Effect of growth temperature on the transcriptome and proteome of Escherichia coli:
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
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Heidelberg
2017
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| Online-Zugang: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Beschreibung: | 171 Seiten Illustrationen 30 cm 1 CD-ROM |
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| 100 | 1 | |a Rudenko, Iaroslav |e Verfasser |0 (DE-588)1155029003 |4 aut | |
| 245 | 1 | 0 | |a Effect of growth temperature on the transcriptome and proteome of Escherichia coli |c presented by Master of Science Iraoslav Rudenko |
| 264 | 1 | |a Heidelberg |c 2017 | |
| 300 | |a 171 Seiten |b Illustrationen |c 30 cm |e 1 CD-ROM | ||
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| 502 | |b Dissertation |c Ruperto-Carola University of Heidelberg |d 2017 | ||
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Datensatz im Suchindex
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| adam_text | TABLE OF CONTENTS
I INTRODUCTION
1 EFFECTS OF TEMPERATURE ON GENE EXPRESSION
1.1 TEMPERATURE AS AN ENVIRONMENTAL
CUE.............................................................................3
1.2 THERMOREGULATION OF GENE EXPRESSION IN
YERSINIA............................................................4
1.3 THERMOREGULATION OF GENE EXPRESSION IN PSEUDOMONAS
...................................................
6
1.4 THERMOREGULATION OF GENE EXPRESSION IN E. C O
LI.............................................................. 8
1.5 GLOBAL REGULATORY MECHANISMS IN E.
COLI.........................................................................9
1.6 REGULATION OF CARBON METABOLISM IN E. COLI........................
11
1.7 ADAPTATION OF E. COLI TO AEROBIC AND ANAEROBIC CONDITIONS
.............................................
13
1.8 CARBON UTILIZATION IN DIFFERENT ENVIRONMENTS
..................................................................
15
1.9 ACID RESISTANCE AND
CHAPERONES.....................................................................................17
2 MOTILITY SYSTEM OF E. COLI
2.1 OVERVIEW OF THE MOTILITY
SYSTEM...................................................................................19
2.2 MOTILITY
APPARATUS...........................................................................................................20
2.3 RECEPTORS AND SIGNAL
TRANSDUCTION..................................................................................22
2.4 REGULATION OF EXPRESSION OF MOTILITY
GENES...................................................................
23
2.5 INVERSE REGULATION OF THE FLHDC AND RPOS REGULONS
.....................................................
26
2.6 REGULATION BY
FLGM........................................................................................................27
2.7 ENVIRONMENTAL TEMPERATURE AND M
OTILITY.......................................................................29
2.8 ANNOTATION OF THE FLHDC-FLIA REGULON
........................................................................31
3 AIMS OF THE CURRENT W
ORK.....................................................................................................33
II RESULTS
4 EFFECT OF GROWTH TEMPERATURE ON TRANSCRIPTOME AND PROTEOME OF E. COLI
4.1 GROWTH TEMPERATURE AFFECTS TRANSCRIPTOME AND
PROTEOME.............................................37
4.2 TRANSCRIPTOME AND PROTEOME COMPARISON AT 27C AND 32C
........................................
39
4.3 TRANSCRIPTOME AND PROTEOME COMPARISON AT 32C AND 37C
........................................46
4.4 TRANSCRIPTOME AND PROTEOME COMPARISON AT 37C AND 42C
........................................
53
4.5 TRANSCRIPTOME AND PROTEOME COMPARISON AT 27C AND 37C
........................................60
4.6 RESPIRATION AND OXIDATIVE STRESS
RESISTANCE.....................................................................68
4.7 ACID RESISTANCE AND
CHAPERONES......................................................................................70
4.8 ARGININE
METABOLISM......................................................................................................72
4.9 THREONINE AND PROPIONATE
METABOLISM...........................................................................73
4.10 PUTRESCINE METABOLISM
............................
76
4.11 QUORUM
SENSING............................................................................................................77
4.12 PHENYLACETIC ACID
METABOLISM.......................................................................................
78
4.13 BIOTIN
METABOLISM.........................................................................................................80
4.14 ENTEROBACTIN
BIOSYNTHESIS.............................................................................................81
4.15 PORINS (ENVZ/OMPR
SYSTEM).........................................................................................
82
4.16 REGULATORY
PROTEINS.......................................................................................................84
5 EFFECTS OF TEMPERATURE ON THE MOTILITY SYSTEM OF E. COLI
5.1 MOTILITY SYSTEM OF E. COLI SHOWED DISTINCT EXPRESSION
PROFILE.......................................86
5.2 FLGM IS RESPONSIBLE FOR 10 FOLD DOWNREGULATION OF THE CLASS 3 GENES
AT 42C
............
89
5.3 FLGM ACCUMULATES AT HIGH TEMPERATURE DUE TO AN INEFFICIENT SECRETION
.........................
90
6 EXPRESSION-PROFILE BASED ANNOTATION OF NEW GENES
6.1 EXPRESSION PROFILES AS A TOOL FOR FUNCTIONAL ANNOTATION OF NEW GENES
...........................
91
6.2 IDENTIFICATION OF FLHDC, FLIA, FLGM CONTROLLED
GENES..................................................93
6.3 OVERLAP OF THE FLHDC, FLIA, FLGM
REGULONS.................................................................95
6.4 CLASSIFICATION OF THE PREDICTED MOTILITY-RELATED
GENES...................................................98
6.5 DELETION OF THE NOVEL GENES AFFECTS MOTILITY AND EXPRESSION OF CLASS
1-2-3 REPORTERS. 107
6.6 OVEREXPRESSION OF THE NOVEL GENES AFFECTS MOTILITY AND EXPRESSION OF
CLASS 1-2-3
REPORTERS
.............................................................................................................................109
III DISCUSSION
7 GROWTH TEMPERATURE ACTS AS A CUE FOR THE LIFE STYLE
CHOICE.................................................115
8 MECHANISMS UNDERLYING THE LOSS OF MOTILITY AT HIGH TEMPERATURE
8.1 LOSS OF MOTILITY AT 42C INVOLVES REGULATION OF MOTILITY SYSTEM ON
MRNA
AND POSTTRANSCRIPTIONAL
LEVELS.............................................................................................
119
8.2 SEVERAL CRUCIAL COMPONENTS OF THE MOTILITY APPARATUS ARE
DOWNREGULATED AT 42C
....
120
8.3 REPRESSION OF MOTILITY GENES AT 42C OCCURS DUE TO THE INEFFICIENT
SECRETION OF
FLGM................................................................................................................122
9 NOVEL GENES RELATED TO THE MOTILITY REGULON OF E. COLI
9.1 TRANSCRIPTIONAL PROFILING CAN BE USED FOR ANNOTATION OF THE
PREVIOUSLY UNCHARACTERIZED
GENES TO THE GIVEN FUNCTIONAL PROCESS
................................................................................
124
9.2 REGULATION OF CLASS 1 AND OVERVIEW OF THE FLHDC REPRESSED GENES
............................
124
9.3 OVERVIEW OF THE NOVEL CLASS 2
GENES...........................................................................125
9.4 OVERVIEW OF THE NOVEL CLASS 3
GENES...........................................................................128
9.5 ROLE OF FLXA IN THE ASSEMBLY OF THE
FLAGELLUM............................................................130
9.6 COOCCURENCE ANALYSIS FROM STRING DATABASE SUGGESTS INVOLVEMENT OF
THE NOVEL TAXIS
GENES IN REGULATION OF THE MOTILITY, POSSIBLY THROUGH YDIV, FLHE AND
YCGR
...................
131
10 OUTLOOK
.....................................................
135
IV MATERIALS AND METHODS
11 MATERIALS
11.1 MEDIA AND
PLATES.........................................................................................................
139
11.2 AGAROSE GEL
ELECTROPHORESIS........................................................................................
140
11.3 RNA GEL
ELECTROPHORESIS.............................................................................................
141
11.4 SECRETION
ASSAY............................................................................................................
142
11.5 80S
PAGE..................................................................................................................
142
11.6 WESTERN
BLOT...............................................................................................................
143
11.7 TOTAL PROTEOME
ISOLATION.............................................................................................
143
11.8 MANIPULATION OF
BACTERIA............................................................................................
145
11.9
ANTIBIOTICS...................................................................................................................
146
11.10
INDUCERS....................................................................................................................146
11.11 STOCK
SOLUTION...........................................................................................................
146
11.12 REACTION
KITS.............................................................................................................
146
12 METHODS
12.1 MOLECULAR
CLONING......................................................
12.1.1 POLYMERASE CHAIN REACTION
..................................
12.1.2 RESTRICTION ENZYMES............................................
12.1.3
LIGATION...............................................................
12.1.4 COMPETENT
CELLS...................................................
12.1.5 ONE-STEP PREPARATION OF COMPETENT CELLS..............
12.1.6 TRANSFORMATION OF CHEMICALLY COMPETENT CELLS
12.1.7 TRANSFORMATION OF THE LIGATION MIXTURE
...............
.
12.1.8 DNA ISOLATION AND SCREENING FOR POSITIVE CLONES,
12.1.9 PI TRANSDUCTION
...................................................
12.1.10 CROSS-OUT OF KANAMYCIN RESISTANCE CASSETTE
.......
12.1.11 GLYCEROL STORAGE OF BACTERIAL STRAINS
..................
12.2 GROWTH AND PREPARATION OF CELLS.................................
12.2.1 E. COLI STRAINS AND PLASMIDS..................................
12.2.2 GROWTH RATE MEASUREMENTS..................................
12.2.3 GROWTH CONDITIONS OF PLANKTONIC CULTURES
............
147
147
149
149
149
149
150
150
150
151
151
151
152
152
152
152
12.3 MOTILITY ASSAY ON SOFT AGAR
PLATES...............................................................................
152
12.4 PROMOTOR ACTIVITY MEASUREMENTS USING FLOW CYTOMETRY
.............................................
153
12.5 PROTEIN SECRETION
ASSAY................................................................................................
153
12.5.1 SAMPLE
PREPARATION..............................................................................................
153
12.5.2 SDS-PAGE (SODIUMDODECYLSULFATE POLYACRYLAMIDE GEL
ELECTROPHORESIS)
........
153
12.5.3 WESTERN
BLOT........................................................................................................
154
12.6 TOTAL PROTEOME
ANALYSIS..............................................................................................
154
12.7 TOTAL TRANSCRIPTOME
ANALYSIS.......................................................................................
155
12.8 ANALYSIS OF TRANSCRIPTOMIC AND PROTEOMIC DATA
..........................................................
155
12.9 ANALYSIS OF OTHER EXPERIMENTAL
DATA...........................................................................
155
V APPENDIX
APPENDIX A
............................................................................................................................
159
A1 LIST OF STRAINS USED IN THIS
STUDY....................................................................................
159
A2 LIST OF PLASMIDS USED IN THIS
STUDY................................................................................
160
A3 CHEMICALS AND
CONSUMABLES.........................................................................................
160
APPENDIX B
............................................................................................................................
163
BIBLIOGRAPHY.......................................................................................................................
163
APPENDIX C
............................................................................................................................
171
SUPPLEMENTARY DATA 1
.........................................................................................................
CD
SUPPLEMENTARY DATA 2
.........................................................................................................
CD
|
| any_adam_object | 1 |
| author | Rudenko, Iaroslav |
| author_GND | (DE-588)1155029003 |
| author_facet | Rudenko, Iaroslav |
| author_role | aut |
| author_sort | Rudenko, Iaroslav |
| author_variant | i r ir |
| building | Verbundindex |
| bvnumber | BV045102353 |
| ctrlnum | (OCoLC)1135387817 (DE-599)DNB1155207785 |
| discipline | Biologie |
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| spelling | Rudenko, Iaroslav Verfasser (DE-588)1155029003 aut Effect of growth temperature on the transcriptome and proteome of Escherichia coli presented by Master of Science Iraoslav Rudenko Heidelberg 2017 171 Seiten Illustrationen 30 cm 1 CD-ROM txt rdacontent n rdamedia nc rdacarrier Dissertation Ruperto-Carola University of Heidelberg 2017 (DE-588)4113937-9 Hochschulschrift gnd-content B:DE-101 application/pdf http://d-nb.info/1155207785/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030492910&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Rudenko, Iaroslav Effect of growth temperature on the transcriptome and proteome of Escherichia coli |
| subject_GND | (DE-588)4113937-9 |
| title | Effect of growth temperature on the transcriptome and proteome of Escherichia coli |
| title_auth | Effect of growth temperature on the transcriptome and proteome of Escherichia coli |
| title_exact_search | Effect of growth temperature on the transcriptome and proteome of Escherichia coli |
| title_full | Effect of growth temperature on the transcriptome and proteome of Escherichia coli presented by Master of Science Iraoslav Rudenko |
| title_fullStr | Effect of growth temperature on the transcriptome and proteome of Escherichia coli presented by Master of Science Iraoslav Rudenko |
| title_full_unstemmed | Effect of growth temperature on the transcriptome and proteome of Escherichia coli presented by Master of Science Iraoslav Rudenko |
| title_short | Effect of growth temperature on the transcriptome and proteome of Escherichia coli |
| title_sort | effect of growth temperature on the transcriptome and proteome of escherichia coli |
| topic_facet | Hochschulschrift |
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