan.,RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
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20
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Gelova SP, Chan K. Mutagenesis induced by protonation of single-stranded DNA is linked to glycolytic sugar metabolism. Mutat Res 2023; 826:111814. [PMID: 36634476 DOI: 10.1016/j.mrfmmm.2023.111814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
Mutagenesis can be thought of as random, in the sense that the occurrence of each mutational event cannot be predicted with precision in space or time. However, when sufficiently large numbers of mutations are analyzed, recurrent patterns of base changes called mutational signatures can be identified. To date, some 60 single base substitution or SBS signatures have been derived from analysis of cancer genomics data. We recently reported that the ubiquitous signature SBS5 matches the pattern of single nucleotide polymorphisms (SNPs) in humans and has analogs in many species. Using a temperature-sensitive single-stranded DNA (ssDNA) mutation reporter system, we also showed that a similar mutational pattern in yeast is dependent on error-prone translesion DNA synthesis (TLS) and glycolytic sugar metabolism. Here, we further investigated mechanisms that are responsible for this form of mutagenesis in yeast. We first confirmed that excess sugar metabolism leads to increased mutation rate, which was detectable by fluctuation assay. Since glycolysis is known to produce excess protons, we then investigated the effects of experimental manipulations on pH and mutagenesis. We hypothesized that yeast metabolizing 8% glucose would produce more excess protons than cells metabolizing 2% glucose. Consistent with this, cells metabolizing 8% glucose had lower intracellular and extracellular pH values. Similarly, deletion of vma3 (encoding a vacuolar H+-ATPase subunit) increased mutagenesis. We also found that treating cells with edelfosine (which renders membranes more permeable, including to protons) or culturing in low pH media increased mutagenesis. Analysis of the mutational pattern attributable to 20 µM edelfosine treatment revealed similarity to the SBS5-like TLS- and glycolysis-dependant mutational patterns previously observed in ssDNA. Altogether, our results agree with multiple biochemical studies showing that protonation of nitrogenous bases can alter base pairing so as to stabilize some mispairs, and shed new light on a common form of intrinsic mutagenesis.
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Affiliation(s)
- Suzana P Gelova
- University of Ottawa Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada; Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, Ontario N0R 1G0, Canada
| | - Kin Chan
- University of Ottawa Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.
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21
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Žunar B, Ito T, Mosrin C, Sugahara Y, Bénédetti H, Guégan R, Vallée B. Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae. Biomater Res 2022; 26:85. [PMID: 36539854 PMCID: PMC9769040 DOI: 10.1186/s40824-022-00337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. METHODS We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. RESULTS When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. CONCLUSIONS F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.
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Affiliation(s)
- Bojan Žunar
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France ,grid.4808.40000 0001 0657 4636Department of Chemistry and Biochemistry, Laboratory for Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Taiga Ito
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Christine Mosrin
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Yoshiyuki Sugahara
- grid.5290.e0000 0004 1936 9975Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Hélène Bénédetti
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
| | - Régis Guégan
- grid.5290.e0000 0004 1936 9975Global Center for Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555 Japan ,grid.112485.b0000 0001 0217 6921Institut des Sciences de la Terre d’Orléans (ISTO), UMR 7327, CNRS-Université d’Orléans, 1A Rue de la Férollerie, 45071 Orléans, Cedex 2 France
| | - Béatrice Vallée
- grid.4444.00000 0001 2112 9282Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, Cedex 2 France
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22
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Delzell S, Nelson SW, Frost MP, Klingbeil MM. Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Polymerase Domain Insertion That Confers Dominant Exonuclease Activity. Biochemistry 2022; 61:2751-2765. [PMID: 36399653 PMCID: PMC9731263 DOI: 10.1021/acs.biochem.2c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/31/2022] [Indexed: 11/19/2022]
Abstract
Trypanosoma brucei and related parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of maxicircles and minicircles. The kDNA structure and replication mechanism are divergent and essential for parasite survival. POLIB is one of three Family A DNA polymerases independently essential to maintain the kDNA network. However, the division of labor among the paralogs, particularly which might be a replicative, proofreading enzyme, remains enigmatic. De novo modeling of POLIB suggested a structure that is divergent from all other Family A polymerases, in which the thumb subdomain contains a 369 amino acid insertion with homology to DEDDh DnaQ family 3'-5' exonucleases. Here we demonstrate recombinant POLIB 3'-5' exonuclease prefers DNA vs RNA substrates and degrades single- and double-stranded DNA nonprocessively. Exonuclease activity prevails over polymerase activity on DNA substrates at pH 8.0, while DNA primer extension is favored at pH 6.0. Mutations that ablate POLIB polymerase activity slow the exonuclease rate suggesting crosstalk between the domains. We show that POLIB extends an RNA primer more efficiently than a DNA primer in the presence of dNTPs but does not incorporate rNTPs efficiently using either primer. Immunoprecipitation of Pol I-like paralogs from T. brucei corroborates the pH selectivity and RNA primer preferences of POLIB and revealed that the other paralogs efficiently extend a DNA primer. The enzymatic properties of POLIB suggest this paralog is not a replicative kDNA polymerase, and the noncanonical polymerase domain provides another example of exquisite diversity among DNA polymerases for specialized function.
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Affiliation(s)
- Stephanie
B. Delzell
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
| | - Scott W. Nelson
- Roy
J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Matthew P. Frost
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
| | - Michele M. Klingbeil
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
- The
Institute for Applied Life Sciences, University
of Massachusetts, Amherst, Massachusetts01003, United States
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23
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Di Gregorio E, Israel S, Staelens M, Tankel G, Shankar K, Tuszyński JA. The distinguishing electrical properties of cancer cells. Phys Life Rev 2022; 43:139-188. [PMID: 36265200 DOI: 10.1016/j.plrev.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
In recent decades, medical research has been primarily focused on the inherited aspect of cancers, despite the reality that only 5-10% of tumours discovered are derived from genetic causes. Cancer is a broad term, and therefore it is inaccurate to address it as a purely genetic disease. Understanding cancer cells' behaviour is the first step in countering them. Behind the scenes, there is a complicated network of environmental factors, DNA errors, metabolic shifts, and electrostatic alterations that build over time and lead to the illness's development. This latter aspect has been analyzed in previous studies, but how the different electrical changes integrate and affect each other is rarely examined. Every cell in the human body possesses electrical properties that are essential for proper behaviour both within and outside of the cell itself. It is not yet clear whether these changes correlate with cell mutation in cancer cells, or only with their subsequent development. Either way, these aspects merit further investigation, especially with regards to their causes and consequences. Trying to block changes at various levels of occurrence or assisting in their prevention could be the key to stopping cells from becoming cancerous. Therefore, a comprehensive understanding of the current knowledge regarding the electrical landscape of cells is much needed. We review four essential electrical characteristics of cells, providing a deep understanding of the electrostatic changes in cancer cells compared to their normal counterparts. In particular, we provide an overview of intracellular and extracellular pH modifications, differences in ionic concentrations in the cytoplasm, transmembrane potential variations, and changes within mitochondria. New therapies targeting or exploiting the electrical properties of cells are developed and tested every year, such as pH-dependent carriers and tumour-treating fields. A brief section regarding the state-of-the-art of these therapies can be found at the end of this review. Finally, we highlight how these alterations integrate and potentially yield indications of cells' malignancy or metastatic index.
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Affiliation(s)
- Elisabetta Di Gregorio
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Autem Therapeutics, 35 South Main Street, Hanover, 03755, NH, USA
| | - Simone Israel
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Autem Therapeutics, 35 South Main Street, Hanover, 03755, NH, USA
| | - Michael Staelens
- Department of Physics, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, T6G 2E1, AB, Canada
| | - Gabriella Tankel
- Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, ON, Canada
| | - Karthik Shankar
- Department of Electrical & Computer Engineering, University of Alberta, 9211 116 Street NW, Edmonton, T6G 1H9, AB, Canada
| | - Jack A Tuszyński
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, Corso Duca degli Abruzzi, 24, Torino, 10129, TO, Italy; Department of Physics, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, T6G 2E1, AB, Canada; Department of Oncology, University of Alberta, 11560 University Avenue, Edmonton, T6G 1Z2, AB, Canada.
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24
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Chang H, Bennett AM, Cameron WD, Floro E, Au A, McFaul CM, Yip CM, Rocheleau JV. Targeting Apollo-NADP + to Image NADPH Generation in Pancreatic Beta-Cell Organelles. ACS Sens 2022; 7:3308-3317. [PMID: 36269889 PMCID: PMC9706804 DOI: 10.1021/acssensors.2c01174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NADPH/NADP+ redox state supports numerous reactions related to cell growth and survival; yet the full impact is difficult to appreciate due to organelle compartmentalization of NADPH and NADP+. To study glucose-stimulated NADPH production in pancreatic beta-cell organelles, we targeted the Apollo-NADP+ sensor by first selecting the most pH-stable version of the single-color sensor. We subsequently targeted mTurquoise2-Apollo-NADP+ to various organelles and confirmed activity in the cytoplasm, mitochondrial matrix, nucleus, and peroxisome. Finally, we measured the glucose- and glutamine-stimulated NADPH responses by single- and dual-color imaging of the targeted sensors. Overall, we developed multiple organelle-targeted Apollo-NADP+ sensors to reveal the prominent role of beta-cell mitochondria in determining NADPH production in the cytoplasm, nucleus, and peroxisome.
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Affiliation(s)
- Huntley
H. Chang
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Alex M. Bennett
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - William D. Cameron
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Eric Floro
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Aaron Au
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. McFaul
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Christopher M. Yip
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Jonathan V. Rocheleau
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada,Toronto
General Hospital Research Institute, University
Health Network, Toronto, Ontario M5G 2C4, Canada,Department
of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada,Banting
and Best Diabetes Centre, University of
Toronto, Toronto, Ontario M5G 2C4, Canada,
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25
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Dykstra JC, van Oort J, Yazdi AT, Vossen E, Patinios C, van der Oost J, Sousa DZ, Kengen SWM. Metabolic engineering of Clostridium autoethanogenum for ethyl acetate production from CO. Microb Cell Fact 2022; 21:243. [DOI: 10.1186/s12934-022-01964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Ethyl acetate is a bulk chemical traditionally produced via energy intensive chemical esterification. Microbial production of this compound offers promise as a more sustainable alternative process. So far, efforts have focused on using sugar-based feedstocks for microbial ester production, but extension to one-carbon substrates, such as CO and CO2/H2, is desirable. Acetogens present a promising microbial platform for the production of ethyl esters from these one-carbon substrates.
Results
We engineered the acetogen C. autoethanogenum to produce ethyl acetate from CO by heterologous expression of an alcohol acetyltransferase (AAT), which catalyzes the formation of ethyl acetate from acetyl-CoA and ethanol. Two AATs, Eat1 from Kluyveromyces marxianus and Atf1 from Saccharomyces cerevisiae, were expressed in C. autoethanogenum. Strains expressing Atf1 produced up to 0.2 mM ethyl acetate. Ethyl acetate production was barely detectable (< 0.01 mM) for strains expressing Eat1. Supplementation of ethanol was investigated as potential boost for ethyl acetate production but resulted only in a 1.5-fold increase (0.3 mM ethyl acetate). Besides ethyl acetate, C. autoethanogenum expressing Atf1 could produce 4.5 mM of butyl acetate when 20 mM butanol was supplemented to the growth medium.
Conclusions
This work offers for the first time a proof-of-principle that autotrophic short chain ester production from C1-carbon feedstocks is possible and offers leads on how this approach can be optimized in the future.
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26
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [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: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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27
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de Castro RJA, Rêgo MTAM, Brandão FS, Pérez ALA, De Marco JL, Poças-Fonseca MJ, Nichols C, Alspaugh JA, Felipe MSS, Alanio A, Bocca AL, Fernandes L. Engineered Fluorescent Strains of Cryptococcus neoformans: a Versatile Toolbox for Studies of Host-Pathogen Interactions and Fungal Biology, Including the Viable but Nonculturable State. Microbiol Spectr 2022; 10:e0150422. [PMID: 36005449 PMCID: PMC9603711 DOI: 10.1128/spectrum.01504-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/05/2022] [Indexed: 12/31/2022] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen known for its remarkable ability to infect and subvert phagocytes. This ability provides survival and persistence within the host and relies on phenotypic plasticity. The viable but nonculturable (VBNC) phenotype was recently described in C. neoformans, whose study is promising in understanding the pathophysiology of cryptococcosis. The use of fluorescent strains is improving host interaction research, but it is still underexploited. Here, we fused histone H3 or the poly(A) binding protein (Pab) to enhanced green fluorescent protein (eGFP) or mCherry, obtaining a set of C. neoformans transformants with different colors, patterns of fluorescence, and selective markers (hygromycin B resistance [Hygr] or neomycin resistance [Neor]). We validated their similarity to the parental strain in the stress response, the expression of virulence-related phenotypes, mating, virulence in Galleria mellonella, and survival within murine macrophages. PAB-GFP, the brightest transformant, was successfully applied for the analysis of phagocytosis by flow cytometry and fluorescence microscopy. Moreover, we demonstrated that an engineered fluorescent strain of C. neoformans was able to generate VBNC cells. GFP-tagged Pab1, a key regulator of the stress response, evidenced nuclear retention of Pab1 and the assembly of cytoplasmic stress granules, unveiling posttranscriptional mechanisms associated with dormant C. neoformans cells. Our results support that the PAB-GFP strain is a useful tool for research on C. neoformans. IMPORTANCE Cryptococcus neoformans is a human-pathogenic yeast that can undergo a dormant state and is responsible for over 180,000 deaths annually worldwide. We engineered a set of fluorescent transformants to aid in research on C. neoformans. A mutant with GFP-tagged Pab1 improved fluorescence-based techniques used in host interaction studies. Moreover, this mutant induced a viable but nonculturable phenotype and uncovered posttranscriptional mechanisms associated with dormant C. neoformans. The experimental use of fluorescent mutants may shed light on C. neoformans-host interactions and fungal biology, including dormant phenotypes.
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Affiliation(s)
- Raffael Júnio Araújo de Castro
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
- CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses et Antifongiques, Institut Pasteur, Paris, France
| | - Marco Túlio Aidar Mariano Rêgo
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Fabiana S. Brandão
- Faculty of Health Science, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Ana Laura Alfonso Pérez
- Department of Cell Biology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasilia, Federal District, Brazil
| | - Janice Lisboa De Marco
- Department of Cell Biology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasilia, Federal District, Brazil
| | - Marcio José Poças-Fonseca
- Department of Genetics and Morphology, Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Connie Nichols
- Duke University School of Medicine, Department of Medicine, Durham, North Carolina, USA
| | - J. Andrew Alspaugh
- Duke University School of Medicine, Department of Medicine, Durham, North Carolina, USA
| | - Maria Sueli S. Felipe
- Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Brasília, Federal District, Brazil
| | - Alexandre Alanio
- CNRS, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses et Antifongiques, Institut Pasteur, Paris, France
- Laboratoire de Mycologie et Parasitologie, AP-HP, Hôpital Saint Louis, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
| | - Larissa Fernandes
- Laboratory of Applied Immunology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Brasília, Federal District, Brazil
- Faculty of Ceilândia, Campus UnB Ceilândia, University of Brasília, Ceilândia Sul, Brasília, Federal District, Brazil
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28
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Regulation of yeast Snf1 (AMPK) by a polyhistidine containing pH sensing module. iScience 2022; 25:105083. [PMID: 36147951 PMCID: PMC9486060 DOI: 10.1016/j.isci.2022.105083] [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: 01/31/2022] [Revised: 08/12/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Cellular regulation of pH is crucial for internal biological processes and for the import and export of ions and nutrients. In the yeast Saccharomyces cerevisiae, the major proton pump (Pma1) is regulated by glucose. Glucose is also an inhibitor of the energy sensor Snf1/AMPK, which is conserved in all eukaryotes. Here, we demonstrate that a poly-histidine (polyHIS) tract in the pre-kinase region (PKR) of Snf1 functions as a pH-sensing module (PSM) and regulates Snf1 activity. This regulation is independent from, and unaffected by, phosphorylation at T210, the major regulatory control of Snf1, but is controlled by the Pma1 plasma-membrane proton pump. By examining the PKR from additional yeast species, and by varying the number of histidines in the PKR, we determined that the polyHIS functions progressively. This regulation mechanism links the activity of a key enzyme with the metabolic status of the cell at any given moment.
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29
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Luzia L, Lao‐Martil D, Savakis P, van Heerden J, van Riel N, Teusink B. pH dependencies of glycolytic enzymes of yeast under in vivo-like assay conditions. FEBS J 2022; 289:6021-6037. [PMID: 35429225 PMCID: PMC9790636 DOI: 10.1111/febs.16459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
Under carbon source transitions, the intracellular pH of Saccharomyces cerevisiae is subject to change. Dynamics in pH modulate the activity of the glycolytic enzymes, resulting in a change in glycolytic flux and ultimately cell growth. To understand how pH affects the global behavior of glycolysis and ethanol fermentation, we measured the activity of the glycolytic and fermentative enzymes in S. cerevisiae under in vivo-like conditions at different pH. We demonstrate that glycolytic enzymes exhibit differential pH dependencies, and optima, in the pH range observed during carbon source transitions. The forward reaction of GAPDH shows the highest decrease in activity, 83%, during a simulated feast/famine regime upon glucose removal (cytosolic pH drop from 7.1 to 6.4). We complement our biochemical characterization of the glycolytic enzymes by fitting the Vmax to the progression curves of product formation or decay over time. The fitting analysis shows that the observed changes in enzyme activities require changes in Vmax , but changes in Km cannot be excluded. Our study highlights the relevance of pH as a key player in metabolic regulation and provides a large set of quantitative data that can be explored to improve our understanding of metabolism in dynamic environments.
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Affiliation(s)
| | | | | | | | - Natal van Riel
- Department of Biomedical EngineeringTU EindhovenNetherlands
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30
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Jin X, Zhou M, Chen S, Li D, Cao X, Liu B. Effects of pH alterations on stress- and aging-induced protein phase separation. Cell Mol Life Sci 2022; 79:380. [PMID: 35750966 PMCID: PMC9232405 DOI: 10.1007/s00018-022-04393-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 01/18/2023]
Abstract
Upon stress challenges, proteins/RNAs undergo liquid–liquid phase separation (LLPS) to fine-tune cell physiology and metabolism to help cells adapt to adverse environments. The formation of LLPS has been recently linked with intracellular pH, and maintaining proper intracellular pH homeostasis is known to be essential for the survival of organisms. However, organisms are constantly exposed to diverse stresses, which are accompanied by alterations in the intracellular pH. Aging processes and human diseases are also intimately linked with intracellular pH alterations. In this review, we summarize stress-, aging-, and cancer-associated pH changes together with the mechanisms by which cells regulate cytosolic pH homeostasis. How critical cell components undergo LLPS in response to pH alterations is also discussed, along with the functional roles of intracellular pH fluctuation in the regulation of LLPS. Further studies investigating the interplay of pH with other stressors in LLPS regulation and identifying protein responses to different pH levels will provide an in-depth understanding of the mechanisms underlying pH-driven LLPS in cell adaptation. Moreover, deciphering aging and disease-associated pH changes that influence LLPS condensate formation could lead to a deeper understanding of the functional roles of biomolecular condensates in aging and aging-related diseases.
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Affiliation(s)
- Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Min Zhou
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shuxin Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Danqi Li
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xiuling Cao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China. .,Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90, Goteborg, Sweden. .,Center for Large-Scale Cell-Based Screening, Faculty of Science, University of Gothenburg, Medicinaregatan 9C, 413 90, Goteborg, Sweden.
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31
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Harbauer AB, Schneider A, Wohlleber D. Analysis of Mitochondria by Single-Organelle Resolution. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:1-16. [PMID: 35303775 DOI: 10.1146/annurev-anchem-061020-111722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cellular organelles are highly specialized compartments with distinct functions. With the increasing resolution of detection methods, it is becoming clearer that same organelles may have different functions or properties not only within different cell populations of a tissue but also within the same cell. Dysfunction or altered function affects the organelle itself and may also lead to malignancies or undesirable cell death. To understand cellular function or dysfunction, it is therefore necessary to analyze cellular components at the single-organelle level. Here, we review the recent advances in analyzing cellular function at single-organelle resolution using high-parameter flow cytometry or multicolor confocal microscopy. We focus on the analysis of mitochondria, as they are organelles at the crossroads of various cellular signaling pathways and functions. However, most of the applied methods/technologies are transferable to any other organelle, such as the endoplasmic reticulum, lysosomes, or peroxisomes.
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Affiliation(s)
- Angelika B Harbauer
- Max Planck Institute of Neurobiology, Martinsried, Germany;
- Institute of Neuronal Cell Biology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Annika Schneider
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany; ,
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32
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Yang YM, Karbstein K. The chaperone Tsr2 regulates Rps26 release and reincorporation from mature ribosomes to enable a reversible, ribosome-mediated response to stress. SCIENCE ADVANCES 2022; 8:eabl4386. [PMID: 35213229 PMCID: PMC8880767 DOI: 10.1126/sciadv.abl4386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/13/2022] [Indexed: 05/04/2023]
Abstract
Although ribosome assembly is quality controlled to maintain protein homeostasis, different ribosome populations have been described. How these form, especially under stress conditions that affect energy levels and stop the energy-intensive production of ribosomes, remains unknown. Here, we demonstrate how a physiologically relevant ribosome population arises during high Na+, sorbitol, or pH stress via dissociation of Rps26 from fully assembled ribosomes to enable a translational response to these stresses. The chaperone Tsr2 releases Rps26 in the presence of high Na+ or pH in vitro and is required for Rps26 release in vivo. Moreover, Tsr2 stores free Rps26 and promotes reincorporation of the protein, thereby repairing the subunit after the Na+ stress subsides. Our data implicate a residue in Rps26 involved in Diamond Blackfan Anemia in mediating the effects of Na+. These data demonstrate how different ribosome populations can arise rapidly, without major energy input and without bypass of quality control mechanisms.
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Affiliation(s)
- Yoon-Mo Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- HHMI Faculty Scholar, Chevy Chase, MD 20815, USA
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33
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Regulation of the Leucine Metabolism in Mortierella alpina. J Fungi (Basel) 2022; 8:jof8020196. [PMID: 35205950 PMCID: PMC8880518 DOI: 10.3390/jof8020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer.
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34
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Gutierrez JI, Brittingham GP, Karadeniz YB, Tran KD, Dutta A, Holehouse AS, Peterson CL, Holt LJ. SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence. eLife 2022; 11:70344. [PMID: 35129437 PMCID: PMC8890752 DOI: 10.7554/elife.70344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.
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Affiliation(s)
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, United States
| | - Yonca B Karadeniz
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Kathleen D Tran
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, United States
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35
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Acevedo Restrepo I, Blandón Naranjo L, Hoyos-Arbeláez J, Víctor Vázquez M, Gutiérrez Granados S, Palacio J. Electrochemical determination of Saccharomyces cerevisiae sp using glassy carbon electrodes modified with oxidized multi-walled carbon nanotubes dispersed in water –Nafion®. Curr Res Food Sci 2022; 5:351-359. [PMID: 35198994 PMCID: PMC8842009 DOI: 10.1016/j.crfs.2022.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Isabel Acevedo Restrepo
- Interdiscliplinary Group of Molecular Studies (GIEM), Chemistry Institute, Faculty of Exact and Natural Sciences, Universidad de Antioquia, Street 67 No. 53-108, Medellín, Colombia
- Corresponding author.
| | - Lucas Blandón Naranjo
- Interdiscliplinary Group of Molecular Studies (GIEM), Chemistry Institute, Faculty of Exact and Natural Sciences, Universidad de Antioquia, Street 67 No. 53-108, Medellín, Colombia
| | - Jorge Hoyos-Arbeláez
- BIOALI Research Group, Food Department, Faculty of Pharmaceutical and Food Sciences, Universidad de Antioquia, Street 67 No. 53-108, Medellín, Colombia
| | - Mario Víctor Vázquez
- Interdiscliplinary Group of Molecular Studies (GIEM), Chemistry Institute, Faculty of Exact and Natural Sciences, Universidad de Antioquia, Street 67 No. 53-108, Medellín, Colombia
| | - Silvia Gutiérrez Granados
- Department of Chemistry, Division of Exact and Natural Sciences, Campus Guanajuato, Universidad de Guanajuato, Cerro de la Venada s/n, Colonia Pueblito de Rocha, 36040, Guanajuato, Mexico
| | - Juliana Palacio
- Materials Science Research Group, Chemistry Institute, Faculty of Exact and Natural Sciences, Universidad de Antioquia, Street 70 No. 52-21, Medellín, Colombia
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36
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Jethva J, Schmidt RR, Sauter M, Selinski J. Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020205. [PMID: 35050092 PMCID: PMC8780655 DOI: 10.3390/plants11020205] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 05/09/2023]
Abstract
Fluctuations in oxygen (O2) availability occur as a result of flooding, which is periodically encountered by terrestrial plants. Plant respiration and mitochondrial energy generation rely on O2 availability. Therefore, decreased O2 concentrations severely affect mitochondrial function. Low O2 concentrations (hypoxia) induce cellular stress due to decreased ATP production, depletion of energy reserves and accumulation of metabolic intermediates. In addition, the transition from low to high O2 in combination with light changes-as experienced during re-oxygenation-leads to the excess formation of reactive oxygen species (ROS). In this review, we will update our current knowledge about the mechanisms enabling plants to adapt to low-O2 environments, and how to survive re-oxygenation. New insights into the role of mitochondrial retrograde signaling, chromatin modification, as well as moonlighting proteins and mitochondrial alternative electron transport pathways (and their contribution to low O2 tolerance and survival of re-oxygenation), are presented.
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Affiliation(s)
- Jay Jethva
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Romy R. Schmidt
- Department of Plant Biotechnology, Faculty of Biology, University of Bielefeld, D-33615 Bielefeld, Germany;
| | - Margret Sauter
- Department of Plant Developmental Biology and Plant Physiology, Faculty of Mathematics and Natural Sciences, Botanical Institute, Christian-Albrechts University, D-24118 Kiel, Germany; (J.J.); (M.S.)
| | - Jennifer Selinski
- Department of Plant Cell Biology, Botanical Institute, Faculty of Mathematics and Natural Sciences, Christian-Albrechts University, D-24118 Kiel, Germany
- Correspondence: ; Tel.: +49-(0)431-880-4245
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Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome. Proc Natl Acad Sci U S A 2022; 119:2023328119. [PMID: 34969852 PMCID: PMC8740578 DOI: 10.1073/pnas.2023328119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that produces an oxidant as byproduct, hydrogen peroxide (H2O2). While much is known about the necessity of scavenging O2•−, it is less clear what the physiological roles of Sod1-derived H2O2 are. We discovered that Sod1-derived H2O2 plays an important role in antioxidant defense by stimulating the production of NADPH, a vital cellular reductant required for reactive oxygen species scavenging enzymes, as well as redox regulating a large network of enzymes. Cu/Zn superoxide dismutase (Sod1) is a highly conserved and abundant antioxidant enzyme that detoxifies superoxide (O2•−) by catalyzing its conversion to dioxygen (O2) and hydrogen peroxide (H2O2). Using Saccharomyces cerevisiae and mammalian cells, we discovered that a major aspect of the antioxidant function of Sod1 is to integrate O2 availability to promote NADPH production. The mechanism involves Sod1-derived H2O2 oxidatively inactivating the glycolytic enzyme, GAPDH, which in turn reroutes carbohydrate flux to the oxidative phase of the pentose phosphate pathway (oxPPP) to generate NADPH. The aerobic oxidation of GAPDH is dependent on and rate-limited by Sod1. Thus, Sod1 senses O2 via O2•− to balance glycolytic and oxPPP flux, through control of GAPDH activity, for adaptation to life in air. Importantly, this mechanism for Sod1 antioxidant activity requires the bulk of cellular Sod1, unlike for its role in protection against O2•− toxicity, which only requires <1% of total Sod1. Using mass spectrometry, we identified proteome-wide targets of Sod1-dependent redox signaling, including numerous metabolic enzymes. Altogether, Sod1-derived H2O2 is important for antioxidant defense and a master regulator of metabolism and the thiol redoxome.
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38
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Nazir R, Mohsin M, Siddiqi TO. Real time optical detection of gold in living cells through genetically-encoded probe. RSC Adv 2022; 12:23193-23203. [PMID: 36090423 PMCID: PMC9380193 DOI: 10.1039/d2ra02574d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
To study the efflux of gold (Au) in living cells, a genetically encoded fluorescence resonance energy transfer (FRET)-based sensor has been developed. The gold-sensing domain GolB from Salmonella typhimurium has been fused to the N- and C-termini of the FRET pair enhanced cyan fluorescent protein (ECFP) and Venus respectively. In living cells, this probe is highly selective and sensitive to gold and it can withstand changes in variable pH ranges. GolSeN-25, the most efficient sensor variant, binds gold with an affinity (Kd) of 0.3 × 10−6 M, covering gold concentrations of nM to μM, and can be used for non-invasive real-time in vivo gold measurement in living cells. A simple and sensitive FRET probe was designed for the detection of gold with high selectivity and can be applied to the analysis of real samples. To study the efflux of gold (Au) in living cells, a genetically encoded fluorescence resonance energy transfer (FRET)-based sensor has been developed.![]()
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Affiliation(s)
- Rahila Nazir
- Metabolic Engineering Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Mohd Mohsin
- Metabolic Engineering Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Tariq Omar Siddiqi
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
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39
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In Vivo Monitoring of Cytosolic pH Using the Ratiometric pH Sensor pHluorin. Methods Mol Biol 2022; 2391:99-107. [PMID: 34686980 DOI: 10.1007/978-1-0716-1795-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytosolic pH (pHcyt) is a key factor controlling cell fate. The genetically encoded pH-sensor pHluorin has proven highly valuable for studies on pHcyt in many living organisms. pHluorin displays a bimodal excitation spectrum with peaks at 395 nm and 475 nm, which is dependent on pH. Here we describe two different protocols for determining pHcyt in the soil-borne fungal pathogen Fusarium oxysporum, based either on population or single-cell analysis.
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40
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Fontana NA, Rosse AD, Watts A, Coelho PSR, Costa-Filho AJ. In vivo observation of amyloid-like fibrils produced under stress. Int J Biol Macromol 2021; 199:42-50. [PMID: 34942208 DOI: 10.1016/j.ijbiomac.2021.12.065] [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: 08/12/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
The participation of amyloids in neurodegenerative diseases and functional processes has triggered the quest for methods allowing their direct detection in vivo. Despite the plethora of data, those methods are still lacking. The autofluorescence from the extended β-sheets of amyloids is here used to follow fibrillation of S. cerevisiae Golgi Reassembly and Stacking Protein (Grh1). Grh1 has been implicated in starvation-triggered unconventional protein secretion (UPS), and here its participation also in heat shock response (HSR) is suggested. Fluorescence Lifetime Imaging (FLIM) is used to detect fibril autofluorescence in cells (E. coli and yeast) under stress (starvation and higher temperature). The formation of Grh1 large complexes under stress is further supported by size exclusion chromatography and ultracentrifugation. The data show for the first time in vivo detection of amyloids without the use of extrinsic probes as well as bring new perspectives on the participation of Grh1 in UPS and HSR.
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Affiliation(s)
- Natália A Fontana
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ariane D Rosse
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Paulo S R Coelho
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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41
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Rieger B, Arroum T, Borowski M, Villalta J, Busch KB. Mitochondrial F 1 F O ATP synthase determines the local proton motive force at cristae rims. EMBO Rep 2021; 22:e52727. [PMID: 34595823 PMCID: PMC8647149 DOI: 10.15252/embr.202152727] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 12/25/2022] Open
Abstract
The classical view of oxidative phosphorylation is that a proton motive force (PMF) generated by the respiratory chain complexes fuels ATP synthesis via ATP synthase. Yet, under glycolytic conditions, ATP synthase in its reverse mode also can contribute to the PMF. Here, we dissected these two functions of ATP synthase and the role of its inhibitory factor 1 (IF1) under different metabolic conditions. pH profiles of mitochondrial sub-compartments were recorded with high spatial resolution in live mammalian cells by positioning a pH sensor directly at ATP synthase's F1 and FO subunits, complex IV and in the matrix. Our results clearly show that ATP synthase activity substantially controls the PMF and that IF1 is essential under OXPHOS conditions to prevent reverse ATP synthase activity due to an almost negligible ΔpH. In addition, we show how this changes lateral, transmembrane, and radial pH gradients in glycolytic and respiratory cells.
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Affiliation(s)
- Bettina Rieger
- Institute of Molecular Cell BiologySchool of BiologyUniversity of MünsterMünsterGermany
| | - Tasnim Arroum
- Institute of Molecular Cell BiologySchool of BiologyUniversity of MünsterMünsterGermany
| | - Marie‐Theres Borowski
- Institute of Molecular Cell BiologySchool of BiologyUniversity of MünsterMünsterGermany
| | - Jimmy Villalta
- Institute of Molecular Cell BiologySchool of BiologyUniversity of MünsterMünsterGermany
| | - Karin B Busch
- Institute of Molecular Cell BiologySchool of BiologyUniversity of MünsterMünsterGermany
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42
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Hansen JM, Horowitz A, Lynch EM, Farrell DP, Quispe J, DiMaio F, Kollman JM. Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. eLife 2021; 10:73368. [PMID: 34734801 PMCID: PMC8641951 DOI: 10.7554/elife.73368] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
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Affiliation(s)
- Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, United States.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, United States
| | - Avital Horowitz
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel P Farrell
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, United States
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43
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Fedotova EI, Dolgacheva LP, Abramov AY, Berezhnov AV. Lactate and Pyruvate Activate Autophagy and Mitophagy that Protect Cells in Toxic Model of Parkinson's Disease. Mol Neurobiol 2021; 59:177-190. [PMID: 34642892 DOI: 10.1007/s12035-021-02583-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Intracellular quality control regulated by autophagy process is important for maintenance of cellular homeostasis. Deregulation of autophagy and more specifically mitophagy leads to accumulation of the misfolded proteins and damaged mitochondria that in turn leads to the cell loss. Alteration of autophagy and mitophagy has shown to be involved in the number of disorders including neurodegenerative diseases. Autophagy and mitophagy could be activated by short-time acidification of the cytosol; however, most of the compounds which can induce it are toxic. Here, we tested several organic compounds which are involved in cellular metabolism on their ability to change intracellular pH and induce mitophagy/autophagy. We have found that lactate and pyruvate are able to reduce intracellular pH in non-toxic concentrations. Short-term (2 h) and long-term (24 h) incubation of the cells with lactate and pyruvateinduced mitophagy and autophagy. Incubation of the SH-SY5Y cells or primary neurons and astrocytes with lactate or pyruvate also activated mitophagy and autophagy after MPP + treatment that led to recovery of mitochondrial function and protection of these cells against apoptotic and necrotic death. Thus, pyruvate- or lactate-induced acidification of cytosol activates cell protective mitophagy and autophagy.
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Affiliation(s)
- Evgeniya I Fedotova
- Institute of Cell Biophysics of the Russian Academy of Sciences, 3 Institutskaya St., 142290, Pushchino, Russia.,Cell Physiology and Pathology Laboratory, Orel State University, 29 Naugorskoe Highway, 302020, Orel, Russia
| | - Ludmila P Dolgacheva
- Institute of Cell Biophysics of the Russian Academy of Sciences, 3 Institutskaya St., 142290, Pushchino, Russia
| | - Andrey Y Abramov
- Cell Physiology and Pathology Laboratory, Orel State University, 29 Naugorskoe Highway, 302020, Orel, Russia.,Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alexey V Berezhnov
- Institute of Cell Biophysics of the Russian Academy of Sciences, 3 Institutskaya St., 142290, Pushchino, Russia. .,Cell Physiology and Pathology Laboratory, Orel State University, 29 Naugorskoe Highway, 302020, Orel, Russia.
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44
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Coordinated glucose-induced Ca 2+ and pH responses in yeast Saccharomyces cerevisiae. Cell Calcium 2021; 100:102479. [PMID: 34610487 DOI: 10.1016/j.ceca.2021.102479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Ca2+ and pH homeostasis are closely intertwined and this interrelationship is crucial in the cells' ability to adapt to varying environmental conditions. To further understand this Ca2+-pH link, cytosolic Ca2+ was monitored using the aequorin-based bioluminescent assay in parallel with fluorescence reporter-based assays to monitor plasma membrane potentials and intracellular (cytosolic and vacuolar) pH in yeast Saccharomyces cerevisiae. At external pH 5, starved yeast cells displayed depolarized membrane potentials and responded to glucose re-addition with small Ca2+ transients accompanied by cytosolic alkalinization and profound vacuolar acidification. In contrast, starved cells at external pH 7 were hyperpolarized and glucose re-addition induced large Ca2+ transients and vacuolar alkalinization. In external Ca2+-free medium, glucose-induced pH responses were not affected but Ca2+ transients were abolished, indicating that the intracellular [Ca2+] increase was not prerequisite for activation of the two primary proton pumps, being Pma1 at the plasma membrane and the vacuolar and Golgi localized V-ATPases. A reduction in Pma1 expression resulted in membrane depolarization and reduced Ca2+ transients, indicating that the membrane hyperpolarization generated by Pma1 activation governed the Ca2+ influx that is associated with glucose-induced Ca2+ transients. Loss of V-ATPase activity through concanamycin A inhibition did not alter glucose-induced cytosolic pH responses but affected vacuolar pH changes and Ca2+ transients, indicating that the V-ATPase established vacuolar proton gradient is substantial for organelle H+/Ca2+ exchange. Finally, a systematic analysis of yeast deletion strains allowed us to reveal an essential role for both the vacuolar H+/Ca2+ exchanger Vcx1 and the Golgi exchanger Gdt1 in the dissipation of intracellular Ca2+.
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45
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Wang P, Li C, Li X, Huang W, Wang Y, Wang J, Zhang Y, Yang X, Yan X, Wang Y, Zhou Z. Complete biosynthesis of the potential medicine icaritin by engineered Saccharomyces cerevisiae and Escherichia coli. Sci Bull (Beijing) 2021; 66:1906-1916. [PMID: 36654400 DOI: 10.1016/j.scib.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/12/2020] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
Icaritin is a prenylflavonoid present in the Chinese herbal medicinal plant Epimedium spp. and is under investigation in a phase III clinical trial for advanced hepatocellular carcinoma. Here, we report the biosynthesis of icaritin from glucose by engineered microbial strains. We initially designed an artificial icaritin biosynthetic pathway by identifying a novel prenyltransferase from the Berberidaceae-family species Epimedium sagittatum (EsPT2) that catalyzes the C8 prenylation of kaempferol to yield 8-prenlykaempferol and a novel methyltransferase GmOMT2 from soybean to transfer a methyl to C4'-OH of 8-prenlykaempferol to produce icaritin. We next introduced 11 heterologous genes and modified 12 native yeast genes to construct a yeast strain capable of producing 8-prenylkaempferol with high efficiency. GmOMT2 was sensitive to low pH and lost its activity when expressed in the yeast cytoplasm. By relocating GmOMT2 into mitochondria (higher pH than cytoplasm) of the 8-prenylkaempferol-producing yeast strain or co-culturing the 8-prenylkaempferol-producing yeast with an Escherichia coli strain expressing GmOMT2, we obtained icaritin yields of 7.2 and 19.7 mg/L, respectively. Beyond the characterizing two previously unknown plant enzymes and conducting the first biosynthesis of icaritin from glucose, we describe two strategies of overcoming the widespread issue of incompatible pH conditions encountered in basic and applied bioproduction research. Our findings will facilitate industrial-scale production of icaritin and other prenylflavonoids.
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Affiliation(s)
- Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chaojing Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodong Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiali Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaoman Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Center of Economic Botany/Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ying Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Center of Economic Botany/Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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46
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Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
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Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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47
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Salsaa M, Aziz K, Lazcano P, Schmidtke MW, Tarsio M, Hüttemann M, Reynolds CA, Kane PM, Greenberg ML. Valproate activates the Snf1 kinase in Saccharomyces cerevisiae by decreasing the cytosolic pH. J Biol Chem 2021; 297:101110. [PMID: 34428448 PMCID: PMC8449051 DOI: 10.1016/j.jbc.2021.101110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022] Open
Abstract
Valproate (VPA) is a widely used mood stabilizer, but its therapeutic mechanism of action is not understood. This knowledge gap hinders the development of more effective drugs with fewer side effects. Using the yeast model to elucidate the effects of VPA on cellular metabolism, we determined that the drug upregulated expression of genes normally repressed during logarithmic growth on glucose medium and increased levels of activated (phosphorylated) Snf1 kinase, the major metabolic regulator of these genes. VPA also decreased the cytosolic pH (pHc) and reduced glycolytic production of 2/3-phosphoglycerate. ATP levels and mitochondrial membrane potential were increased, and glucose-mediated extracellular acidification decreased in the presence of the drug, as indicated by a smaller glucose-induced shift in pH, suggesting that the major P-type proton pump Pma1 was inhibited. Interestingly, decreasing the pHc by omeprazole-mediated inhibition of Pma1 led to Snf1 activation. We propose a model whereby VPA lowers the pHc causing a decrease in glycolytic flux. In response, Pma1 is inhibited and Snf1 is activated, resulting in increased expression of normally repressed metabolic genes. These findings suggest a central role for pHc in regulating the metabolic program of yeast cells.
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Affiliation(s)
- Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Kerestin Aziz
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Michael W Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Christian A Reynolds
- Department of Emergency Medicine, School of Medicine, Wayne State University, Detroit, Michigan, USA; Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
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48
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Teixeira V, Martins TS, Prinz WA, Costa V. Target of Rapamycin Complex 1 (TORC1), Protein Kinase A (PKA) and Cytosolic pH Regulate a Transcriptional Circuit for Lipid Droplet Formation. Int J Mol Sci 2021; 22:9017. [PMID: 34445723 PMCID: PMC8396576 DOI: 10.3390/ijms22169017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Lipid droplets (LDs) are ubiquitous organelles that fulfill essential roles in response to metabolic cues. The identification of several neutral lipid synthesizing and regulatory protein complexes have propelled significant advance on the mechanisms of LD biogenesis in the endoplasmic reticulum (ER). However, our understanding of signaling networks, especially transcriptional mechanisms, regulating membrane biogenesis is very limited. Here, we show that the nutrient-sensing Target of Rapamycin Complex 1 (TORC1) regulates LD formation at a transcriptional level, by targeting DGA1 expression, in a Sit4-, Mks1-, and Sfp1-dependent manner. We show that cytosolic pH (pHc), co-regulated by the plasma membrane H+-ATPase Pma1 and the vacuolar ATPase (V-ATPase), acts as a second messenger, upstream of protein kinase A (PKA), to adjust the localization and activity of the major transcription factor repressor Opi1, which in turn controls the metabolic switch between phospholipid metabolism and lipid storage. Together, this work delineates hitherto unknown molecular mechanisms that couple nutrient availability and pHc to LD formation through a transcriptional circuit regulated by major signaling transduction pathways.
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Affiliation(s)
- Vitor Teixeira
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Telma S. Martins
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - William A. Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA;
| | - Vítor Costa
- Yeast Signalling Networks, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (T.S.M.); (V.C.)
- Yeast Signalling Networks, IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
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49
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Dong C, Shi Z, Huang L, Zhao H, Xu Z, Lian J. Cloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiae. Biotechnol Bioeng 2021; 118:4269-4277. [PMID: 34273106 DOI: 10.1002/bit.27896] [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: 01/09/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022]
Abstract
Mitochondrion is generally considered as the most promising subcellular organelle for compartmentalization engineering. Much progress has been made in reconstituting whole metabolic pathways in the mitochondria of yeast to harness the precursor pools (i.e., pyruvate and acetyl-CoA), bypass competing pathways, and minimize transportation limitations. However, only a few mitochondrial targeting sequences (MTSs) have been characterized (i.e., MTS of COX4), limiting the application of compartmentalization engineering for multigene biosynthetic pathways in the mitochondria of yeast. In the present study, based on the mitochondrial proteome, a total of 20 MTSs were cloned and the efficiency of these MTSs in targeting heterologous proteins, including the Escherichia coli FabI and enhanced green fluorescence protein (EGFP) into the mitochondria was evaluated by growth complementation and confocal microscopy. After systematic characterization, six of the well-performed MTSs were chosen for the colocalization of complete biosynthetic pathways into the mitochondria. As proof of concept, the full α-santalene biosynthetic pathway consisting of 10 expression cassettes capable of converting acetyl-coA to α-santalene was compartmentalized into the mitochondria, leading to a 3.7-fold improvement in the production of α-santalene. The newly characterized MTSs should contribute to the expanded metabolic engineering and synthetic biology toolbox for yeast mitochondrial compartmentalization engineering.
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Affiliation(s)
- Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhuwei Shi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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50
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Gao X, Xu K, Ahmad N, Qin L, Li C. Recent advances in engineering of microbial cell factories for intelligent pH regulation and tolerance. Biotechnol J 2021; 16:e2100151. [PMID: 34164941 DOI: 10.1002/biot.202100151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/12/2022]
Abstract
pH regulation is a serious concern in the industrial fermentation process as pH adjustment heavily utilizes acid/base and pollutes the environment. Under pH-stress conditions, microbial growth and production of valuable target products may be severely affected. Furthermore, some strains generating acidic or alkaline products require self pH regulation and increased tolerance against pH-stress. For pH control, synthetic biology has provided advanced engineering approaches to construct robust and more intelligent microbial strains, exhibiting tolerance to pH-stress to cope with limitations of pH regulation. This study reviewed the current progress of advanced strain evolution strategies to engineer pH-stress tolerant strains via synthetic biology. In addition, a large number of pH-responsive elements, including promoters, riboswitches, and some proteins have been investigated and applied for construction of pH-responsive genetic circuits and intelligent pH-responsive microbial strains.
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Affiliation(s)
- Xiaopeng Gao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China.,School of Life Science, Yan'an University, Shanxi, PR China
| | - Ke Xu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China.,Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Department of Life Science, Tangshan Normal University, Tangshan, PR China
| | - Nadeem Ahmad
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, PR China.,School of Life Science, Yan'an University, Shanxi, PR China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
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