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Dive into the research topics where Paulina Deptula is active.

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Featured researches published by Paulina Deptula.


Microbial Cell Factories | 2015

BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B12 by Propionibacterium freudenreichii

Paulina Deptula; Petri Kylli; Bhawani Chamlagain; Liisa Holm; Risto Kostiainen; Vieno Piironen; Kirsi Savijoki; Pekka Varmanen

BackgroundPropionibacterium freudenreichii is a food grade bacterium that has gained attention as a producer of appreciable amounts of cobalamin, a cobamide with activity of vitamin B12. Production of active form of vitamin is a prerequisite for attempts to naturally fortify foods with B12 by microbial fermentation. Active vitamin B12 is distinguished from the pseudovitamin by the presence of 5,6-dimethylbenzimidazole (DMBI) as the lower ligand. Genomic data indicate that P. freudenreichii possesses a fusion gene, bluB/cobT2, coding for a predicted phosphoribosyltransferase/nitroreductase, which is presumably involved in production of vitamin B12. Understanding the mechanisms affecting the synthesis of different vitamin forms is useful for rational strain selection and essential for engineering of strains with improved B12 production properties.ResultsHere, we investigated the activity of heterologously expressed and purified fusion enzyme BluB/CobT2. Our results show that BluB/CoBT2 is responsible for the biosynthesis of the DMBI base and its activation into α-ribazole phosphate, preparing it for attachment as the lower ligand of cobalamin. The fusion enzyme was found to be efficient in metabolite channeling and the enzymes’ inability to react with adenine, a lower ligand present in the pseudovitamin, revealed a mechanism favoring the production of the active form of the vitamin. P. freudenreichii did not produce cobalamin under strictly anaerobic conditions, confirming the requirement of oxygen for DMBI synthesis. In vivo experiments also revealed a clear preference for incorporating DMBI over adenine into cobamide under both microaerobic and anaerobic conditions.ConclusionsThe herein described BluB/CobT2 is responsible for the production and activation of DMBI. Fusing those two activities results in high pressure towards production of the true vitamin B12 by efficiently activating DMBI formed within the same enzymatic complex. This indicates that BluB/CobT2 is the crucial enzyme in the B12 biosynthetic pathway of P. freudenreichii. The GRAS organism status and the preference for synthesizing active vitamin form make P. freudenreichii a unique candidate for the in situ production of vitamin B12 within food products.


Frontiers in Microbiology | 2017

Food-Like Growth Conditions Support Production of Active Vitamin B12 by Propionibacterium freudenreichii 2067 without DMBI, the Lower Ligand Base, or Cobalt Supplementation

Paulina Deptula; Bhawani Chamlagain; Minnamari Edelmann; Panchanit Sangsuwan; Tuula A. Nyman; Kirsi Savijoki; Vieno Piironen; Pekka Varmanen

Propionibacterium freudenreichii is a traditional dairy bacterium and a producer of short chain fatty acids (propionic and acetic acids) as well as vitamin B12. In food applications, it is a promising organism for in situ fortification with B12 vitamin since it is generally recognized as safe (GRAS) and it is able to synthesize biologically active form of the vitamin. In the present study, vitamin B12 and pseudovitamin biosynthesis by P. freudenreichii was monitored by UHPLC as a function of growth in food-like conditions using a medium mimicking cheese environment, without cobalt or 5,6-dimethylbenzimidazole (DMBI) supplementation. Parallel growth experiments were performed in industrial-type medium known to support the biosynthesis of vitamin B12. The production of other key metabolites in the two media were determined by HPLC, while the global protein production was compared by gel-based proteomics to assess the effect of growth conditions on the physiological status of the strain and on the synthesis of different forms of vitamin. The results revealed distinct protein and metabolite production, which reflected the growth conditions and the potential of P. freudenreichii for synthesizing nutritionally relevant amounts of active vitamin B12 regardless of the metabolic state of the cells.


BMC Genomics | 2017

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Paulina Deptula; Pia Laine; Richard J. Roberts; Olli-Pekka Smolander; Helena Vihinen; Vieno Piironen; Lars Paulin; Eija Jokitalo; Kirsi Savijoki; Petri Auvinen; Pekka Varmanen

BackgroundPropionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species.ResultsWe used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm.ConclusionThe complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.


Food Science and Nutrition | 2018

In situ production of active vitamin B12 in cereal matrices using Propionibacterium freudenreichii

Bhawani Chamlagain; Tessa A. Sugito; Paulina Deptula; Minnamari Edelmann; Susanna Kariluoto; Pekka Varmanen; Vieno Piironen

Abstract The in situ production of active vitamin B12 was investigated in aqueous cereal‐based matrices with three strains of food‐grade Propionibacterium freudenreichii. Matrices prepared from malted barley flour (33% w/v; BM), barley flour (6%; BF), and wheat aleurone (15%; AM) were fermented. The effect of cobalt and the lower ligand 5,6‐dimethylbenzimidazole (DMBI) or its natural precursors (riboflavin and nicotinamide) on active B12 production was evaluated. Active B12 production was confirmed by UHPLC–UV–MS analysis. A B12 content of 12–37 μg·kg−1 was produced in BM; this content increased 10‐fold with cobalt and reached 940–1,480 μg·kg−1 with both cobalt and DMBI. With riboflavin and nicotinamide, B12 production in cobalt‐supplemented BM increased to 712 μg·kg−1. Approximately, 10 μg·kg−1 was achieved in BF and AM and was increased to 80 μg·kg−1 in BF and 260 μg·kg−1 in AM with cobalt and DMBI. The UHPLC and microbiological assay (MBA) results agreed when both cobalt and DMBI or riboflavin and nicotinamide were supplemented. However, MBA gave ca. 20%–40% higher results in BM and AM supplemented with cobalt, indicating the presence of human inactive analogues, such as pseudovitamin B12. This study demonstrates that cereal products can be naturally fortified with active B12 to a nutritionally relevant level by fermenting with P. freudenreichii.


Microbial Biotechnology | 2018

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains

Esther Frohnmeyer; Paulina Deptula; Tuula A. Nyman; Pia Laine; Helena Vihinen; Lars Paulin; Petri Auvinen; Eija Jokitalo; Vieno Piironen; Pekka Varmanen; Kirsi Savijoki

This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain‐specific variation in secretion of adhesins/invasins (SlpA, InlA), cell‐wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) and moonlighting (DnaK, GroEL, GaPDH, IDH, ENO, ClpB) enzymes and/or proteins. Detailed secretome comparison suggested that one of the cereal strains (JS14) released a tip fimbrillin (FimB) in to the extracellular milieu, which was in line with the electron microscopy and genomic analyses, indicating the lack of surface‐associated fimbrial‐like structures, predicting a mutated type‐2 fimbrial gene cluster (fimB‐fimA‐srtC2) and production of anchorless FimB. Instead, the cereal strain produced high amounts of SlpB that tentatively mediated adherent growth on hydrophilic surface and adherence to hydrophobic material. One of the dairy strains (JS22), producing non‐covalently bound surface‐proteins (LspA, ClpB, AraI) and releasing SlpA and InlA into the culture medium, was found to form clumps under physiological conditions. The JS22 strain lacked SlpB and displayed a non‐clumping and biofilm‐forming phenotype only under conditions of increased ionic strength (300 mM NaCl). However, this strain cultured under the same conditions was not adherent to hydrophobic support, which supports the contributory role of SlpB in mediating hydrophobic interactions. Thus, this study reports significant secretome variation in P. freudenreichii and suggests that strain‐specific differences in protein export, modification and protein–protein interactions have been the driving forces behind the adaptation of this bacterial species.


International Journal of Systematic and Evolutionary Microbiology | 2018

Acidipropionibacterium virtanenii sp. nov., isolated from malted barley

Paulina Deptula; Olli-Pekka Smolander; Pia Laine; Richard J. Roberts; Minnamari Edelmann; Petri Peltola; Vieno Piironen; Lars Paulin; Erna Storgårds; Kirsi Savijoki; Arja Laitila; Petri Auvinen; Pekka Varmanen

A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici). The subsequent comparison of the whole 16S rRNA gene with other representatives of the genus Acidipropionibacterium revealed that the strain belongs to a novel species, most closely related to Acidipropionibacterium microaerophilum and Acidipropionibacterium acidipropionici, with similarity values of 98.46 and 98.31 %, respectively. The whole genome sequencing using PacBio RS II platform allowed further comparison of the genome with all of the other DNA sequences available for the type strains of the Acidipropionibacterium species. Those comparisons revealed the highest similarity of strain JS278T to A. acidipropionici, which was confirmed by the average nucleotide identity analysis. The genome of strain JS278T is intermediate in size compared to the A. acidipropionici and Acidipropionibacterium jensenii at 3 432 872 bp, the G+C content is 68.4 mol%. The strain fermented a wide range of carbon sources, and produced propionic acid as the major fermentation product. Besides its poor ability to grow at 37 °C and positive catalase reaction, the observed phenotype was almost indistinguishable from those of A. acidipropionici and A. jensenii. Based on our findings, we conclude that the organism represents a novel member of the genus Acidipropionibacterium, for which we propose the name Acidipropionibacteriumvirtanenii sp. nov. The type strain is JS278T (=VTT E-113202T=DSM 106790T).


Lwt - Food Science and Technology | 2016

Effect of the lower ligand precursors on vitamin B12 production by food-grade Propionibacteria

Bhawani Chamlagain; Paulina Deptula; Minnamari Edelmann; Susanna Kariluoto; Franck Grattepanche; Christophe Lacroix; Pekka Varmanen; Vieno Piironen


Standards in Genomic Sciences | 2015

Complete genome sequence of Propionibacterium freudenreichii DSM 20271T

Patrik Koskinen; Paulina Deptula; Olli-Pekka Smolander; Fitsum Tamene; Juhana Kammonen; Kirsi Savijoki; Lars Paulin; Vieno Piironen; Petri Auvinen; Pekka Varmanen


Journal of Cereal Science | 2018

In situ fortification of vitamin B12 in wheat flour and wheat bran by fermentation with Propionibacterium freudenreichii

Chong Xie; Rossana Coda; Bhawani Chamlagain; Minnamari Edelmann; Paulina Deptula; Pekka Varmanen; Vieno Piironen; Kati Katina


International Journal of Food Microbiology | 2016

Letter to the editor on ‘Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri, IJFM. 206:56–59’

Pekka Varmanen; Paulina Deptula; Bhawani Chamlagain; Vieno Piironen

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Lars Paulin

University of Helsinki

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Pia Laine

University of Helsinki

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