1
|
McDonnell L, Evans S, Lu Z, Suchoronczak M, Leighton J, Ordeniza E, Ritchie B, Valado N, Walsh N, Antoney J, Wang C, Luna-Flores CH, Scott C, Speight R, Vickers CE, Peng B. Cyanamide-inducible expression of homing nuclease I- SceI for selectable marker removal and promoter characterisation in Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 9:820-827. [PMID: 39072146 PMCID: PMC11277796 DOI: 10.1016/j.synbio.2024.06.009] [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: 04/07/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
In synthetic biology, microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale. Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements, such as the galactose-inducible (GAL) promoter in S. cerevisiae. Here, we prototyped the cyanamide-induced I- SceI expression, which triggered double-strand DNA breaks (DSBs) for selectable marker removal. We further combined cyanamide-induced I- SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter substitution, which simplified the molecular cloning procedure for promoter characterisation. We then characterised three tetracycline-inducible promoters showing differential strength, a non-leaky β-estradiol-inducible promoter, cyanamide-inducible DDI2 promoter, bidirectional MAL32/MAL31 promoters, and five pairs of bidirectional GAL1/GAL10 promoters. Overall, alternative regulatory controls for genome engineering tools can be developed to facilitate genomic engineering for synthetic biology and metabolic engineering applications.
Collapse
Affiliation(s)
- Liam McDonnell
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Samuel Evans
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Zeyu Lu
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mitch Suchoronczak
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Jonah Leighton
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Eugene Ordeniza
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Blake Ritchie
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Nik Valado
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Niamh Walsh
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - James Antoney
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Chengqiang Wang
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong Province, 271018, People's Republic of China
| | - Carlos Horacio Luna-Flores
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, 2601, Australia
| | - Robert Speight
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia
| | - Claudia E. Vickers
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Bingyin Peng
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
2
|
Mahdizade AH, Hoseinnejad A, Ghazanfari M, Boozhmehrani MJ, Bahreiny SS, Abastabar M, Galbo R, Giuffrè L, Haghani I, Romeo O. The TAC1 Gene in Candida albicans: Structure, Function, and Role in Azole Resistance: A Mini-Review. Microb Drug Resist 2024; 30:288-296. [PMID: 38770776 DOI: 10.1089/mdr.2023.0334] [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] [Indexed: 05/22/2024] Open
Abstract
Candidiasis is a common fungal infection caused by Candida species, with Candida albicans being the most prevalent. Resistance to azole drugs, commonly used to treat Candida infections, poses a significant challenge. Transcriptional activator candidate 1 (TAC1) gene has emerged as a key player in regulating drug resistance in C. albicans. This review explores the structure and function of the TAC1 gene and its role in azole resistance. This gene encodes a transcription factor that controls the expression of genes involved in drug resistance, such as efflux pump genes (CDR1, CDR2, and MDR1) and ERG11. Mutations in TAC1 can increase these genes' expression and confer resistance to azoles. Various TAC1 gene mutations, mostly gain-of-function mutations, have been identified, which upregulate CDR1 and CDR2 expression, resulting in azole resistance. Understanding the mechanisms of azole resistance mediated by the TAC1 gene is crucial for the strategies in the effective antifungal development pipeline.
Collapse
Affiliation(s)
- Amir Hossein Mahdizade
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Akbar Hoseinnejad
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mona Ghazanfari
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Javad Boozhmehrani
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Medical Parasitology, Faculty of Medicine, Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Sobhan Bahreiny
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Abastabar
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Roberta Galbo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Letterio Giuffrè
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Iman Haghani
- Invasive Fungi Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| |
Collapse
|
3
|
Cheah LC, Liu L, Plan MR, Peng B, Lu Z, Schenk G, Vickers CE, Sainsbury F. Product Profiles of Promiscuous Enzymes Can be Altered by Controlling In Vivo Spatial Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303415. [PMID: 37750486 PMCID: PMC10646250 DOI: 10.1002/advs.202303415] [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: 05/26/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Enzyme spatial organization is an evolved mechanism for facilitating multi-step biocatalysis and can play an important role in the regulation of promiscuous enzymes. The latter function suggests that artificial spatial organization can be an untapped avenue for controlling the specificity of bioengineered metabolic pathways. A promiscuous terpene synthase (nerolidol synthase) is co-localized and spatially organized with the preceding enzyme (farnesyl diphosphate synthase) in a heterologous production pathway, via translational protein fusion and/or co-encapsulation in a self-assembling protein cage. Spatial organization enhances nerolidol production by ≈11- to ≈62-fold relative to unorganized enzymes. More interestingly, striking differences in the ratio of end products (nerolidol and linalool) are observed with each spatial organization approach. This demonstrates that artificial spatial organization approaches can be harnessed to modulate the product profiles of promiscuous enzymes in engineered pathways in vivo. This extends the application of spatial organization beyond situations where multiple enzymes compete for a single substrate to cases where there is competition among multiple substrates for a single enzyme.
Collapse
Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Present address:
Australian Centre for Disease Preparedness5 Portarlington RdEast GeelongVIC3219Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Manuel R. Plan
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| |
Collapse
|
4
|
Giuraniuc CV, Parkin C, Almeida MC, Fricker M, Shadmani P, Nye S, Wehmeier S, Chawla S, Bedekovic T, Lehtovirta-Morley L, Richards DM, Gow NA, Brand AC. Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans. mBio 2023; 14:e0115723. [PMID: 37750683 PMCID: PMC10653887 DOI: 10.1128/mbio.01157-23] [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: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Intracellular calcium signaling plays an important role in the resistance and adaptation to stresses encountered by fungal pathogens within the host. This study reports the optimization of the GCaMP fluorescent calcium reporter for live-cell imaging of dynamic calcium responses in single cells of the pathogen, Candida albicans, for the first time. Exposure to membrane, osmotic or oxidative stress generated both specific changes in single cell intracellular calcium spiking and longer calcium transients across the population. Repeated treatments showed that calcium dynamics become unaffected by some stresses but not others, consistent with known cell adaptation mechanisms. By expressing GCaMP in mutant strains and tracking the viability of individual cells over time, the relative contributions of key signaling pathways to calcium flux, stress adaptation, and cell death were demonstrated. This reporter, therefore, permits the study of calcium dynamics, homeostasis, and signaling in C. albicans at a previously unattainable level of detail.
Collapse
Affiliation(s)
- C. V. Giuraniuc
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - C. Parkin
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - M. C. Almeida
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - M. Fricker
- School of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - P. Shadmani
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Nye
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Wehmeier
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - S. Chawla
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - T. Bedekovic
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - L. Lehtovirta-Morley
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - D. M. Richards
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - N. A. Gow
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - A. C. Brand
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
5
|
Hartmann FSF, Weiß T, Kastberg LLB, Workman CT, Seibold GM. Precise and versatile microplate reader-based analyses of biosensor signals from arrayed microbial colonies. Front Microbiol 2023; 14:1187228. [PMID: 37389345 PMCID: PMC10303141 DOI: 10.3389/fmicb.2023.1187228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in Corynebacterium glutamicum, or promoter activity using GFP as reporter in Saccharomyces cerevisiae, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in Escherichia coli colonies. Applicability of this novel technique was further demonstrated by assessing redox states in C. glutamicum colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
Collapse
|
6
|
Brockhurst M, Cavet J, Diggle SP, Grainger D, Mangenelli R, Sychrova H, Martin-Verstraete I, Welch M, Palmer T, Thomas GH. Shaping microbiology for 75 years: highlights of research published in Microbiology. Part 1 - Physiology and growth. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37379229 DOI: 10.1099/mic.0.001356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Affiliation(s)
- Michael Brockhurst
- Division of Evolution, Infection and Genomics, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Jennifer Cavet
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Stephen P Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Hana Sychrova
- Institute of Physiology of the Czech Academy of Sciences, Laboratory of Membrane Transport, 14200 Prague 4, Czech Republic
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
| |
Collapse
|
7
|
Deligönül N, Yildiz I, Bilgin S, Gokce I, Isildak O. Green Fluorescent Protein-Multi Walled Carbon Nanotube based Polymeric Membrane Electrode for Bismuth Ion Detection. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
8
|
Xu Y, Geng Z, Yang C, Zhou H, Wang Y, Kuerban B, Luo G. Effect of N-acetyl-l-cysteine on Cell Phenotype and Autophagy in Pichia pastoris Expressing Human Serum Albumin and Porcine Follicle-Stimulating Hormone Fusion Protein. Molecules 2023; 28:molecules28073041. [PMID: 37049804 PMCID: PMC10095845 DOI: 10.3390/molecules28073041] [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: 02/11/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Pichia pastoris is widely used for the production of recombinant proteins, but the low secretion efficiency hinders its wide application in biopharmaceuticals. Our previous study had shown that N-acetyl-l-cysteine (NAC) promotes human serum albumin and porcine follicle-stimulating hormone fusion protein (HSA-pFSHβ) secretion by increasing intracellular GSH levels, but the downstream impact mechanism is not clear. In this study, we investigated the roles of autophagy as well as cell phenotype in NAC promoting HSA-pFSHβ secretion. Our results showed that NAC slowed down the cell growth rate, and its effects were unaffected by Congo Red and Calcofluor White. Moreover, NAC affected cell wall composition by increasing chitin content and decreasing β-1,3-glucan content. In addition, the expressions of vesicular pathway and autophagy-related genes were significantly decreased after NAC treatment. Further studies revealed that autophagy, especially the cytoplasm-to-vacuole targeting (Cvt) pathway, mitophagy and pexophagy, was significantly increased with time, and NAC has a promoting effect on autophagy, especially at 48 h and 72 h of NAC treatment. However, the disruption of mitophagy receptor Atg32, but not pexophagy receptor Atg30, inhibited HSA-pFSHβ production, and neither of them inhibited the NAC-promoted effect of HSA-pFSHβ. In conclusion, vesicular transport, autophagy and cell wall are all involved in the NAC-promoted HSA-pFSHβ secretion and that disruption of the autophagy receptor alone does not inhibit the effect of NAC.
Collapse
Affiliation(s)
- Yingqing Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Zijian Geng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Chengxi Yang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Hongwei Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yixing Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Buayisham Kuerban
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Gang Luo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| |
Collapse
|
9
|
Cheah LC, Liu L, Stark T, Plan MR, Peng B, Lu Z, Schenk G, Sainsbury F, Vickers CE. Metabolic flux enhancement from the translational fusion of terpene synthases is linked to terpene synthase accumulation. Metab Eng 2023; 77:143-151. [PMID: 36990382 DOI: 10.1016/j.ymben.2023.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
The end-to-end fusion of enzymes that catalyse successive steps in a reaction pathway is a metabolic engineering strategy that has been successfully applied in a variety of pathways and is particularly common in terpene bioproduction. Despite its popularity, limited work has been done to interrogate the mechanism of metabolic enhancement from enzyme fusion. We observed a remarkable >110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), corresponding with increases of a similar magnitude in terpene synthase levels. Our data demonstrate that increased in vivo enzyme levels - resulting from improved expression and/or improved protein stability - is a major driver of catalytic enhancement from enzyme fusion.
Collapse
Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Terra Stark
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Manuel R Plan
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia; School of Biological and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia.
| |
Collapse
|
10
|
Brown AJP. Fungal resilience and host-pathogen interactions: Future perspectives and opportunities. Parasite Immunol 2023; 45:e12946. [PMID: 35962618 PMCID: PMC10078341 DOI: 10.1111/pim.12946] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
We are constantly exposed to the threat of fungal infection. The outcome-clearance, commensalism or infection-depends largely on the ability of our innate immune defences to clear infecting fungal cells versus the success of the fungus in mounting compensatory adaptive responses. As each seeks to gain advantage during these skirmishes, the interactions between host and fungal pathogen are complex and dynamic. Nevertheless, simply compromising the physiological robustness of fungal pathogens reduces their ability to evade antifungal immunity, their virulence, and their tolerance against antifungal therapy. In this article I argue that this physiological robustness is based on a 'Resilience Network' which mechanistically links and controls fungal growth, metabolism, stress resistance and drug tolerance. The elasticity of this network probably underlies the phenotypic variability of fungal isolates and the heterogeneity of individual cells within clonal populations. Consequently, I suggest that the definition of the fungal Resilience Network represents an important goal for the future which offers the clear potential to reveal drug targets that compromise drug tolerance and synergise with current antifungal therapies.
Collapse
Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
| |
Collapse
|
11
|
Vold VA, Glanville S, Klaerke DA, Pedersen PA. pXOOY: A dual-function vector for expression of membrane proteins in Saccharomyces cerevisiae and Xenopus laevis oocytes. PLoS One 2023; 18:e0281868. [PMID: 36809531 PMCID: PMC9942955 DOI: 10.1371/journal.pone.0281868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
On the quest for solving structures of membrane proteins by X-ray crystallography or cryo-EM, large quantities of ultra-pure protein are a paramount prerequisite. Obtaining enough protein of such high standard is not a trivial task, especially for difficult-to-express membrane proteins. Producing membrane protein for structural studies is often performed in Escherichia coli or Saccharomyces cerevisiae and is frequently complemented with functional studies. Ion channels and electrogenic receptors are traditionally studied in terms of their electrophysiological behavior, which cannot be performed in neither E. coli nor yeast. Therefore, they are frequently characterized in mammalian cells or in Xenopus laevis oocytes. To avoid generating two different plasmids, we here describe the construction of a dual-function plasmid, pXOOY, for membrane protein production in yeast and for electrophysiology in oocytes. pXOOY was constructed such that all elements required for oocyte expression were copied from the dual Xenopus-mammalian vector pXOOM and meticulously introduced into the high-yield yeast expression vector pEMBLyex4. pXOOY is thus designed to preserve the high yield of protein from pEMBLyex4 while simultaneously permitting in vitro transcription for expression in oocytes. We evaluated the performance of pXOOY by comparing expression of two yeast codon optimized human potassium channels, ohERG and ohSlick (Slo2.1) from pXOOY to expression of these channels obtained from the reference vectors pEMBLyex4 and pXOOM. Our proof-of-concept study indicates that accumulation in PAP1500 yeast cells was higher when the channels were expressed from pXOOY, which was verified both qualitatively and quantitatively. Two-electrode voltage clamp measurements in oocytes showed that the pXOOY constructs encoding ohERG and ohSlick gave currents with full preservation of electrophysiological characteristics. Our results show that it is possible to design a dual-function Xenopus-yeast vector without compromising expression in yeast and simultaneously maintaining channel activity in oocytes.
Collapse
Affiliation(s)
- Victoria Amstrup Vold
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sebastian Glanville
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dan Arne Klaerke
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (PAP); (DAK)
| | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
- * E-mail: (PAP); (DAK)
| |
Collapse
|
12
|
Jung SJ, Yun M, Yim C, Hong S, Huh WK, Kim H. Expression level of Sec62 modulates membrane insertion of marginally hydrophobic segments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184051. [PMID: 36122759 DOI: 10.1016/j.bbamem.2022.184051] [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: 06/26/2022] [Revised: 08/08/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
In the endoplasmic reticulum (ER) membrane, transmembrane (TM) domain insertion occurs through the Sec61 channel with its auxiliary components, including Sec62. Sec62 interacts with the Sec61 channel and is located on the front side of the Sec61 lateral gate, an entry site for TM domains to the lipid bilayer. Overexpression of Sec62 led to a growth defect in yeast, and we investigated its effects on protein translocation and membrane insertion by pulse labeling of Sec62 client proteins. Our data show that the insertion efficiency of marginally hydrophobic TM segments is reduced upon Sec62 overexpression. This result suggests a potential regulatory role of Sec62 as a gatekeeper of the lateral gate, thereby modulating the insertion threshold of TM segments.
Collapse
Affiliation(s)
- Sung-Jun Jung
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Mekang Yun
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Chewon Yim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Sujin Hong
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Won-Ki Huh
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea
| | - Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, South Korea.
| |
Collapse
|
13
|
Colombari B, Tagliazucchi D, Odorici A, Pericolini E, Foltran I, Pinetti D, Meto A, Peppoloni S, Blasi E. Pomegranate Extract Affects Fungal Biofilm Production: Consumption of Phenolic Compounds and Alteration of Fungal Autoinducers Release. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14146. [PMID: 36361021 PMCID: PMC9657062 DOI: 10.3390/ijerph192114146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Candida albicans expresses numerous virulence factors that contribute to pathogenesis, including its dimorphic transition and even biofilm formation, through the release of specific quorum sensing molecules, such as the autoinducers (AI) tyrosol and farnesol. In particular, once organized as biofilm, Candida cells can elude conventional antifungal therapies and the host's immune defenses as well. Accordingly, biofilm-associated infections become a major clinical challenge underlining the need of innovative antimicrobial approaches. The aim of this in vitro study was to assess the effects of pomegranate peel extract (PomeGr) on C. albicans growth and biofilm formation; in addition, the release of tyrosol and farnesol was investigated. The phenolic profile of PomeGr was assessed by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS) analysis before and after exposure to C. albicans. Here, we showed that fungal growth, biofilm formation and AI release were altered by PomeGr treatment. Moreover, the phenolic content of PomeGr was substantially hampered upon exposure to fungal cells; particularly pedunculagin, punicalin, punicalagin, granatin, di-(HHDP-galloyl-hexoside)-pentoside and their isomers as well as ellagic acid-hexoside appeared highly consumed, suggesting their role as bioactive molecules against Candida. Overall, these new insights on the anti-Candida properties of PomeGr and its potential mechanisms of action may represent a relevant step in the design of novel therapeutic approaches against fungal infections.
Collapse
Affiliation(s)
- Bruna Colombari
- Laboratory of Microbiology and Virology, Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Davide Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola, 2—Pad. Besta, 42100 Reggio Emilia, Italy
| | - Alessandra Odorici
- Laboratory of Microbiology and Virology, School of Doctorate in Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Eva Pericolini
- Laboratory of Microbiology and Virology, Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Ismaela Foltran
- Incos-Cosmeceutica Industriale, Funo di Argelato, 40050 Bologna, Italy
| | - Diego Pinetti
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S), University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Aida Meto
- Laboratory of Microbiology and Virology, Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
- Department of Dentistry, Faculty of Dental Sciences, University of Aldent, 1007 Tirana, Albania
| | - Samuele Peppoloni
- Laboratory of Microbiology and Virology, Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Elisabetta Blasi
- Laboratory of Microbiology and Virology, Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| |
Collapse
|
14
|
Shang L, Zhang Y, Liu Y, Jin C, Yuan Y, Tian C, Ni M, Bo X, Zhang L, Li D, He F, Wang J. A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:795-807. [PMID: 34314873 PMCID: PMC9880813 DOI: 10.1016/j.gpb.2021.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 12/14/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023]
Abstract
Genome-wide physical protein-protein interaction (PPI) mapping remains a major challenge for current technologies. Here, we reported a high-efficiency BiFC-seq method, yeast-enhanced green fluorescent protein-based bimolecular fluorescence complementation (yEGFP-BiFC) coupled with next-generation DNA sequencing, for interactome mapping. We first applied yEGFP-BiFC method to systematically investigate an intraviral network of the Ebola virus. Two-thirds (9/14) of known interactions of EBOV were recaptured, and five novel interactions were discovered. Next, we used the BiFC-seq method to map the interactome of the tumor protein p53. We identified 97 interactors of p53, more than three-quarters of which were novel. Furthermore, in a more complex background, we screened potential interactors by pooling two BiFC libraries together and revealed a network of 229 interactions among 205 proteins. These results show that BiFC-seq is a highly sensitive, rapid, and economical method for genome-wide interactome mapping.
Collapse
Affiliation(s)
- Limin Shang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuehui Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Li Zhang
- Department of Rehabilitation Medicine, Nan Lou; Key Laboratory of Wound Repair and Regeneration of PLA, College of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.
| |
Collapse
|
15
|
Perruca-Foncillas R, Davidsson J, Carlquist M, Gorwa-Grauslund MF. Assessment of fluorescent protein candidates for multi-color flow cytometry analysis of Saccharomyces cerevisiae. BIOTECHNOLOGY REPORTS 2022; 34:e00735. [PMID: 35686015 PMCID: PMC9171426 DOI: 10.1016/j.btre.2022.e00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/25/2022]
Abstract
In vivo fluorescence of candidate fluorescent proteins was assessed in Saccharomyces cerevisiae. eEGFP, CyOFP1opt and mBeRFPopt were found to be suitable for multicolour flow cytometry. Successful protein selection and equipment configuration allowed potential tri-color flow cytometry with 488 nm single-laser excitation.
Transcription factor-based biosensors represent promising tools in the construction and evaluation of efficient cell factories for the sustainable production of fuels, chemicals and pharmaceuticals. They can notably be designed to follow the production of a target compound or to monitor key cellular properties, such as stress or starvation. In most cases, the biosensors are built with fluorescent protein (FP) genes as reporter genes because of the direct correlation between promoter activity and fluorescence level that can be measured using, for instance, flow cytometry or fluorometry. The expansion of available FPs offers the possibility of using several FPs - and biosensors – in parallel in one host, with simultaneous detection using multicolor flow cytometry. However, the technique is currently limited by the unavailability of combinations of FP whose genes can be successfully expressed in the host and whose fluorescence can be efficiently distinguished from each other. In the present study, the broad collection of available FPs was explored and four different FPs were successfully expressed in the yeast Saccharomyces cerevisiae: yEGFP, mEGFP, CyOFP1opt and mBeRFPopt. After studying their fluorescence signals, population heterogeneity and possible interactions, we recommend two original combinations of FPs for bi-color flow cytometry: mEGFP together with either CyOFP1opt or mBeRFPopt, as well as the combination of all three FPs mEGFP, CyOFP1opt and mBeRFPopt for tri-color flow cytometry. These combinations will allow to perform different types of bi-color or possibly tri-color flow cytometry and FACS experiments with yeast, such as phenotype evaluation, screening or sorting, by single-laser excitation with a standard 488 nm blue laser.
Collapse
|
16
|
Ring J, Tadic J, Ristic S, Poglitsch M, Bergmann M, Radic N, Mossmann D, Liang Y, Maglione M, Jerkovic A, Hajiraissi R, Hanke M, Küttner V, Wolinski H, Zimmermann A, Domuz Trifunović L, Mikolasch L, Moretti DN, Broeskamp F, Westermayer J, Abraham C, Schauer S, Dammbrueck C, Hofer SJ, Abdellatif M, Grundmeier G, Kroemer G, Braun RJ, Hansen N, Sommer C, Ninkovic M, Seba S, Rockenfeller P, Vögtle F, Dengjel J, Meisinger C, Keller A, Sigrist SJ, Eisenberg T, Madeo F. The HSP40 chaperone Ydj1 drives amyloid beta 42 toxicity. EMBO Mol Med 2022; 14:e13952. [PMID: 35373908 PMCID: PMC9081910 DOI: 10.15252/emmm.202113952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 01/22/2023] Open
Abstract
Amyloid beta 42 (Abeta42) is the principal trigger of neurodegeneration during Alzheimer's disease (AD). However, the etiology of its noxious cellular effects remains elusive. In a combinatory genetic and proteomic approach using a yeast model to study aspects of intracellular Abeta42 toxicity, we here identify the HSP40 family member Ydj1, the yeast orthologue of human DnaJA1, as a crucial factor in Abeta42-mediated cell death. We demonstrate that Ydj1/DnaJA1 physically interacts with Abeta42 (in yeast and mouse), stabilizes Abeta42 oligomers, and mediates their translocation to mitochondria. Consequently, deletion of YDJ1 strongly reduces co-purification of Abeta42 with mitochondria and prevents Abeta42-induced mitochondria-dependent cell death. Consistently, purified DnaJ chaperone delays Abeta42 fibrillization in vitro, and heterologous expression of human DnaJA1 induces formation of Abeta42 oligomers and their deleterious translocation to mitochondria in vivo. Finally, downregulation of the Ydj1 fly homologue, Droj2, improves stress resistance, mitochondrial morphology, and memory performance in a Drosophila melanogaster AD model. These data reveal an unexpected and detrimental role for specific HSP40s in promoting hallmarks of Abeta42 toxicity.
Collapse
|
17
|
Dean N, Jones R, DaSilva J, Chionchio G, Ng H. The Mnn10/Anp1-dependent N-linked outer chain glycan is dispensable for Candida albicans cell wall integrity. Genetics 2022; 221:6554200. [PMID: 35333306 PMCID: PMC9071539 DOI: 10.1093/genetics/iyac048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Candida albicans cell wall glycoproteins, and in particular their mannose-rich glycans, are important for maintaining cellular integrity as well as host recognition, adhesion, and immunomodulation. The asparagine (N)-linked mannose outer chain of these glycoproteins is produced by Golgi mannosyltransferases (MTases). The outer chain is composed of a linear backbone of ∼50 α1,6-linked mannoses, which acts as a scaffold for addition of ∼150 or more mannoses in other linkages. Here, we describe the characterization of C. albicans OCH1, MNN9, VAN1, ANP1, MNN10, and MNN11, which encode the conserved Golgi MTases that sequentially catalyze the α1,6 mannose outer chain backbone. Candida albicans och1Δ/Δ, mnn9Δ/Δ, and van1Δ/Δ mutants block the earliest steps of backbone synthesis and like their Saccharomyces cerevisiae counterparts, have severe cell wall and growth phenotypes. Unexpectedly, and in stark contrast to S. cerevisiae, loss of Anp1, Mnn10, or Mnn11, which together synthesize most of the backbone, have no obvious deleterious phenotypes. These mutants were unaffected in cell morphology, growth, drug sensitivities, hyphal formation, and macrophage recognition. Analyses of secreted glycosylation reporters demonstrated that anp1Δ/Δ, mnn10Δ/Δ, and mnn11Δ/Δ strains accumulate glycoproteins with severely truncated N-glycan chains. This hypo-mannosylation did not elicit increased chitin deposition in the cell wall, which in other yeast and fungi is a key compensatory response to cell wall integrity breaches. Thus, C. albicans has evolved an alternate mechanism to adapt to cell wall weakness when N-linked mannan levels are reduced.
Collapse
Affiliation(s)
- Neta Dean
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
- Corresponding author: Department of Biochemistry and Cell Biology, Life Sciences Bldg Room 310, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Rachel Jones
- Department of Anesthesiology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Gregory Chionchio
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Henry Ng
- Department of Physiology, University of California, San Francisco, CA 94143, USA
| |
Collapse
|
18
|
Hector RE, Mertens JA, Nichols NN. Increased expression of the fluorescent reporter protein ymNeonGreen in Saccharomyces cerevisiae by reducing RNA secondary structure near the start codon. BIOTECHNOLOGY REPORTS 2022; 33:e00697. [PMID: 35036336 PMCID: PMC8749125 DOI: 10.1016/j.btre.2021.e00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/06/2022]
Abstract
Stable secondary RNA structure 3′ of the start codon inhibits ymNeonGreen expression. Removing secondary RNA structure increased expression in S. cerevisiae and E. coli. Expression was increased 2-fold in S. cerevisiae. Expression was increased 3.8-fold in E. coli. Increased expression in S. cerevisiae was promoter independent.
Expression of a new fluorescent reporter protein called mNeonGreen, that is not based on the jellyfish green fluorescent protein (GFP) sequence, shows increased brightness and folding speed compared to enhanced GFP. However, in vivo brightness of mNeonGreen and its yeast-optimized variant ymNeonGreen in S. cerevisiae is lower than expected, limiting the use of this high quantum yield, fast-folding reporter in budding yeast. This study shows that secondary RNA structure near the start codon in the ymNeonGreen ORF inhibits expression in S. cerevisiae. Removing secondary structure, without altering the ymNeonGreen protein sequence, led to a 2 and 4-fold increase in fluorescence when expressed in S. cerevisiae and E. coli, respectively. In S. cerevisiae, increased fluorescence was seen with strong and weak promoters and led to higher transcript levels suggesting greater transcript stability and improved expression in the absence of stable secondary RNA structure near the start codon.
Collapse
|
19
|
Virolainen MS, Søltoft CL, Pedersen PA, Ellgaard L. Production of an Active, Human Membrane Protein in Saccharomyces cerevisiae: Full-Length FICD. Int J Mol Sci 2022; 23:ijms23052458. [PMID: 35269596 PMCID: PMC8910494 DOI: 10.3390/ijms23052458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/10/2022] Open
Abstract
The human Fic domain-containing protein (FICD) is a type II endoplasmic reticulum (ER) membrane protein that is important for the maintenance of ER proteostasis. Structural and in vitro biochemical characterisation of FICD AMPylase and deAMPylase activity have been restricted to the soluble ER-luminal domain produced in Escherichia coli. Information about potentially important features, such as structural motifs, modulator binding sites or other regulatory elements, is therefore missing for the approximately 100 N-terminal residues including the transmembrane region of FICD. Expressing and purifying the required quantity and quality of membrane proteins is demanding because of the low yields and poor stability often observed. Here, we produce full-length FICD by combining a Saccharomyces cerevisiae-based platform with green fluorescent protein (GFP) tagging to optimise the conditions for expression, solubilisation and purification. We subsequently employ these conditions to purify milligram quantities of His-tagged FICD per litre of culture, and show that the purified, detergent-solubilised membrane protein is an active deAMPylating enzyme. Our work provides a straightforward methodology for producing not only full-length FICD, but also other membrane proteins in S. cerevisiae for structural and biochemical characterisation.
Collapse
Affiliation(s)
- Minttu S. Virolainen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
| | - Cecilie L. Søltoft
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
| | - Per A. Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2200 Copenhagen, Denmark
- Correspondence: (P.A.P.); (L.E.)
| | - Lars Ellgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; (M.S.V.); (C.L.S.)
- Correspondence: (P.A.P.); (L.E.)
| |
Collapse
|
20
|
Cheah LC, Stark T, Adamson LSR, Abidin RS, Lau YH, Sainsbury F, Vickers CE. Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast. ACS Synth Biol 2021; 10:3251-3263. [PMID: 34591448 PMCID: PMC8689640 DOI: 10.1021/acssynbio.1c00045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 12/29/2022]
Abstract
Metabolic pathways are commonly organized by sequestration into discrete cellular compartments. Compartments prevent unfavorable interactions with other pathways and provide local environments conducive to the activity of encapsulated enzymes. Such compartments are also useful synthetic biology tools for examining enzyme/pathway behavior and for metabolic engineering. Here, we expand the intracellular compartmentalization toolbox for budding yeast (Saccharomyces cerevisiae) with Murine polyomavirus virus-like particles (MPyV VLPs). The MPyV system has two components: VP1 which self-assembles into the compartment shell and a short anchor, VP2C, which mediates cargo protein encapsulation via binding to the inner surface of the VP1 shell. Destabilized green fluorescent protein (GFP) fused to VP2C was specifically sorted into VLPs and thereby protected from host-mediated degradation. An engineered VP1 variant displayed improved cargo capture properties and differential subcellular localization compared to wild-type VP1. To demonstrate their ability to function as a metabolic compartment, MPyV VLPs were used to encapsulate myo-inositol oxygenase (MIOX), an unstable and rate-limiting enzyme in d-glucaric acid biosynthesis. Strains with encapsulated MIOX produced ∼20% more d-glucaric acid compared to controls expressing "free" MIOX─despite accumulating dramatically less expressed protein─and also grew to higher cell densities. This is the first demonstration in yeast of an artificial biocatalytic compartment that can participate in a metabolic pathway and establishes the MPyV platform as a promising synthetic biology tool for yeast engineering.
Collapse
Affiliation(s)
- Li Chen Cheah
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO
Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
| | - Terra Stark
- Metabolomics
Australia (Queensland Node), The University
of Queensland, St Lucia, Queensland 4072, Australia
| | - Lachlan S. R. Adamson
- School
of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Rufika S. Abidin
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yu Heng Lau
- School
of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Frank Sainsbury
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO
Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre
for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Claudia E. Vickers
- Australian
Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO
Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre
for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- ARC Centre
of Excellence in Synthetic Biology, Queensland
University of Technology, Brisbane
City, Queensland 4000, Australia
| |
Collapse
|
21
|
Van Genechten W, Van Dijck P, Demuyser L. Fluorescent toys 'n' tools lighting the way in fungal research. FEMS Microbiol Rev 2021; 45:fuab013. [PMID: 33595628 PMCID: PMC8498796 DOI: 10.1093/femsre/fuab013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
Collapse
Affiliation(s)
- Wouter Van Genechten
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200g, 3001 Leuven-Heverlee, Belgium
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| | - Liesbeth Demuyser
- VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001 Leuven-heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Belgium
| |
Collapse
|
22
|
Kassem N, Araya-Secchi R, Bugge K, Barclay A, Steinocher H, Khondker A, Wang Y, Lenard AJ, Bürck J, Sahin C, Ulrich AS, Landreh M, Pedersen MC, Rheinstädter MC, Pedersen PA, Lindorff-Larsen K, Arleth L, Kragelund BB. Order and disorder-An integrative structure of the full-length human growth hormone receptor. SCIENCE ADVANCES 2021; 7:7/27/eabh3805. [PMID: 34193419 PMCID: PMC8245047 DOI: 10.1126/sciadv.abh3805] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 05/13/2023]
Abstract
Because of its small size (70 kilodalton) and large content of structural disorder (>50%), the human growth hormone receptor (hGHR) falls between the cracks of conventional high-resolution structural biology methods. Here, we study the structure of the full-length hGHR in nanodiscs with small-angle x-ray scattering (SAXS) as the foundation. We develop an approach that combines SAXS, x-ray diffraction, and NMR spectroscopy data obtained on individual domains and integrate these through molecular dynamics simulations to interpret SAXS data on the full-length hGHR in nanodiscs. The hGHR domains reorient freely, resulting in a broad structural ensemble, emphasizing the need to take an ensemble view on signaling of relevance to disease states. The structure provides the first experimental model of any full-length cytokine receptor in a lipid membrane and exemplifies how integrating experimental data from several techniques computationally may access structures of membrane proteins with long, disordered regions, a widespread phenomenon in biology.
Collapse
Affiliation(s)
- Noah Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Raul Araya-Secchi
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Abigail Barclay
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Helena Steinocher
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Adree Khondker
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Aneta J Lenard
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Cagla Sahin
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Michael Landreh
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Martin Cramer Pedersen
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| | - Lise Arleth
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| |
Collapse
|
23
|
Sophon N, Phiwpesh C, Darith S, Cherdshewasart W, Boonchird C. Improved yeast-screening assay for phytoestrogens. Biosci Biotechnol Biochem 2021; 85:1422-1432. [PMID: 33770159 DOI: 10.1093/bbb/zbab051] [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: 01/28/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022]
Abstract
A yeast estrogen screening (YES) assay was improved to increase sensitivity for detection of phytoestrogens. New yeast strains minus one or the other of transporters Pdr5 or Snq2 and harboring yEGFP as a reporter gene were developed. The new strains showed 2-100-fold improvement in sensitivity for detection of standard estrogens and antiestrogens. In addition, the assay time (1 h) using the newly developed strains was shorter than that (4 h) previously reported. Furthermore, the snq2-minus strains were most effective for detection of estrogenic activity while the pdr5-minus strains were most effective for detection of antiestrogenic activity. The efficacy of the new methods was evaluated and confirmed by testing with 23 Thai medicinal plant species. The new strains were also tested for detection of xenoestrogens. The results revealed that the newly developed YES methods were specific and rapid and suitable for simple high-throughput screening or detection of estrogen-like compounds.
Collapse
Affiliation(s)
- Natthida Sophon
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Ratchathewi, Bangkok, Thailand
| | - Choladda Phiwpesh
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Ratchathewi, Bangkok, Thailand
| | - Sieng Darith
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Ratchathewi, Bangkok, Thailand
| | - Wichai Cherdshewasart
- Department of Biology, Faculty of Science, Chulalongkorn University, Phyathai Road, Bangkok, Thailand
| | - Chuenchit Boonchird
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Ratchathewi, Bangkok, Thailand
| |
Collapse
|
24
|
Møller LB, Mogensen M, Weaver DD, Pedersen PA. Occipital Horn Syndrome as a Result of Splice Site Mutations in ATP7A. No Activity of ATP7A Splice Variants Missing Exon 10 or Exon 15. Front Mol Neurosci 2021; 14:532291. [PMID: 33967692 PMCID: PMC8097048 DOI: 10.3389/fnmol.2021.532291] [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: 10/14/2020] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Disease-causing variants in ATP7A lead to two different phenotypes associated with copper deficiency; a lethal form called Menkes disease (MD), leading to early death, and a much milder form called occipital horn syndrome (OHS). Some investigators have proposed that an ATP7A transcript missing exon 10 leads to a partly active protein product resulting in the OHS phenotype. Here, we describe an individual with OHS, a biology professor, who survived until age 62 despite a splice site mutation, leading to skipping of exon 15. ATP7A transcripts missing exon 10, or exon 15 preserve the reading frame, but it is unknown if either of these alternative transcripts encode functional protein variants. We have investigated the molecular consequence of splice site mutations leading to skipping of exon 10 or exon 15 which have been identified in individuals with OHS, or MD. By comparing ATP7A expression in fibroblasts from three individuals with OHS (OHS-fibroblasts) to ATP7A expression in fibroblasts from two individuals with MD (MD-fibroblasts), we demonstrate that transcripts missing either exon 10 or exon 15 were present in similar amounts in OHS-fibroblasts and MD-fibroblasts. No ATP7A protein encoded from these transcripts could be detected in the OHS and MD fibroblast. These results, combined with the observation that constructs encoding ATP7A cDNA sequences missing either exon 10, or exon 15 were unable to complement the high iron requirement of the ccc2Δ yeast strain, provide evidence that neither a transcript missing exon 10 nor a transcript missing exon 15 results in functional ATP7A protein. In contrast, higher amounts of wild-type ATP7A transcript were present in the OHS-fibroblasts compared with the MD-fibroblasts. We found that the MD-fibroblasts contained between 0 and 0.5% of wild-type ATP7A transcript, whereas the OHS-fibroblasts contained between 3 and 5% wild-type transcripts compared with the control fibroblasts. In summary these results indicate that protein variants encoded by ATP7A transcripts missing either exon 10 or exon 15 are not functional and not responsible for the OHS phenotype. In contrast, expression of only 3-5% of wild-type transcript compared with the controls permits the OHS phenotype.
Collapse
Affiliation(s)
- Lisbeth Birk Møller
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Mie Mogensen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - David D Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | | |
Collapse
|
25
|
Romero-Suarez D, Wulff T, Rong Y, Jakočiu̅nas T, Yuzawa S, Keasling JD, Jensen MK. A Reporter System for Cytosolic Protein Aggregates in Yeast. ACS Synth Biol 2021; 10:466-477. [PMID: 33577304 DOI: 10.1021/acssynbio.0c00476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein misfolding and aggregation are linked to neurodegenerative diseases of mammals and suboptimal protein expression within biotechnology. Tools for monitoring protein aggregates are therefore useful for studying disease-related aggregation and for improving soluble protein expression in heterologous hosts for biotechnology purposes. In this work, we developed a promoter-reporter system for aggregated protein on the basis of the yeast native response to misfolded protein. To this end, we first studied the proteome of yeast in response to the expression of folded soluble and aggregation-prone protein baits and identified genes encoding proteins related to protein folding and the response to heat stress as well as the ubiquitin-proteasome system that are over-represented in cells expressing an aggregation-prone protein. From these data, we created and validated promoter-reporter constructs and further engineered the best performing promoters by increasing the copy number of upstream activating sequences and optimization of culture conditions. Our best promoter-reporter has an output dynamic range of approximately 12-fold upon expression of the aggregation-prone protein and responded to increasing levels of aggregated protein. Finally, we demonstrate that the system can discriminate between yeast cells expressing different prion precursor proteins and select the cells expressing folded soluble protein from mixed populations. Our reporter system is thus a simple tool for diagnosing protein aggregates in living cells and should be applicable for the health and biotechnology industries.
Collapse
Affiliation(s)
- David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Yixin Rong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tadas Jakočiu̅nas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, Guangdong 518055, China
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| |
Collapse
|
26
|
Klimova N, Chu S, Turcotte B. A lacZ reporter with high activity in the human fungal pathogen Candida albicans. FEMS Yeast Res 2021; 21:6147040. [PMID: 33620462 DOI: 10.1093/femsyr/foab013] [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: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 11/14/2022] Open
Abstract
Reporter genes are useful tools to study gene transcription in various organisms. For example, the lacZ gene encoding β-galactosidase has been extensively used as a reporter in bacteria, budding yeast, fruit fly, mouse etc. However, use of this gene in the human fungal pathogen Candida albicans has been limited, probably due to low β-galactosidase activity. Here, we describe a reporter derived from the Vibrio cholerae lacZ gene in which codons have been optimized for expression in C. albicans. The constitutively active ACT1 promoter was fused to this synthetic lacZ reporter and integrated in the C. albicans genome. High β-galactosidase activity in liquid assays was observed for this reporter as well as coloration on X-gal plates. When the lacZ reporter expression was driven by the MET3 promoter, β-galactosidase activity in liquid assays and coloration on X-gal plates was higher in the absence of methionine, thus recapitulating the regulation of the native MET3 gene. This synthetic lacZ gene extends the toolbox of C. albicans reagents by providing a useful reporter for analysis of promoter activity in this organism of medical importance.
Collapse
Affiliation(s)
- Natalia Klimova
- Department of Medicine, McGill University Health Centre, McGill University, Montréal H3A 1A1, Québec, Canada
| | - Siwei Chu
- Department of Medicine, McGill University Health Centre, McGill University, Montréal H3A 1A1, Québec, Canada
| | - Bernard Turcotte
- Department of Medicine, McGill University Health Centre, McGill University, Montréal H3A 1A1, Québec, Canada.,Department of Biochemistry, McGill University Health Centre, McGill University, Montréal H3A 1A1, Québec, Canada.,Department of Microbiology and Immunology, McGill University Health Centre, McGill University, Montréal H3A 1A1, Québec, Canada
| |
Collapse
|
27
|
Juin C, Perrin F, Puy T, Bernard C, Mollichella ML, Girardot M, Costa D, Guillard J, Imbert C. Anti-biofilm activity of a semi-synthetic molecule obtained from resveratrol against Candida albicans biofilm. Med Mycol 2021; 58:530-542. [PMID: 31504755 DOI: 10.1093/mmy/myz087] [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: 06/04/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 01/08/2023] Open
Abstract
Candida albicans can form biofilm on tissues and medical devices, becoming, in that case, less susceptible to antifungal agents. Treatment of candidiasis associated with the formation of C. albicans biofilms is restricted to echinocandins and lipid forms of amphotericin B. This study investigated the activity of micafungin and resveratrol modified molecule (EB487) against C. albicans biofilms. The anti-biofilm growth (Bgrowth) and anti-preformed biofilm (Bpreformed) activities of micafungin (0 to 3.94 μM) and EB487 (0 to 20.32 mM) were comparatively studied separately and combined, using XTT, flow cytometry and cell counts approaches. Concentrations causing 50% inhibition of the studied steps (IC50) were evaluated. When tested separately, IC50 Bgrowth was obtained for 4.8 mM and 0.13 μM of EB487 and micafungin respectively, and IC50 Bpreformed for 3.6 mM and 0.06 μM of EB487 and micafungin respectively. Micafungin used alone was not able to totally eradicate fungi. Micafungin combined with EB487 displayed synergistic activity (both anti-growth- and anti-preformed biofilm-activities). Optimal combination concentrations were EB487 (≤9.12 mM -strain ATCC 28367™ or ≤8.12 mM -strain CAI4-p), micafungin (≤0.05 μM for both) and caused a total eradication of fungi. Dose reduction indexes obtained using these concentrations were at least 9 (micafungin) and 3.2 (EB487) for both anti-biofilm growth- and anti-preformed biofilm-activities. Combinations indexes were consistently below one, demonstrating a synergistic relationship between micafungin and EB487 in these conditions. This study demonstrated the strong anti-biofilm activity of EB487 and highlighted its synergistic potential when combined with micafungin. EB487 is a promising semi-synthetic molecule with prophylactic and curative interests in fighting C. albicans biofilms.
Collapse
Affiliation(s)
- Camille Juin
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Flavie Perrin
- University of Poitiers, Institute of Chemistry, Materials and Naturals Resources of Poitiers, IC2MP, UMR CNRS 7285, University of Poitiers, 4 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9, France
| | - Thomas Puy
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Clément Bernard
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Marie Laure Mollichella
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Marion Girardot
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Damien Costa
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| | - Jérôme Guillard
- University of Poitiers, Institute of Chemistry, Materials and Naturals Resources of Poitiers, IC2MP, UMR CNRS 7285, University of Poitiers, 4 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9, France
| | - Christine Imbert
- Université de Poitiers, Laboratoire Ecologie Biologie des Interactions, UMR CNRS 7267, 1 rue Michel Brunet TSA 51106 86073 Poitiers Cedex 9 France
| |
Collapse
|
28
|
Brouwer I, Patel HP, Meeussen JVW, Pomp W, Lenstra TL. Single-Molecule Fluorescence Imaging in Living Saccharomyces cerevisiae Cells. STAR Protoc 2020; 1:100142. [PMID: 33377036 PMCID: PMC7757289 DOI: 10.1016/j.xpro.2020.100142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This protocol describes how to image fluorescently tagged proteins, RNA, or DNA inside living Saccharomyces cerevisiae cells at the single-molecule level. Imaging inside living cells, as opposed to fixed materials, gives access to real-time kinetic information. Although various single-molecule imaging applications are discussed, we focus on imaging of gene transcription at the single-RNA level. To obtain the best possible results, it is important that both imaging parameters and yeast culture conditions are optimized. Here, both aspects are described. For complete details on the use and execution of this protocol, please refer to Lenstra et al. (2015) and Donovan et al. (2019).
Collapse
Affiliation(s)
- Ineke Brouwer
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Heta Piyush Patel
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | | | - Wim Pomp
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tineke Laura Lenstra
- Division of Gene Regulation, Oncode Institute, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| |
Collapse
|
29
|
Sprenger M, Brunke S, Hube B, Kasper L. A TRP1-marker-based system for gene complementation, overexpression, reporter gene expression and gene modification in Candida glabrata. FEMS Yeast Res 2020; 20:6027539. [PMID: 33289831 PMCID: PMC7787354 DOI: 10.1093/femsyr/foaa066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 01/14/2023] Open
Abstract
Although less prevalent than its relative Candida albicans, the yeast Candida glabrata is a successful pathogen of humans, which causes life-threatening candidiasis. It is thus vital to understand the pathogenicity mechanisms and contributing genes in C. glabrata. However, gene complementation as a tool for restoring the function of a previously deleted gene is not standardized in C. glabrata, and it is less frequently used than in C. albicans. In this study, we established a gene complementation strategy using genomic integration at the TRP1 locus. We prove that our approach can not only be used for integration of complementation cassettes, but also for overexpression of markers like fluorescent proteins and the antigen ovalbumin, or of potential pathogenicity-related factors like the biotin transporter gene VHT1. With urea amidolyase Dur1,2 as an example, we demonstrate the application of the gene complementation approach for the expression of sequence-modified genes. With this approach, we found that a lysine-to-arginine mutation in the biotinylation motif of Dur1,2 impairs urea-dependent growth of C. glabrata and C. albicans. Taken together, the TRP1-based gene complementation approach is a valuable tool for investigating novel gene functions and for elucidating their role in the pathobiology of C. glabrata.
Collapse
Affiliation(s)
- Marcel Sprenger
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Sascha Brunke
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Lydia Kasper
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| |
Collapse
|
30
|
Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H. Genetic profiling of protein burden and nuclear export overload. eLife 2020; 9:54080. [PMID: 33146608 PMCID: PMC7673788 DOI: 10.7554/elife.54080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/01/2020] [Indexed: 12/11/2022] Open
Abstract
Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
Collapse
Affiliation(s)
- Reiko Kintaka
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Shotaro Namba
- Matching Program Course, Okayama University, Okayama, Japan
| | - Hisaaki Kato
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Tokyo, Japan
| | - Shinsuke Ohnuki
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Ohya
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Brenda J Andrews
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Charles Boone
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada.,RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| |
Collapse
|
31
|
Kreimendahl S, Schwichtenberg J, Günnewig K, Brandherm L, Rassow J. The selectivity filter of the mitochondrial protein import machinery. BMC Biol 2020; 18:156. [PMID: 33121519 PMCID: PMC7596997 DOI: 10.1186/s12915-020-00888-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background The uptake of newly synthesized nuclear-encoded mitochondrial proteins from the cytosol is mediated by a complex of mitochondrial outer membrane proteins comprising a central pore-forming component and associated receptor proteins. Distinct fractions of proteins initially bind to the receptor proteins and are subsequently transferred to the pore-forming component for import. The aim of this study was the identification of the decisive elements of this machinery that determine the specific selection of the proteins that should be imported. Results We identified the essential internal targeting signal of the members of the mitochondrial metabolite carrier proteins, the largest protein family of the mitochondria, and we investigated the specific recognition of this signal by the protein import machinery at the mitochondrial outer surface. We found that the outer membrane import receptors facilitated the uptake of these proteins, and we identified the corresponding binding site, marked by cysteine C141 in the receptor protein Tom70. However, in tests both in vivo and in vitro, the import receptors were neither necessary nor sufficient for specific recognition of the targeting signals. Although these signals are unrelated to the amino-terminal presequences that mediate the targeting of other mitochondrial preproteins, they were found to resemble presequences in their strict dependence on a content of positively charged residues as a prerequisite of interactions with the import pore. Conclusions The general import pore of the mitochondrial outer membrane appears to represent not only the central channel of protein translocation but also to form the decisive general selectivity filter in the uptake of the newly synthesized mitochondrial proteins.
Collapse
Affiliation(s)
- Sebastian Kreimendahl
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Jan Schwichtenberg
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Kathrin Günnewig
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Lukas Brandherm
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Joachim Rassow
- Institute for Biochemistry and Pathobiochemistry, Ruhr-University Bochum, 44780, Bochum, Germany.
| |
Collapse
|
32
|
Molbaek K, Tejada M, Ricke CH, Scharff-Poulsen P, Ellekvist P, Helix-Nielsen C, Kumar N, Klaerke DA, Pedersen PA. Purification and initial characterization of Plasmodium falciparum K + channels, PfKch1 and PfKch2 produced in Saccharomyces cerevisiae. Microb Cell Fact 2020; 19:183. [PMID: 32957994 PMCID: PMC7507820 DOI: 10.1186/s12934-020-01437-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
Resistance towards known antimalarial drugs poses a significant problem, urging for novel drugs that target vital proteins in the malaria parasite Plasmodium falciparum. However, recombinant production of malaria proteins is notoriously difficult. To address this, we have investigated two putative K+ channels, PfKch1 and PfKch2, identified in the P. falciparum genome. We show that PfKch1 and PfKch2 and a C-terminally truncated version of PfKch1 (PfKch11−1094) could indeed be functionally expressed in vivo, since a K+-uptake deficient Saccharomyces cerevisiae strain was complemented by the P. falciparum cDNAs. PfKch11−1094-GFP and GFP-PfKch2 fusion proteins were overexpressed in yeast, purified and reconstituted in lipid bilayers to determine their electrophysiological activity. Single channel conductance amounted to 16 ± 1 pS for PfKch11−1094-GFP and 28 ± 2 pS for GFP-PfKch2. We predicted regulator of K+-conductance (RCK) domains in the C-terminals of both channels, and we accordingly measured channel activity in the presence of Ca2+.
Collapse
Affiliation(s)
- Karen Molbaek
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Maria Tejada
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark
| | - Christina Hoeier Ricke
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark
| | - Peter Scharff-Poulsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark
| | - Peter Ellekvist
- Medical Department, Herlev-Gentofte Hospital, Herlev, 2730, Denmark
| | - Claus Helix-Nielsen
- Aquaporin A/S, Kgs Lyngby, 2800, Denmark.,Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, 2800, Denmark.,University of Maribor, Laboratory for Water Biophysics and Membrane Technology, Maribor, 2000, Slovenia
| | - Nirbhay Kumar
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington DC, 20052-0066, USA
| | - Dan A Klaerke
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, 1870, Denmark.
| | | |
Collapse
|
33
|
Engineering an oleaginous yeast Candida tropicalis SY005 for enhanced lipid production. Appl Microbiol Biotechnol 2020; 104:8399-8411. [DOI: 10.1007/s00253-020-10830-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 12/23/2022]
|
34
|
Kemppainen M, Chowdhury J, Lundberg-Felten J, Pardo A. Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes. Curr Genet 2020; 66:791-811. [PMID: 32170354 DOI: 10.1007/s00294-020-01060-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 10/24/2022]
Abstract
For long time, studies on ectomycorrhiza (ECM) have been limited by inefficient expression of fluorescent proteins (FPs) in the fungal partner. To convert this situation, we have evaluated the basic requirements of FP expression in the model ECM homobasidiomycete Laccaria bicolor and established eGFP and mCherry as functional FP markers. Comparison of intron-containing and intronless FP-expression cassettes confirmed that intron-processing is indispensable for efficient FP expression in Laccaria. Nuclear FP localization was obtained via in-frame fusion of FPs between the intron-containing genomic gene sequences of Laccaria histone H2B, while cytosolic FP expression was produced by incorporating the intron-containing 5' fragment of the glyceraldehyde-3-phosphate dehydrogenase encoding gene. In addition, we have characterized the consensus Kozak sequence of strongly expressed genes in Laccaria and demonstrated its boosting effect on transgene mRNA accumulation. Based on these results, an Agrobacterium-mediated transformation compatible plasmid set was designed for easy use of FPs in Laccaria. The four cloning plasmids presented here allow fast and highly flexible construction of C-terminal in-frame fusions between the sequences of interest and the two FPs, expressed either from the endogenous gene promoter, allowing thus evaluation of the native regulation modes of the gene under study, or alternatively, from the constitutive Agaricus bisporus gpdII promoter for enhanced cellular protein localization assays. The molecular tools described here for cell-biological studies in Laccaria can also be exploited in studies of other biotrophic or saprotrophic basidiomycete species susceptible to genetic transformation.
Collapse
Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina.
| | - Jamil Chowdhury
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Judith Lundberg-Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina
| |
Collapse
|
35
|
Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis. Nat Commun 2020; 11:2926. [PMID: 32522991 PMCID: PMC7286901 DOI: 10.1038/s41467-020-16804-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/27/2020] [Indexed: 12/29/2022] Open
Abstract
Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis. Changes in osmotic homeostasis alter metabolites and therefore chemical milieu of the cells. Here, the authors show that altering metabolites in E. coli also change the cellular capacity for buffering mutations that impair protein folding and influences proteostasis irrespective of molecular chaperones
Collapse
|
36
|
Lodens S, Roelants SLKW, Luyten G, Geys R, Coussement P, De Maeseneire SL, Soetaert W. Unraveling the regulation of sophorolipid biosynthesis in Starmerella bombicola. FEMS Yeast Res 2020; 20:5824630. [DOI: 10.1093/femsyr/foaa021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
ABSTRACTStarmerella bombicola very efficiently produces the secondary metabolites sophorolipids (SLs). Their biosynthesis is not-growth associated and highly upregulated in the stationary phase. Despite high industrial and academic interest, the underlying regulation of SL biosynthesis remains unknown. In this paper, potential regulation of SL biosynthesis through the telomere positioning effect (TPE) was investigated, as the SL gene cluster is located adjacent to a telomere. An additional copy of this gene cluster was introduced elsewhere in the genome to investigate if this results in a decoy of regulation. Indeed, for the new strain, the onset of SL production was shifted to the exponential phase. This result was confirmed by RT-qPCR analysis. The TPE effect was further investigated by developing and applying a suitable reporter system for this non-conventional yeast, enabling non-biased comparison of gene expression between the subtelomeric CYP52M1- and the URA3 locus. This was done with a constitutive endogenous promotor (pGAPD) and one of the endogenous promotors of the SL biosynthetic gene cluster (pCYP52M1). A clear positioning effect was observed for both promotors with significantly higher GFP expression levels at the URA3 locus. No clear GFP upregulation was observed in the stationary phase for any of the new strains.
Collapse
Affiliation(s)
- Sofie Lodens
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sophie L K W Roelants
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Goedele Luyten
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Robin Geys
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Pieter Coussement
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| |
Collapse
|
37
|
Presenting a codon-optimized palette of fluorescent proteins for use in Candida albicans. Sci Rep 2020; 10:6158. [PMID: 32273559 PMCID: PMC7145796 DOI: 10.1038/s41598-020-63308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Fluorescent proteins with varying colors are indispensable tools for the life sciences research community. These fluorophores are often developed for use in mammalian systems, with incremental enhancements or new versions published frequently. However, the successful application of these labels in other organisms in the tree of life, such as the fungus Candida albicans, can be difficult to achieve due to the difficulty in engineering constructs for good expression in these organisms. In this contribution, we present a palette of Candida-optimized fluorescent proteins ranging from cyan to red and assess their application potential. We also compare a range of reported expression optimization techniques, and find that none of these strategies is generally applicable, and that even very closely related proteins require the application of different strategies to achieve good expression. In addition to reporting new fluorescent protein variants for applications in Candida albicans, our work highlights the ongoing challenges in optimizing protein expression in heterologous systems.
Collapse
|
38
|
Kassem N, Kassem MM, Pedersen SF, Pedersen PA, Kragelund BB. Yeast recombinant production of intact human membrane proteins with long intrinsically disordered intracellular regions for structural studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183272. [PMID: 32169592 DOI: 10.1016/j.bbamem.2020.183272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 01/07/2023]
Abstract
Membrane proteins exist in lipid bilayers and mediate solute transport, signal transduction, cell-cell communication and energy conversion. Their activities are fundamental for life, which make them prominent subjects of study, but access to only a limited number of high-resolution structures complicates their mechanistic understanding. The absence of such structures relates mainly to difficulties in expressing and purifying high quality membrane protein samples in large quantities. An additional layer of complexity stems from the presence of intra- and/or extra-cellular domains constituted by unstructured intrinsically disordered regions (IDR), which can be hundreds of residues long. Although IDRs form key interaction hubs that facilitate biological processes, these are regularly removed to enable structural studies. To advance mechanistic insight into intact intrinsically disordered membrane proteins, we have developed a protocol for their purification. Using engineered yeast cells for optimized expression and purification, we have purified to homogeneity two very different human membrane proteins each with >300 residues long IDRs; the sodium proton exchanger 1 and the growth hormone receptor. Subsequent to their purification we have further explored their incorporation into membrane scaffolding protein nanodiscs, which will enable future structural studies.
Collapse
Affiliation(s)
- Noah Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maher M Kassem
- Machine Learning, Department of Computer Science, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen Ø, Denmark
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
| | - Per Amstrup Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
| |
Collapse
|
39
|
Establishment of tetracycline-regulated bimolecular fluorescence complementation assay to detect protein-protein interactions in Candida albicans. Sci Rep 2020; 10:2936. [PMID: 32076074 PMCID: PMC7031294 DOI: 10.1038/s41598-020-59891-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/03/2020] [Indexed: 01/05/2023] Open
Abstract
To visualize protein-protein interactions in Candida albicans with the bimolecular fluorescence complementation (BiFC) approach, we created a Tet-on system with the plasmids pWTN1 and pWTN2. Both plasmids bear a hygromycin B-resistant marker (CaHygB) that is compatible with the original Tet-on plasmid pNIM1, which carries a nourseothricin-resistant marker (CaSAT1). By using GFPmut2 and mCherry as reporters, we found that the two complementary Tet-on plasmids act synergistically in C. albicans with doxycycline in a dose-dependent manner and that expression of the fusion proteins, CaCdc11-GFPmut2 and mCherry-CaCdc10, derived from this system, is septum targeted. Furthermore, to allow detection of protein-protein interactions with the reassembly of a split fluorescent protein, we incorporated mCherry into our system. We generated pWTN1-RN and pNIM1-RC, which express the N-terminus (amino acids 1–159) and C-terminus (amino acids 160–237) of mCherry, respectively. To verify BiFC with mCherry, we created the pWTN1-CDC42-RN (or pWTN1-RN-CDC42) and pNIM1-RC-RDI1 plasmids. C. albicans cells containing these plasmids treated with doxycycline co-expressed the N- and C-terminal fragments of mCherry either N-terminally or C-terminally fused with CaCdc42 and CaRdi1, respectively, and the CaCdc42-CaRdi1 interaction reconstituted a functional form of mCherry. The establishment of this Tet-on-based BiFC system in C. albicans should facilitate the exploration of protein-protein interactions under a variety of conditions.
Collapse
|
40
|
Kozlova NV, Pichon C, Rahmouni AR. mRNA with Mammalian Codon Bias Accumulates in Yeast Mutants with Constitutive Stress Granules. Int J Mol Sci 2020; 21:ijms21041234. [PMID: 32059599 PMCID: PMC7072924 DOI: 10.3390/ijms21041234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Stress granules and P bodies are cytoplasmic structures assembled in response to various stress factors and represent sites of temporary storage or decay of mRNAs. Depending on the source of stress, the formation of these structures may be driven by distinct mechanisms, but several stresses have been shown to stabilize mRNAs via inhibition of deadenylation. A recent study identified yeast gene deletion mutants with constitutive stress granules and elevated P bodies; however, the mechanisms which trigger its formation remain poorly understood. Here, we investigate the possibility of accumulating mRNA with mammalian codon bias, which we termed the model RNA, in these mutants. We found that the model RNA accumulates in dcp2 and xrn1 mutants and in four mutants with constitutive stress granules overlapping with P bodies. However, in eight other mutants with constitutive stress granules, the model RNA is downregulated, or its steady state levels vary. We further suggest that the accumulation of the model RNA is linked to its protection from the main mRNA surveillance path. However, there is no obvious targeting of the model RNA to stress granules or P bodies. Thus, accumulation of the model RNA and formation of constitutive stress granules occur independently and only some paths inducing formation of constitutive stress granules will stabilize mRNA as well.
Collapse
Affiliation(s)
- Natalia V. Kozlova
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Colléguim Sciences et Techniques, Université d’Orléans, 45071 Orléans, France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
| |
Collapse
|
41
|
Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S. ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO J 2020; 39:e102586. [PMID: 31802527 PMCID: PMC6960443 DOI: 10.15252/embj.2019102586] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
ER-phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER-phagy can occur by macroautophagic and microautophagic mechanisms. While dedicated machinery for macro-ER-phagy has been discovered, the molecules and mechanisms mediating micro-ER-phagy remain unknown. Here, we first show that micro-ER-phagy in yeast involves the conversion of stacked cisternal ER into multilamellar ER whorls during microautophagic uptake into lysosomes. Second, we identify the conserved Nem1-Spo7 phosphatase complex and the ESCRT machinery as key components for micro-ER-phagy. Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements. Finally, we provide evidence that the ESCRT machinery directly functions in scission of the lysosomal membrane to complete the microautophagic uptake of ER. These findings establish a framework for a mechanistic understanding of micro-ER-phagy and, thus, a comprehensive appreciation of the role of autophagy in ER homeostasis.
Collapse
Affiliation(s)
- Jasmin A Schäfer
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Julia P Schessner
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Peter W Bircham
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Laboratory of Systems BiologyVIB Center for Microbiology/Laboratory of Genetics and GenomicsCMPGKU LeuvenLeuvenBelgium
| | - Takuma Tsuji
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Charlotta Funaya
- Electron Microscopy Core FacilityHeidelberg UniversityHeidelbergGermany
| | - Oliver Pajonk
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Katharina Schaeff
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Giulia Ruffini
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Dimitrios Papagiannidis
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Michael Knop
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Sebastian Schuck
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| |
Collapse
|
42
|
Moriya H. The expression level and cytotoxicity of green fluorescent protein are modulated by an additional N-terminal sequence. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
43
|
Hohnholz R, Achstetter T. Recombination in yeast based on six base pairs of homologous sequences: Structural instability in two sets of isomeric model expression plasmids. Yeast 2019; 37:207-216. [DOI: 10.1002/yea.3393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ruben Hohnholz
- Department of Industrial MicrobiologyCity University of Applied Sciences Bremen Bremen Germany
| | - Tilman Achstetter
- Department of Industrial MicrobiologyCity University of Applied Sciences Bremen Bremen Germany
| |
Collapse
|
44
|
Hector RE, Mertens JA, Nichols NN. Development and characterization of vectors for tunable expression of both xylose-regulated and constitutive gene expression in Saccharomyces yeasts. N Biotechnol 2019; 53:16-23. [DOI: 10.1016/j.nbt.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
|
45
|
Muncanovic D, Justesen MH, Preisler SS, Pedersen PA. Characterization of Hailey-Hailey Disease-mutants in presence and absence of wild type SPCA1 using Saccharomyces cerevisiae as model organism. Sci Rep 2019; 9:12442. [PMID: 31455819 PMCID: PMC6712213 DOI: 10.1038/s41598-019-48866-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Hailey-Hailey disease is an autosomal genetic disease caused by mutations in one of the two ATP2C1 alleles encoding the secretory pathway Ca2+/Mn2+-ATPase, hSPCA1. The disease almost exclusively affects epidermis, where it mainly results in acantholysis of the suprabasal layers. The etiology of the disease is complex and not well understood. We applied a yeast based complementation system to characterize fourteen disease-causing ATP2C1 missense mutations in presence or absence of wild type ATP2C1 or ATP2A2, encoding SERCA2. In our yeast model system, mutations in ATP2C1 affected Mn2+ transport more than Ca2+ transport as twelve out of fourteen mutations were unable to complement Mn2+ sensitivity while thirteen out of fourteen to some extent complemented the high Ca2+requirement. Nine out of fourteen mutations conferred a cold sensitive complementation capacity. In absence of a wild type ATP2C1 allele, twelve out of fourteen mutations induced an unfolded protein response indicating that in vivo folding of hSPCA1 is sensitive to disease causing amino acid substitutions and four of the fourteen mutations caused the hSPCA1 protein to accumulate in the vacuolar membrane. Co-expression of either wild type ATP2C1 or ATP2A2 prevented induction of the unfolded protein response and hSPCA1 mis-localization.
Collapse
Affiliation(s)
- Daniel Muncanovic
- Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, OE, Denmark
| | - Mette Heberg Justesen
- Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, OE, Denmark
| | - Sarah Spruce Preisler
- Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, OE, Denmark
| | - Per Amstrup Pedersen
- Department of Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, OE, Denmark.
| |
Collapse
|
46
|
Petersen SD, Zhang J, Lee JS, Jakociunas T, Grav LM, Kildegaard HF, Keasling JD, Jensen MK. Modular 5'-UTR hexamers for context-independent tuning of protein expression in eukaryotes. Nucleic Acids Res 2019; 46:e127. [PMID: 30124898 PMCID: PMC6265478 DOI: 10.1093/nar/gky734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/01/2018] [Indexed: 11/25/2022] Open
Abstract
Functional characterization of regulatory DNA elements in broad genetic contexts is a prerequisite for forward engineering of biological systems. Translation initiation site (TIS) sequences are attractive to use for regulating gene activity and metabolic pathway fluxes because the genetic changes are minimal. However, limited knowledge is available on tuning gene outputs by varying TISs in different genetic and environmental contexts. Here, we created TIS hexamer libraries in baker’s yeast Saccharomyces cerevisiae directly 5′ end of a reporter gene in various promoter contexts and measured gene activity distributions for each library. Next, selected TIS sequences, resulted in almost 10-fold changes in reporter outputs, were experimentally characterized in various environmental and genetic contexts in both yeast and mammalian cells. From our analyses, we observed strong linear correlations (R2 = 0.75–0.98) between all pairwise combinations of TIS order and gene activity. Finally, our analysis enabled the identification of a TIS with almost 50% stronger output than a commonly used TIS for protein expression in mammalian cells, and selected TISs were also used to tune gene activities in yeast at a metabolic branch point in order to prototype fitness and carotenoid production landscapes. Taken together, the characterized TISs support reliable context-independent forward engineering of translation initiation in eukaryotes.
Collapse
Affiliation(s)
- Søren D Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jae S Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tadas Jakociunas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lise M Grav
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helene F Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.,Joint BioEnergy Institute, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA 94720, USA.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
47
|
Rao L, Berger F, Nicholas MP, Gennerich A. Molecular mechanism of cytoplasmic dynein tension sensing. Nat Commun 2019; 10:3332. [PMID: 31350388 PMCID: PMC6659695 DOI: 10.1038/s41467-019-11231-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cytoplasmic dynein is the most complex cytoskeletal motor protein and is responsible for numerous biological functions. Essential to dynein’s function is its capacity to respond anisotropically to tension, so that its microtubule-binding domains bind microtubules more strongly when under backward load than forward load. The structural mechanisms by which dynein senses directional tension, however, are unknown. Using a combination of optical tweezers, mutagenesis, and chemical cross-linking, we show that three structural elements protruding from the motor domain—the linker, buttress, and stalk—together regulate directional tension-sensing. We demonstrate that dynein’s anisotropic response to directional tension is mediated by sliding of the coiled-coils of the stalk, and that coordinated conformational changes of dynein’s linker and buttress control this process. We also demonstrate that the stalk coiled-coils assume a previously undescribed registry during dynein’s stepping cycle. We propose a revised model of dynein’s mechanochemical cycle which accounts for our findings. The cytoplasmic motor protein dynein senses directional tension; its microtubule-binding domains bind microtubules more strongly when under backward load. Here the authors use optical tweezers to show that the linker, buttress, and stalk domains together regulate directional tension-sensing.
Collapse
Affiliation(s)
- Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Florian Berger
- Laboratory of Sensory Neuroscience, Rockefeller University, New York, NY, 10065, USA
| | - Matthew P Nicholas
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Medical Scientist Training Program, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Flaum Eye Institute, University of Rochester Medical Center, 210 Crittenden Blvd, Rochester, NY, 14642, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| |
Collapse
|
48
|
Shellhammer JP, Pomeroy AE, Li Y, Dujmusic L, Elston TC, Hao N, Dohlman HG. Quantitative analysis of the yeast pheromone pathway. Yeast 2019; 36:495-518. [PMID: 31022772 DOI: 10.1002/yea.3395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 01/04/2023] Open
Abstract
The pheromone response pathway of the yeast Saccharomyces cerevisiae is a well-established model for the study of G proteins and mitogen-activated protein kinase (MAPK) cascades. Our longstanding ability to combine sophisticated genetic approaches with established functional assays has provided a thorough understanding of signalling mechanisms and regulation. In this report, we compare new and established methods used to quantify pheromone-dependent MAPK phosphorylation, transcriptional induction, mating morphogenesis, and gradient tracking. These include both single-cell and population-based assays of activity. We describe several technical advances, provide example data for benchmark mutants, highlight important differences between newer and established methodologies, and compare the advantages and disadvantages of each as applied to the yeast model. Quantitative measurements of pathway activity have been used to develop mathematical models and reveal new regulatory mechanisms in yeast. It is our expectation that experimental and computational approaches developed in yeast may eventually be adapted to human systems biology and pharmacology.
Collapse
Affiliation(s)
- James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Amy E Pomeroy
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yang Li
- Division of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Lorena Dujmusic
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nan Hao
- Division of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| |
Collapse
|
49
|
Takagi J, Singh-Babak SD, Lohse MB, Dalal CK, Johnson AD. Candida albicans white and opaque cells exhibit distinct spectra of organ colonization in mouse models of infection. PLoS One 2019; 14:e0218037. [PMID: 31170229 PMCID: PMC6553767 DOI: 10.1371/journal.pone.0218037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Candida albicans, a species of fungi, can thrive in diverse niches of its mammalian hosts; it is a normal resident of the GI tract and mucosal surfaces but it can also enter the bloodstream and colonize internal organs causing serious disease. The ability of C. albicans to thrive in these different host environments has been attributed, at least in part, to its ability to assume different morphological forms. In this work, we examine one such morphological change known as white-opaque switching. White cells are the default state of C. albicans, and most animal studies have been carried out exclusively with white cells. Here, we compared the proliferation of white and opaque cells in two murine models of infection and also monitored, using specially constructed strains, switching between the two states in the host. We found that white cells outcompeted opaque cells in many niches; however, we show for the first time that in some organs (specifically, the heart and spleen), opaque cells competed favorably with white cells and, when injected on their own, could colonize these organs. In environments where the introduced white cells outcompeted the introduced opaque cells, we observed high rates of opaque-to-white switching. We did not observe white-to-opaque switching in any of the niches we examined.
Collapse
Affiliation(s)
- Julie Takagi
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Sheena D. Singh-Babak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Matthew B. Lohse
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Chiraj K. Dalal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States of America
- * E-mail: (ADJ); (CKD)
| | - Alexander D. Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States of America
- * E-mail: (ADJ); (CKD)
| |
Collapse
|
50
|
Chapuis AF, Ballou ER, MacCallum DM. A Bright Future for Fluorescence Imaging of Fungi in Living Hosts. J Fungi (Basel) 2019; 5:jof5020029. [PMID: 30987114 PMCID: PMC6616859 DOI: 10.3390/jof5020029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 12/24/2022] Open
Abstract
Traditional in vivo investigation of fungal infection and new antifungal therapies in mouse models is usually carried out using post mortem methodologies. However, biomedical imaging techniques focusing on non-invasive techniques using bioluminescent and fluorescent proteins have become valuable tools. These new techniques address ethical concerns as they allow reduction in the number of animals required to evaluate new antifungal therapies. They also allow better understanding of the growth and spread of the pathogen during infection. In this review, we concentrate on imaging technologies using different fungal reporter proteins. We discuss the advantages and limitations of these different reporters and compare the efficacy of bioluminescent and fluorescent proteins for fungal research.
Collapse
Affiliation(s)
- Ambre F Chapuis
- MRC Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Elizabeth R Ballou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Donna M MacCallum
- MRC Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| |
Collapse
|