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Article ; Online: The Effect of Calorie Restriction on Protein Quality Control in Yeast.

Uvdal, Petter / Shashkova, Sviatlana

2023 Volume 13, Issue 5

Abstract: Initially, protein aggregates were regarded as a sign of a pathological state of the cell. Later, it was found that these assemblies are formed in response to stress, and that some of them serve as signalling mechanisms. This review has a particular ... ...

Abstract	Initially, protein aggregates were regarded as a sign of a pathological state of the cell. Later, it was found that these assemblies are formed in response to stress, and that some of them serve as signalling mechanisms. This review has a particular focus on how intracellular protein aggregates are related to altered metabolism caused by different glucose concentrations in the extracellular environment. We summarise the current knowledge of the role of energy homeostasis signalling pathways in the consequent effect on intracellular protein aggregate accumulation and removal. This covers regulation at different levels, including elevated protein degradation and proteasome activity mediated by the Hxk2 protein, the enhanced ubiquitination of aberrant proteins through Torc1/Sch9 and Msn2/Whi2, and the activation of autophagy mediated through
MeSH term(s)	Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Caloric Restriction ; Protein Aggregates ; Glucose/metabolism ; DNA-Binding Proteins/metabolism ; Transcription Factors/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; Protein Aggregates ; Glucose (IY9XDZ35W2) ; MSN2 protein, S cerevisiae ; DNA-Binding Proteins ; Transcription Factors ; Whi2 protein, S cerevisiae
Language	English
Publishing date	2023-05-15
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13050841
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Copy Number Analysis of the Yeast Histone Deacetylase Complex Component Cti6 Directly in Living Cells.

Shashkova, Sviatlana / Nyström, Thomas / Leake, Mark C

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2476, Page(s) 183–190

Abstract: Proteins are one of the key components of cellular life that play a crucial role in most biological processes. Therefore, quantification of protein copy numbers is essential for revealing and better understanding of cellular behavior and functions. Here ... ...

Abstract	Proteins are one of the key components of cellular life that play a crucial role in most biological processes. Therefore, quantification of protein copy numbers is essential for revealing and better understanding of cellular behavior and functions. Here we describe a single-molecule fluorescence-based method of protein copy number quantification directly in living cells. This enables quick and reliable estimations and comparison of the protein of interest abundance without implementing large-scale studies.
MeSH term(s)	Carrier Proteins/metabolism ; DNA Copy Number Variations ; Histone Deacetylases/metabolism ; Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Carrier Proteins ; Cti6 protein, S cerevisiae ; Proteins ; Saccharomyces cerevisiae Proteins ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2022-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2221-6_14
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Article ; Online: Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae.

Persson, Sebastian / Shashkova, Sviatlana / Österberg, Linnea / Cvijovic, Marija

FEMS yeast research

2022 Volume 22, Issue 1

Abstract: Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy homeostasis upon glucose derepression; hence, it plays an important role in ... ...

Abstract	Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy homeostasis upon glucose derepression; hence, it plays an important role in various processes, such as metabolism, cell cycle and autophagy. To unravel its behaviour, SNF1 signalling has been extensively studied. However, the pathway components are strongly interconnected and inconstant; therefore, elucidating its dynamic behaviour based on experimental data only is challenging. To tackle this complexity, systems biology approaches have been successfully employed. This review summarizes the progress, advantages and disadvantages of the available mathematical modelling frameworks covering Boolean, dynamic kinetic, single-cell models, which have been used to study processes and phenomena ranging from crosstalks to sources of cell-to-cell variability in the context of SNF1 signalling. Based on the lessons from existing models, we further discuss how to develop a consensus dynamic mechanistic model of the entire SNF1 pathway that can provide novel insights into the dynamics of nutrient signalling.
MeSH term(s)	Glucose/metabolism ; Protein Serine-Threonine Kinases ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction
Chemical Substances	Saccharomyces cerevisiae Proteins ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2022-03-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2036775-2
ISSN	1567-1364 ; 1567-1356
ISSN (online)	1567-1364
ISSN	1567-1356
DOI	10.1093/femsyr/foac012
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Article ; Online: Growth Rate Evaluation of the Budding Yeast Saccharomyces cerevisiae Cells Carrying Endogenously Expressed Fluorescent Protein Fusions.

Schneider, Kara L / Reibenspies, Lucas E / Nyström, Thomas / Shashkova, Sviatlana

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2564, Page(s) 213–222

Abstract: Fluorescent proteins within fluorescent fusions have been reported to affect cellular growth fitness via altering native protein function and intracellular localization. Here we report in detail a procedure to analyze the growth characteristics of yeast ... ...

Abstract	Fluorescent proteins within fluorescent fusions have been reported to affect cellular growth fitness via altering native protein function and intracellular localization. Here we report in detail a procedure to analyze the growth characteristics of yeast cells expressing such fusions in comparison to unmodified parental strain. This approach can serve as an initial step in fluorescent protein characterization in vivo.
MeSH term(s)	Coloring Agents/metabolism ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomycetales/metabolism
Chemical Substances	Coloring Agents ; Luminescent Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2022-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2667-2_10
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Article: Fine-Tuning of Energy Levels Regulates

Persson, Sebastian / Welkenhuysen, Niek / Shashkova, Sviatlana / Cvijovic, Marija

Frontiers in physiology

2020 Volume 11, Page(s) 954

Abstract: Nutrient sensing pathways are playing an important role in cellular response to different energy levels. In budding yeast, ...

Abstract	Nutrient sensing pathways are playing an important role in cellular response to different energy levels. In budding yeast,
Language	English
Publishing date	2020-08-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2020.00954
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Article ; Online: The effect of stress on biophysical characteristics of misfolded protein aggregates in living Saccharomyces cerevisiae cells.

Schnitzer, Barbara / Welkenhuysen, Niek / Leake, Mark C / Shashkova, Sviatlana / Cvijovic, Marija

Experimental gerontology

2022 Volume 162, Page(s) 111755

Abstract: Aggregation of misfolded or damaged proteins is often attributed to numerous metabolic and neurodegenerative disorders. To reveal underlying mechanisms and cellular responses, it is crucial to investigate protein aggregate dynamics in cells. Here, we ... ...

Abstract	Aggregation of misfolded or damaged proteins is often attributed to numerous metabolic and neurodegenerative disorders. To reveal underlying mechanisms and cellular responses, it is crucial to investigate protein aggregate dynamics in cells. Here, we used super-resolution single-molecule microscopy to obtain biophysical characteristics of individual aggregates of a model misfolded protein ∆ssCPY* labelled with GFP. We demonstrated that oxidative and hyperosmotic stress lead to increased aggregate stoichiometries but not necessarily the total number of aggregates. Moreover, our data suggest the importance of the thioredoxin peroxidase Tsa1 for the controlled sequestering and clearance of aggregates upon both conditions. Our work provides novel insights into the understanding of the cellular response to stress via revealing the dynamical properties of stress-induced protein aggregates.
MeSH term(s)	Oxidation-Reduction ; Protein Aggregates ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins
Chemical Substances	Protein Aggregates ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2022-02-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390992-x
ISSN	1873-6815 ; 0531-5565
ISSN (online)	1873-6815
ISSN	0531-5565
DOI	10.1016/j.exger.2022.111755
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Zs.A 579: Show issues

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Article ; Online: Comparison of endogenously expressed fluorescent protein fusions behaviour for protein quality control and cellular ageing research.

Schneider, Kara L / Wollman, Adam J M / Nyström, Thomas / Shashkova, Sviatlana

Scientific reports

2021 Volume 11, Issue 1, Page(s) 12819

Abstract: The yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress ... ...

Abstract	The yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. While concerns that bigger protein tags, such as genetically encoded fluorescent tags, may affect protein behaviour and function have been around for quite some time, experimental evidence of how exactly the physiology of the protein of interest is altered within fluorescent protein fusions remains limited. To address this issue, we performed a comparative assessment of endogenously expressed Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on such a tag within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects may play a role in other eukaryotic systems.
MeSH term(s)	Cellular Senescence ; Fluorescent Dyes/metabolism ; Green Fluorescent Proteins/metabolism ; Heat-Shock Proteins/metabolism ; Hot Temperature ; Intracellular Space/metabolism ; Protein Aggregates ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Fluorescent Dyes ; Heat-Shock Proteins ; Protein Aggregates ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; HsP104 protein, S cerevisiae (143012-44-6) ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2021-06-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-92249-1
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Article ; Online: Single-molecule fluorescence microscopy review: shedding new light on old problems.

Shashkova, Sviatlana / Leake, Mark C

Bioscience reports

2017 Volume 37, Issue 4

Abstract: Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many ... ...

Abstract	Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called 'green revolution', has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called 'super-resolution' fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques.
MeSH term(s)	Animals ; Green Fluorescent Proteins ; Humans ; Microscopy, Fluorescence/methods ; Microscopy, Fluorescence/trends ; Single Molecule Imaging/methods ; Single Molecule Imaging/trends
Chemical Substances	Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2017-07-21
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20170031
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Zs.A 1676: Show issues

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Article ; Online: Correlative single-molecule fluorescence barcoding of gene regulation in Saccharomyces cerevisiae.

Shashkova, Sviatlana / Nyström, Thomas / Leake, Mark C / Wollman, Adam J M

Methods (San Diego, Calif.)

2020 Volume 193, Page(s) 62–67

Abstract: Most cells adapt to their environment by switching combinations of genes on and off through a complex interplay of transcription factor proteins (TFs). The mechanisms by which TFs respond to signals, move into the nucleus and find specific binding sites ... ...

Abstract	Most cells adapt to their environment by switching combinations of genes on and off through a complex interplay of transcription factor proteins (TFs). The mechanisms by which TFs respond to signals, move into the nucleus and find specific binding sites in target genes is still largely unknown. Single-molecule fluorescence microscopes, which can image single TFs in live cells, have begun to elucidate the problem. Here, we show that different environmental signals, in this case carbon sources, yield a unique single-molecule fluorescence pattern of foci of a key metabolic regulating transcription factor, Mig1, in the nucleus of the budding yeast, Saccharomyces cerevisiae. This pattern serves as a 'barcode' of the gene regulatory state of the cells which can be correlated with cell growth characteristics and other biological function.
MeSH term(s)	Fluorescence ; Gene Expression Regulation ; Gene Expression Regulation, Fungal ; Repressor Proteins ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	MIG1 protein, S cerevisiae ; Repressor Proteins ; Saccharomyces cerevisiae Proteins ; Transcription Factors
Language	English
Publishing date	2020-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2020.10.009
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Zs.A 3239: Show issues

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Article: Correlative single-molecule fluorescence barcoding of gene regulation in Saccharomyces cerevisiae

Shashkova, Sviatlana / Nyström, Thomas / Leake, Mark C. / Wollman, Adam J.M.

Methods. 2021 Sept., v. 193

2021

Abstract	Most cells adapt to their environment by switching combinations of genes on and off through a complex interplay of transcription factor proteins (TFs). The mechanisms by which TFs respond to signals, move into the nucleus and find specific binding sites in target genes is still largely unknown. Single-molecule fluorescence microscopes, which can image single TFs in live cells, have begun to elucidate the problem. Here, we show that different environmental signals, in this case carbon sources, yield a unique single-molecule fluorescence pattern of foci of a key metabolic regulating transcription factor, Mig1, in the nucleus of the budding yeast, Saccharomyces cerevisiae. This pattern serves as a ‘barcode’ of the gene regulatory state of the cells which can be correlated with cell growth characteristics and other biological function.
Keywords	Saccharomyces cerevisiae ; carbon ; cell growth ; fluorescence ; genes ; transcription factors ; yeasts
Language	English
Dates of publication	2021-09
Size	p. 62-67.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2020.10.009
Database	NAL-Catalogue (AGRICOLA)

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