Holdings: Effect of growth temperature on the transcriptome and proteome of Escherichia coli

Effect of growth temperature on the transcriptome and proteome of Escherichia coli:

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Bibliographic Details
Main Author:	Rudenko, Iaroslav (Author)
Format:	Thesis Book
Language:	English
Published:	Heidelberg 2017
Subjects:	Hochschulschrift
Online Access:	Inhaltsverzeichnis Inhaltsverzeichnis
Physical Description:	171 Seiten Illustrationen 30 cm 1 CD-ROM

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MARC


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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
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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
url	http://d-nb.info/1155207785/04 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
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