Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii

Bacterial microcompartments (BMCs) are proteinaceous prokaryotic organelles that enable the utilization of substrates such as 1,2-propanediol and ethanolamine. BMCs are mostly linked to the survival of particular pathogenic bacteria by providing a growth advantage through utilization of 1,2-propanediol and ethanolamine which are abundantly present in the human gut. Although a 1,2-propanediol utilization cluster was found in the probiotic bacterium Propionibacterium freudenreichii, BMC-mediated metabolism of 1,2-propanediol has not been demonstrated experimentally in P. freudenreichii. In this study we show that P. freudenreichii DSM 20271 metabolizes 1,2-propanediol in anaerobic conditions to propionate and 1-propanol. Furthermore, 1,2-propanediol induced the formation of BMCs, which were visualized by transmission electron microscopy and resembled BMCs found in other bacteria. Proteomic analysis of 1,2-propanediol grown cells compared to L-lactate grown cells showed significant upregulation of proteins involved in propanediol-utilization (pdu-cluster), DNA repair mechanisms and BMC shell proteins while proteins involved in oxidative phosphorylation were down-regulated. 1,2-Propanediol utilizing cells actively produced vitamin B12 (cobalamin) in similar amounts as cells growing on L-lactate. The ability to metabolize 1,2-propanediol may have implications for human gut colonization and modulation, and can potentially aid in delivering propionate and vitamin B12 in situ.

[1]  James W. Wilson.  Manipulating microcompartment operons to study mechanism and function. , 2021, Current opinion in microbiology.

[2]  T. Lithgow,et al.  Formation and function of bacterial organelles , 2020, Nature Reviews Microbiology.

[3]  M. Taga,et al.  Sharing vitamins: Cobamides unveil microbial interactions , 2020, Science.

[4]  J. Walter,et al.  Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts , 2020, Applied and Environmental Microbiology.

[5]  Richard A. Notebaart,et al.  Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization Stimulates Anaerobic Growth of Listeria monocytogenes EGDe , 2019, Front. Microbiol..

[6]  I. Thiele,et al.  Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome , 2019, Front. Genet..

[7]  C. Kerfeld,et al.  Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles , 2019, mBio.

[8]  C. Kerfeld,et al.  Bacterial microcompartments. , 2010, Annual review of microbiology.

[9]  P. Auvinen,et al.  De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii , 2017, BMC Genomics.

[10]  W. D. de Vos,et al.  Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B12 Production by Intestinal Symbionts , 2017, mBio.

[11]  C. Kerfeld,et al.  Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell , 2017, Science.

[12]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[13]  Christopher M. Jakobson,et al.  Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle , 2016, PLoS pathogens.

[14]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..

[15]  Seth D. Axen,et al.  A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method , 2014, PLoS Comput. Biol..

[16]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[17]  Aurélie Le Cam,et al.  A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment , 2013, BMC Genomics.

[18]  J. Blanchard,et al.  The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly , 2013 .

[19]  Kerstin Kaufmann,et al.  Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues , 2012, Nature Protocols.

[20]  T. van de Wiele,et al.  Glycerol Supplementation Enhances L. reuteri’s Protective Effect against S. Typhimurium Colonization in a 3-D Model of Colonic Epithelium , 2012, PloS one.

[21]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[22]  S. D. de Vries,et al.  Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins. , 2011, Journal of proteomics.

[23]  J. Roth,et al.  Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota , 2011, Proceedings of the National Academy of Sciences.

[24]  W. Verstraete,et al.  Propionate as a health-promoting microbial metabolite in the human gut. , 2011, Nutrition reviews.

[25]  T. Bobik,et al.  Genetic Analysis of the Protein Shell of the Microcompartments Involved in Coenzyme B12-Dependent 1,2-Propanediol Degradation by Salmonella , 2011, Journal of bacteriology.

[26]  G. Jan,et al.  Dairy propionibacteria as human probiotics: A review of recent evidence , 2010 .

[27]  J. Gibrat,et al.  The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications , 2010, PloS one.

[28]  Junfeng Xue,et al.  Exogenous or l-Rhamnose-Derived 1,2-Propanediol Is Metabolized via a pduD-Dependent Pathway in Listeria innocua , 2008, Applied and Environmental Microbiology.

[29]  T. Yeates,et al.  Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. , 2008, Structure.

[30]  A. Thierry,et al.  Safety assessment of dairy microorganisms: Propionibacterium and Bifidobacterium. , 2008, International journal of food microbiology.

[31]  T. Bobik,et al.  Microcompartments for B12-Dependent 1,2-Propanediol Degradation Provide Protection from DNA and Cellular Damage by a Reactive Metabolic Intermediate , 2008, Journal of bacteriology.

[32]  S. Salminen,et al.  In vitro analysis of probiotic strain combinations to inhibit pathogen adhesion to human intestinal mucus , 2007 .

[33]  Peer Bork,et al.  Systematic Association of Genes to Phenotypes by Genome and Literature Mining , 2005, PLoS biology.

[34]  Y. Huang,et al.  In vitro assessment of the upper gastrointestinal tolerance of potential probiotic dairy propionibacteria. , 2004, International journal of food microbiology.

[35]  Bernhard Schink,et al.  Energetics and kinetics of lactate fermentation to acetate and propionate via methylmalonyl-CoA or acrylyl-CoA. , 2002, FEMS microbiology letters.

[36]  N. Yoda,et al.  Effect of Ingested Culture of Propionibacterium freudenreichii ET-3 on Fecal Microflora and Stool Frequency in Healthy Females , 2002 .

[37]  H. Kurihara,et al.  Effects of Culture-Powder of Propionibacterium freudenreichii ET-3 on Fecal Microflora of Normal Adults , 1999 .

[38]  R. Jonas,et al.  Effect of oxygen supply on biomass, organic acids and vitamin B12 production by Propionibacterium shermanii , 1998 .

[39]  J. Roth,et al.  The control region of the pdu/cob regulon in Salmonella typhimurium , 1994, Journal of bacteriology.

[40]  D. Andersson,et al.  Vitamin B12 repression of the cob operon in Salmonella typhimurium: translational control of the cbiA gene , 1994, Molecular microbiology.

[41]  S. Meguro,et al.  Growth stimulator for bifidobacteria produced by Propionibacterium freudenreichii and several intestinal bacteria. , 1994, Journal of dairy science.

[42]  T. Toraya,et al.  Fermentation of 1,2-Propanediol and 1,2-Ethanediol by Some Genera of Enterobacteriaceae, Involving Coenzyme B12-Dependent Diol Dehydratase , 1979 .

[43]  M. P. Bryant,et al.  Bacterial species of the rumen. , 1959, Bacteriological reviews.

[44]  C. Eyers.  Universal sample preparation method for proteome analysis , 2009 .

[45]  G. Macfarlane,et al.  Carbohydrate Fermentation, Energy Transduction and Gas Metabolism in the Human Large Intestine , 1997 .

[46]  N. Doblhamer.  Vitamin B12. , 1950, Wiener medizinische Wochenschrift.

[47]  Howard C. Berg,et al.  Genetic analysis , 1957, Nature Biotechnology.