Differential proteome analysis of selected lactic acid bacteria, stress response and database construction [Elektronische Ressource] / Oliver Drews

Sujets

• Biologie

Informations

• Publié par: technische_universitat_munchen
• Publié le: 01 janvier 2005
• Nombre de lectures: 66
• Langue: English
• Poids de l'ouvrage: 7 Mo

Extrait

Technische Universität München

FG Proteomik



Differential proteome analysis of
selected lactic acid bacteria,
stress response and database construction


Oliver Drews


Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan
für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur
Erlangung des akademischen Grades eines

Doktors der Naturwissenschaften (Dr. rer. nat.)

genehmigten Dissertation.



Vorsitzender: Univ.-Prof. Dr. A. Delgado
Prüfer der Dissertation: 1. apl. Prof. Dr. A. Görg
2. Univ.-Prof. Dr. K.-H. Schleifer
3. Univ.-Prof. Dr. Dr. h.c. (Zonguldak Univ./Türkei) H. Parlar

Die Dissertation wurde am 29.11.2004 bei der Technischen Universität München
eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für
Ernährung, Landnutzung und Umwelt am 25.01.2005 angenommen. Acknowledgements

The work presented in this thesis was done under the guidance of Prof. Dr.
Görg at the FG Proteomics of the Technische Universität München, Germany, in the
period between April 2000 and November 2003. I would like to thank my supervisor
Prof. Dr. Görg for excellent research facilities, her confidence and the freedom to
pursue the projects with own ideas, helpful discussions and unrestricted support in all
concerns. This work was supported by the Deutsche Forschungsgemeinschaft (FOR
358/1).
I especially thank Prof. Dr. Parlar and Prof Dr. Schleifer for kindly accepting to
co-examine this thesis, as well as Prof. Dr. Delgado for accepting the position as
chairman in my examination and his valuable discussions in the high pressure
research group.
My further thanks go to Dr. Walter Weiss for productive collaboration and
helpful discussions on proteomics and manuscripts, and Dr. Gerold Reil of the
Institute for Chemisch-Technische Analyse und Chemische Lebensmitteltechnologie,
who kindly identified proteins by MALDI-TOF MS.
In addition, at this point, I express my gratitude to Dr. Robin Wait of the Imperial
College in London for his excellent support in protein identification by tandem mass
spectrometry.
I thank Prof. Dr. Vogel for providing his microbiological view of high pressure
and the high pressure apparatus. Thanks also to Maher Korakli and Adriana Molina-
Höppner for sharing distinctive high pressure moments and working with me under
pressure.
Burghardt Scheibe, Kay Junghanns, Reiner Westermeier and all other
Amersham guys, who are now GE guys, deserve my gratitude for equipping me with
the latest Amersham gadgets for proteomics and giving me nice diversions
(especially from Elsendorf), whenever they crossed the lab.
Special thanks go also to Daikun Preuss (Daikun Solutions) for his
ingeniousness in realization of the online access to the proteome database. Similar
thanks go to (Gel-)Carsten Lück, our computer specialist, for untiringly listening to
questions like: Have you ever had the problem with Windows blablabla…?
Thanks also to Christian Obermaier, Günter Boguth and Robert Wildgruber for
being there in the very beginning and providing a hot start in 2D electrophoresis, as
well as all other former and present lab members for sharing jokes and having fun.
As always, also my chaos team Darius and Simon deserve my credits for the
latest PhD gossip and adventurous tours outside the lab.
My mom, Wilfried and my grandma deserve my deepest gratitude for providing
save haven and unconditional support whenever I needed them. I will give you tips
on your future graduate studies too, mom!
Finally and most importantly, Maren Engelhardt receives the most thanks of all
for countless hours of proofreading manuscripts, reminding me to get some sleep late
at night, keeping me healthy with tiger food and running during stressful periods, and
all the other little things with which she enriches my life. All the best for 10 years of
Otter relationship!
IIPublications

Wildgruber R., Reil G., Drews O., Parlar H., Görg A.: Web-based two-dimensional
database of Saccharomyces cerevisiae proteins using immobilized pH gradients from
pH 6 to pH 12 and MALDI-TOF MS. Proteomics. 2002 Jun; 2(6):727-32.

Drews O., Weiss W., Reil G., Parlar H., Wait R., Görg A.: High pressure effects step-
wise altered protein expression in Lactobacillus sanfranciscensis. Proteomics. 2002
Jun; 2(6):765-74.

Görg A., Drews O., Weiss, W.: Separation of Proteins Using Two–dimensional Gel
Electrophoresis. Chapter 16 in: Purifying Proteins for Proteomics: A Laboratory
Manual (Richard J. Simpson, ed.), Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, NY, 2004: p. 391-430.

Drews O., Reil G., Parlar H., Görg A.: Setting up standards and a reference map for
the alkaline proteome of the Gram-positive bacterium Lactococcus lactis. Proteomics.
2004 May; 4(5):1293-1304.

Drews O. and Görg A.: DynaProt 2D: an advanced proteomic database for dynamic
online access to proteomes and two-dimensional electrophoresis gels. Nucleic Acids
Res. 2005 Jan; 33: in press

Drews O., Reil G., Parlar H., Görg A.: Analysis of the heat shock response of
Lactococcus lactis with advanced proteomic tools reveals altered abundance of
proteins implicated in the purine metabolism. in preparation
Görg A.: High pressure induced alterations in the
proteome of Lactococcus lactis point out harmful effects at sublethal pressures. in
preparation

Poster Presentations

O. Drews, W. Weiss, R.F. Vogel, A. Görg: Stressproteine von Milchsäurebakterien
nach subletaler Hochdruckbehandlung. Hochdruck-Workshop, 2001, Freising,
Germany

O. Drews, W. Weiss, G. Reil; H. Parlar, R. Wait and A. Görg: Lactic Acid Bacteria
Under Pressure; P-71, Proteomic Forum, International Meeting on Proteome
Analysis, 2001, Munich, Germany

G. Reil, O. Drews, R. Wildgruber, B. Boguth, H. Parlar, A. Görg: 2D Reference Map
of alkaline E. coli proteins using Immobilized pH Gradients up to pH 12 and MALDI-
TOF MS; P-112, Proteomic Forum, International Meeting on Proteome Analysis,
2001, Munich, Germany

R. Wildgruber, G. Reil, O. Drews, H. Parlar, A. Görg,; Web-based 2D-Database of
Saccharomyces cerevisae proteins using Immobilized pH Gradients from pH 6 to pH
12 and MALDI-TOF MS; P-113, Proteomic Forum, International Meeting on
Proteome Analysis, 2001, Munich, Germany

IIIO. Drews, R. Wait, G. Reil, H. Parlar, W. Weiss, A. Görg: Lactobacillus
ndsanfranciscensis under Pressure; I-32, 102 General Meeting of the American
Society for Microbiology, 2002, Salt Lake City, UT, USA

G. Reil, O. Drews, R. Wildgruber, H. Parlar, A. Görg; 2D Reference maps of alkaline
E. coli and S. cerevisiae proteins using immobilized pH grafients up to pH 12 and
MALDI-TOF MS; P-96, From Genome To Proteome: Functional Proteomics, 5th
Siena Meeting, 2002, Siena, Italy

O. Drews, W. Weiss, R. Wait and A. Görg: Stress Response of Lactic Acid Bacteria -
A closer view; P-108, From Genome To Proteome: Functional Proteomics, 5th Siena
Meeting, 2002, Siena, Italy

A. Köpf, O.Drews, W. Weiss and A. Görg: Sample Prefractionation with Sephadex-
IEF; P-5, Proteomic Forum, International Meeting on Proteome Analysis, 2003,
Munich, Germany

L. Thoenes, O. Drews, A. Görg and W. Weiss: Protein Carbamylation – An Actual
Problem in 2-D Electrophoresis?; P-9, Proteomic Forum, International Meeting on
Proteome Analysis, 2003, Munich, Germany

O. Drews and A. Görg: Current 2D Electrophoresis based Technologies in Stress
Response Assessment: Fluorescence- (DIGE) & Radioactive Pulse Labeling; P-113,
Proteomic Forum, International Meeting on Proteome Analysis, 2003, Munich,
Germany

O. Drews, G. Reil, H. Parlar and A. Görg: Mapping of Minimal Differences in the
Alkaline Proteome of Two Lactococcal Strains by Difference Gel Electrophoresis; P-
166, Proteomic Forum, International Meeting on Proteome Analysis, 2003, Munich,
Germany

C. Lück, O. Drews, G. Reil; H. Parlar and A. Görg: Towards a Database of Very
Alkaline Corynebacterium glutamicum Proteins; P-193, Proteomic Forum,
International Meeting on Proteome Analysis, 2003, Munich, Germany

M. Thiel, O. Drews, A Köpf, H. Behrendt, A. Görg, C. Traidl-Hoffmann: Proteomic
Approach for the Analysis of Allergen Carriers; 16. Mainzer Allergie-Workshop, 2004,
Mainz, Germany

Oral Presentations

O. Drews, A. Köpf, C. Lück, G. Reil, W. Weiss, A. Görg: Challenges and routines of
2-D electrophoresis. Perfection in view?; Journadas sobre Proteómica, 05.02.03,
Cordoba, Spain

O. Drews, A. Görg: 2D Electrophoresis: From Basics to Challenges.; From 2D to
MALDI-TOF, 24.06.03, Alghero, Italy
IVContents
1 INTRODUCTION.........................................................................................1
1.1 Aim of the study.....................................................................