A Proteomic View of Probiotic Lactobacillus Rhamnosus GG
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Helsingin yliopiston digitaalinen arkisto Department of Veterinary Biosciences Faculty of Veterinary Medicine University of Helsinki Helsinki, Finland A proteomic view of probioƟ c Lactobacillus rhamnosus GG KerƩ u Koskenniemi ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Veterinary Medicine of the University of Helsinki, for public examinaƟ on in the Walter Auditorium, Agnes Sjöbergin katu 2, Helsinki, on January 13th 2012, at 12 o’clock noon. Helsinki 2012 Supervisor Docent Pekka Varmanen Division of Food Technology Department of Food and Environmental Sciences University of Helsinki Helsinki, Finland Reviewers Professor Sirpa Kärenlampi Department of Biosciences University of Eastern Finland Kuopio, Finland Docent Jaana Mättö Finnish Red Cross Blood Service Helsinki, Finland Opponent Professor Oscar Kuipers Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen, the Netherlands. Layout: Tinde Päivärinta Cover fi gure: A 2-D DIGE gel image (photo Kerttu Koskenniemi) ISBN 978-952-10-7403-5 (paperback) ISBN 978-952-10-7404-2 (PDF) ISSN 1799-7372 http://ethesis.helsinki.fi Unigrafi a Helsinki 2012 CONTENTS Abstract List of abbreviations List of original publications 1. Review of the literature ..........................................................................................1 1.1. Probiotic bacteria .....................................................................................................1 1.1.1. Common properties of probiotic bacteria .............................................. 1 1.1.1.1. Probiotic mechanisms .................................................................. 1 1.1.1.2. Main properties of probiotic bacteria .........................................2 1.1.1.3. Health-benefi cial eff ects of probiotics ........................................2 1.1.2. Lactobacilli ..................................................................................................3 1.1.2.1. Lactobacillus rhamnosus GG ........................................................3 1.1.3. Bifi dobacteria and propionibacteria ........................................................ 5 1.2. Proteomics ................................................................................................................. 5 1.2.1. Proteomic methods ........................................................................................5 1.3. Proteomics of potential probiotic bacteria ............................................................6 1.3.1. Basic proteome research ..........................................................................10 1.3.1.1. Proteome maps ............................................................................10 1.3.1.2. Comparison of growth phases ...................................................11 1.3.1.3. Comparison of diff erent strains and growth media ...............11 1.3.1.4. Development of proteomic methods ........................................12 1.3.2. Proteomics of stress responses of potentially probiotic bacteria ........13 1.3.2.1. Bile stress ......................................................................................13 1.3.2.2. Acid stress ....................................................................................22 1.3.2.3. Other stresses ...............................................................................23 1.3.3. Studies of the cell envelope proteomes and secretomes of potentially probiotic bacteria ..................................................................24 1.3.3.1. Cell envelope proteome ..............................................................24 1.3.3.2. Secretome .....................................................................................26 1.3.3.3. Surfome and secretome predictions .........................................27 1.3.4. Other proteomic studies of potentially probiotic bacteria .....................28 2. Aims of the study ..................................................................................................30 3. Materials and methods .........................................................................................31 3.1. Bacterial strain and growth conditions ...............................................................31 3.2. Proteomic methods ................................................................................................31 3.2.1. Protein extraction .....................................................................................31 3.2.2. Labeling of protein samples ....................................................................31 3.2.3. 2-D GE and image analysis .....................................................................32 3.3. Protein identifi cation by MS .................................................................................32 3.4. Transcriptomic methods .......................................................................................32 3.4.1. Experimental design, RNA methods, cDNA synthesis, and labeling 32 3.4.2. Scanning, image analysis, and data analyses .........................................33 3.5. Analysis of the phosphoproteome ........................................................................33 3.5.1. Protein extraction .....................................................................................33 3.5.2. 2-D GE and image analysis .....................................................................33 3.5.3. Phosphopeptide identifi cation ................................................................33 4. Results and discussion ..........................................................................................34 4.1. Eff ect of the growth medium on the proteome of L. rhamnosus GG ..............34 4.2. Growth phase-associated changes in L. rhamnosus GG ....................................35 4.3. Bile stress response of L. rhamnosus GG .............................................................37 4.4. Eff ect of growth pH on L. rhamnosus GG ...........................................................38 4.5. Protein phosphorylation in L. rhamnosus GG ....................................................39 4.6. Proteome map of L. rhamnosus GG .....................................................................39 5. Concluding remarks and future prospects ..........................................................43 6. Acknowledgements ...............................................................................................45 7. References .........................................................................................................46 Original publications ABSTRACT Lactobacillus rhamnosus GG is a probiotic bacterium that is known worldwide. Since its discovery in 1985, the health eff ects and biology of this health-promoting strain have been researched at an increasing rate. However, knowledge of the molecular biology responsible for these health eff ects is limited, even though research in this area has con- tinued to grow since the publication of the whole genome sequence of L. rhamnosus GG in 2009. Probiotic strains encounter various stress conditions during the production, product formulation, and passage through the gastro-intestinal tract (GIT), which may aff ect the functionality of these organisms. In this thesis, the molecular biology of L. rhamnosus GG was explored by mapping the changes in protein levels in response to diverse stress factors and environmental conditions. Th e proteomics data were supple- mented with transcriptome level mapping of gene expression. Th e harsh conditions of the GIT, which involve acidic conditions and detergent-like bile acids, are a notable challenge to the survival of probiotic bacteria. To simulate GIT condi- tions, L. rhamnosus GG was exposed to a sudden bile stress, and several stress response mechanisms were revealed. A noteworthy site of bile stress responses was the cell enve- lope, which was modifi ed in several ways to relieve the harmful eff ects of bile and to improve the adhesion properties of L. rhamnosus GG before the entrance to the gut, e.g., debasing of the negative charge of the cell envelope and reduction in the thickness of the exopolysaccharide layer. Mechanisms for recognizing bile compounds and actively removing them from the cell were activated by bile exposure, and several bile-induced changes in central metabolism were also detected. L. rhamnosus GG also responded in various ways to mild acid stress. Probiotic bacteria may face mild acid stress in dairy pro- duction because the pH is lowered by the production of acid by fermenting bacteria in fermented milk products. Th e acid stress response of L. rhamnosus GG included changes in central metabolism and in specifi c responses, such as the induction of proton-trans- locating ATPase, a membrane transporter used for increasing intracellular pH. Th ese results clearly showed that L. rhamnosus GG possesses a large repertoire of mechanisms for responding to stress conditions, which probably explains its good survival in GIT. Adaptation to diff erent growth conditions was studied by comparing the proteome lev- el responses of L. rhamnosus GG to diff erent growth media and to diff erent phases of growth. Th e growth phase-dependent changes were also mapped at the transcriptome level. Th e growth of L. rhamnosus GG in a rich laboratory medium, MRS (de Man – Rogosa – Sharpe),