Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability:
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
Heidelberg
2022
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Physical Description: | v, 170 Seiten Illustrationen, Diagramme 30 cm |
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MARC
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| 100 | 1 | |a Bosch, Katharina |d 1989- |e Verfasser |0 (DE-588)1278718362 |4 aut | |
| 245 | 1 | 0 | |a Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |c presented by M.Sc. Katharina Bosch |
| 264 | 1 | |a Heidelberg |c 2022 | |
| 300 | |a v, 170 Seiten |b Illustrationen, Diagramme |c 30 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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| 502 | |b Dissertation |c Ruperto Carola University Heidelberg, Germany |d 2022 | ||
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Record in the Search Index
| _version_ | 1804185095752384512 |
|---|---|
| adam_text | TABLE
OF
CONTENTS
ACKNOWLEDGEMENTS
1
SUMMARY
3
ZUSAMMENFASSUNG
5
1.
INTRODUCTION
11
1.1.
SOURCES
AND
REGULATION
OF
OXIDANTS
........................................................
11
1.1.1.
HYDROGEN
PEROXIDE
AND
OTHER
BIOLOGICALLY
RELEVANT
OXIDANTS
.
.
12
1.1.2.
REGULATION
OF
OXIDANTS
................................................................
15
1.1.3.
METAL-BASED
OXIDANT
SCAVENGERS
.................................................
15
1.1.4.
THE
GLUTATHIONE
SYSTEM
.............................................................
15
1.1.5.
THE
THIOREDOXIN
SYSTEM
.............................................................
16
1.2.
PROTEIN
THIOL
OXIDATION
AND
SIGNALLING
...................................................
17
1.3.
ROGFP2
....................................................................................................
19
1.4.
YEAST
AS
A
MODEL
ORGANISM
FOR
REDOX
BIOLOGY
...........................................
21
1.5.
OBJECTIVE
.....................................................................................................
24
2.
MATERIALS
AND
METHODS
29
2.1.
MATERIALS
.....................................................................................................
29
2.1.1.
CHEMICALS
AND
BIOCHEMICALS
..........................................................
31
2.1.2.
KITS,
ENZYMES
AND
OTHERS
.............................................................
31
2.1.3.
ANTIBODIES
.....................................................................................
32
2.1.4.
OLIGONUCLEOTIDES
AND
PLASMIDS
.......................................................
33
2.1.5.
BUFFERS
AND
MEDIA
.........................................................................
42
2.1.6.
BIOLOGICAL
MATERIAL
.........................................................................
43
2.1.7.
SOFTWARE
...............................................................
44
2.2.
METHODS
........................................................................................................
45
2.2.1.
YEAST
GROWTH
CONDITIONS
................................................................
45
2.2.2.
TRANSFORMATION
OF
YEAST
................................................................
46
7
2.2.3.
LIBRARY
CONSTRUCTION
AND
VALIDATION
...............................................
47
2.2.4.
ADDITIONAL
YEAST
STRAINS
..................................................................
48
2.2.5.
LIBRARY
MEASUREMENT
........................................................................
48
2.2.6.
DATA
ANALYSIS
....................................................................................
49
2.2.7.
PLATE
READER
MEASUREMENTS
.......................................................
49
2.2.8.
MICROSCOPY
........................................................................................
50
2.2.9.
CELL
LYSIS,
SDS-PAGE,
AND
IMMUNOBLOTTING
...................
YY
.
.
.
50
2.2.10.
COVALENT
MODIFICATION
WITH
METHOXYPOLYETHYLENEGLYCOL
MALEIMIDE
(PEG-MAL)
....................................................................
50
2.2.11.
FLOW
CYTOMETRY
...............................................................................
51
2.2.12.
METABOLIC
SHIFT
EXPERIMENT
OF
SELECTED
STRAINS
...........................
51
2.2.13.
HYPOXIA
MEASUREMENTS
...................................................................
51
2.2.14.
ASNL-ROGFP2
MICROSCOPY
AND
PLATE
READER
ASSAY
......................
52
3.
RESULTS
53
3.1.
LIBRARY
CONSTRUCTION,
MEASUREMENT
AND
ANALYSIS
.........................................
53
3.2.
IDENTIFICATION
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
...........................
.
63
3.3.
IDENTIFICATION
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
USING
AN
ALTERNATIVE
APPROACH
.........................................................................................................
73
3.4.
FUSION
PROTEIN
SPECIFIC
REDOX
DIFFERENCES
ACROSS
DIFFERENT
METABOLIC
CONDITIONS
......................................................................................................
81
3.5.
OXIDATION
OF
ASNL-ROGFP2
CORRELATES
WITH
THE
FORMATION
OF
CYTOOPHIDIAE
...................................................................................................
86
4.
DISCUSSION
93
4.1.
CHALLENGES
OF
C-TERMINAL
TAGGING
IN
GENERAL
...........................................
93
4.2.
CHALLENGES
OF
ENDOGENOUS
C-TERMINAL
TAGGING
WITH
ROGFP2
...................
94
4.3.
GENERAL
OBSERVATIONS
...................................................................................
96
4.4.
LOCAL
AND
CONTEXT
SPECIFIC
ROGFP2
OXIDATION
...........................................
97
4.5.
POSSIBLE
OXIDATION
OF
ROGFP2
ASSOCIATED
PROTEINS
................................
100
4.6.
CONCLUSIONS
AND
FUTURE
DIRECTIONS
............................................................
101
5.
REFERENCES
107
8
APPENDICES
121
A.
APPENDIX
123
A.1.
LIST
OF
ROGFP2
FUSION
PROTEINS
FOUND
TO
BE
OXIDISED
USING
THE
R/R
APPROACH
..............................................................................................
123
A.
2.
GO
ENRICHMENT
INCLUDING
SEMANTIC
SIMILARITY
CLUSTERING
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
(R/R
APPROACH)
.......................................
126
A.
3.
LIST
OF
ROGFP2
FUSION
PROTEINS
FOUND
TO
BE
OXIDISED
USING
THE
485/485
APPROACH
..............................................................................................
131
A.
4.
GO
ENRICHMENT
INCLUDING
SEMANTIC
SIMILARITY
CLUSTERING
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
(485/485
APPROACH)
.................................
148
9
|
| adam_txt |
TABLE
OF
CONTENTS
ACKNOWLEDGEMENTS
1
SUMMARY
3
ZUSAMMENFASSUNG
5
1.
INTRODUCTION
11
1.1.
SOURCES
AND
REGULATION
OF
OXIDANTS
.
11
1.1.1.
HYDROGEN
PEROXIDE
AND
OTHER
BIOLOGICALLY
RELEVANT
OXIDANTS
.
.
12
1.1.2.
REGULATION
OF
OXIDANTS
.
15
1.1.3.
METAL-BASED
OXIDANT
SCAVENGERS
.
15
1.1.4.
THE
GLUTATHIONE
SYSTEM
.
15
1.1.5.
THE
THIOREDOXIN
SYSTEM
.
16
1.2.
PROTEIN
THIOL
OXIDATION
AND
SIGNALLING
.
17
1.3.
ROGFP2
.
19
1.4.
YEAST
AS
A
MODEL
ORGANISM
FOR
REDOX
BIOLOGY
.
21
1.5.
OBJECTIVE
.
24
2.
MATERIALS
AND
METHODS
29
2.1.
MATERIALS
.
29
2.1.1.
CHEMICALS
AND
BIOCHEMICALS
.
31
2.1.2.
KITS,
ENZYMES
AND
OTHERS
.
31
2.1.3.
ANTIBODIES
.
32
2.1.4.
OLIGONUCLEOTIDES
AND
PLASMIDS
.
33
2.1.5.
BUFFERS
AND
MEDIA
.
42
2.1.6.
BIOLOGICAL
MATERIAL
.
43
2.1.7.
SOFTWARE
.
44
2.2.
METHODS
.
45
2.2.1.
YEAST
GROWTH
CONDITIONS
.
45
2.2.2.
TRANSFORMATION
OF
YEAST
.
46
7
2.2.3.
LIBRARY
CONSTRUCTION
AND
VALIDATION
.
47
2.2.4.
ADDITIONAL
YEAST
STRAINS
.
48
2.2.5.
LIBRARY
MEASUREMENT
.
48
2.2.6.
DATA
ANALYSIS
.
49
2.2.7.
PLATE
READER
MEASUREMENTS
.
49
2.2.8.
MICROSCOPY
.
50
2.2.9.
CELL
LYSIS,
SDS-PAGE,
AND
IMMUNOBLOTTING
.
YY
.
.
.
50
2.2.10.
COVALENT
MODIFICATION
WITH
METHOXYPOLYETHYLENEGLYCOL
MALEIMIDE
(PEG-MAL)
.
50
2.2.11.
FLOW
CYTOMETRY
.
51
2.2.12.
METABOLIC
SHIFT
EXPERIMENT
OF
SELECTED
STRAINS
.
51
2.2.13.
HYPOXIA
MEASUREMENTS
.
51
2.2.14.
ASNL-ROGFP2
MICROSCOPY
AND
PLATE
READER
ASSAY
.
52
3.
RESULTS
53
3.1.
LIBRARY
CONSTRUCTION,
MEASUREMENT
AND
ANALYSIS
.
53
3.2.
IDENTIFICATION
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
.
.
63
3.3.
IDENTIFICATION
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
USING
AN
ALTERNATIVE
APPROACH
.
73
3.4.
FUSION
PROTEIN
SPECIFIC
REDOX
DIFFERENCES
ACROSS
DIFFERENT
METABOLIC
CONDITIONS
.
81
3.5.
OXIDATION
OF
ASNL-ROGFP2
CORRELATES
WITH
THE
FORMATION
OF
CYTOOPHIDIAE
.
86
4.
DISCUSSION
93
4.1.
CHALLENGES
OF
C-TERMINAL
TAGGING
IN
GENERAL
.
93
4.2.
CHALLENGES
OF
ENDOGENOUS
C-TERMINAL
TAGGING
WITH
ROGFP2
.
94
4.3.
GENERAL
OBSERVATIONS
.
96
4.4.
LOCAL
AND
CONTEXT
SPECIFIC
ROGFP2
OXIDATION
.
97
4.5.
POSSIBLE
OXIDATION
OF
ROGFP2
ASSOCIATED
PROTEINS
.
100
4.6.
CONCLUSIONS
AND
FUTURE
DIRECTIONS
.
101
5.
REFERENCES
107
8
APPENDICES
121
A.
APPENDIX
123
A.1.
LIST
OF
ROGFP2
FUSION
PROTEINS
FOUND
TO
BE
OXIDISED
USING
THE
R/R
APPROACH
.
123
A.
2.
GO
ENRICHMENT
INCLUDING
SEMANTIC
SIMILARITY
CLUSTERING
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
(R/R
APPROACH)
.
126
A.
3.
LIST
OF
ROGFP2
FUSION
PROTEINS
FOUND
TO
BE
OXIDISED
USING
THE
485/485
APPROACH
.
131
A.
4.
GO
ENRICHMENT
INCLUDING
SEMANTIC
SIMILARITY
CLUSTERING
OF
OXIDISED
ROGFP2
FUSION
PROTEINS
(485/485
APPROACH)
.
148
9 |
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| author_GND | (DE-588)1278718362 |
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| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV048918064 |
| illustrated | Illustrated |
| index_date | 2024-07-03T21:55:08Z |
| indexdate | 2024-07-10T09:49:47Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-034182159 |
| oclc_num | 1372146732 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | v, 170 Seiten Illustrationen, Diagramme 30 cm |
| publishDate | 2022 |
| publishDateSearch | 2022 |
| publishDateSort | 2022 |
| record_format | marc |
| spelling | Bosch, Katharina 1989- Verfasser (DE-588)1278718362 aut Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability presented by M.Sc. Katharina Bosch Heidelberg 2022 v, 170 Seiten Illustrationen, Diagramme 30 cm txt rdacontent n rdamedia nc rdacarrier Dissertation Ruperto Carola University Heidelberg, Germany 2022 (DE-588)4113937-9 Hochschulschrift gnd-content B:DE-101 application/pdf https://d-nb.info/1278052933/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034182159&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p dnb 20230215 DE-101 https://d-nb.info/provenance/plan#dnb |
| spellingShingle | Bosch, Katharina 1989- Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| subject_GND | (DE-588)4113937-9 |
| title | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| title_auth | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| title_exact_search | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| title_exact_search_txtP | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| title_full | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability presented by M.Sc. Katharina Bosch |
| title_fullStr | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability presented by M.Sc. Katharina Bosch |
| title_full_unstemmed | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability presented by M.Sc. Katharina Bosch |
| title_short | Proteome-wide roGFP2-tagging reveals protein context-specific thiol oxidation and its modulation by nutrient availability |
| title_sort | proteome wide rogfp2 tagging reveals protein context specific thiol oxidation and its modulation by nutrient availability |
| topic_facet | Hochschulschrift |
| url | https://d-nb.info/1278052933/04 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034182159&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT boschkatharina proteomewiderogfp2taggingrevealsproteincontextspecificthioloxidationanditsmodulationbynutrientavailability |
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