Comparative genomics of Propionibacterium freudenreichii
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ABSTRACT:
PROVIDER: PRJEB14036 | ENA |
REPOSITORIES: ENA
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Project description:Propionibacterium freudenreichii overview
| PRJNA35885 | ENA
Project description:Propionibacterium freudenreichii is an important starter culture used in the manufacture of Swiss-type cheeses. We have generated the complete genome sequence of a Propionibacterium freudenreichii ssp. shermanii strain JS at the Institute of Biotechnology, University of Helsinki, by using a combination of pyrosequencing with GS FLX and GS FLX Titanium series reagents (Roche) and SOLiD 4 (Life Technologies), ABI 3130xl Genetic Analyzer (Life Technologies), and PacBio RS II (Pacific Biosciences) instruments. Initial genome annotation was carried out using RAST, and additional functional annotation information for each CDS was obtained from BLANNOTATOR, CDD, and KAAS. Accession number for genome sequence is PRJEB12148. This submission is for the transcriptome analysis of Propionibakcterium freudenreichii in cheese ripening under warm and cold conditions. The RNA reads were mapped to the reference genome PRJEB12148.
2016-04-14 | E-MTAB-4593 | biostudies-arrayexpress
Project description:This study was performed to monitor ethylene glycol metabolism by Propionibacterium freudenreichii and to elucidate the metabolic pathway involved.
2024-08-09 | PXD037369 | Pride
Project description:Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The cold adaptation of the type strain was studied previously. The aim of this study was to investigate the adaptation of 6 other P. freudenreichii strains at cold temperature by means of a global gene expression profile. The temporal transcriptomic response of 6 P. freudenreichii strains was analyzed at 2 times of growth, during growth at 30°C then after 3 days 4°C, in the constant presence of lactate as the main carbon source.
2012-07-06 | GSE34227 | GEO
Project description:Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The aim of this study was to investigate the adaptation of P. freudenreichii at cold temperature by means of the first global gene expression profile for this species. The temporal transcriptomic response of P. freudenreichii was analyzed at five times of growth, during growth at 30°C then for 9 days at 4°C, in the constant presence of lactate as the main carbon source. P. freudenreichii response was also investigated by RT-qPCR for 30 genes, by proteomics and metabolomics (main metabolites quantified in culture supernatant). Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from warm to cold temperature (P < 0.05 and |fold change| > 1). Most of the down-expressed genes were involved in cell machinery (cell division, protein turnover, translation, transcription and DNA replication). During incubation at cold temperature, P. freudenreichii accumulated carbon supplies by up-regulating genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis and in glycogen synthesis. Interestingly, some genes involved in the formation of important flavor compounds of cheese, coding for an extracellular lipolytic esterases and enzymes of the pathways of formation of branched-chain compounds, were not significantly affected by cold. In conclusion, P. freudenreichii is metabolically active at cold temperature and induces pathways to maintain its long-term viability, which could explain its contribution to cheese ripening even at low temperature.
2011-12-01 | GSE30841 | GEO
Project description:Propionibacterium freudenreichii MJ2 Genome sequencing and assembly
| PRJNA918783 | ENA
Project description:Adaptation of Propionibacterium freudenreichii to the colon environment
| PRJNA215993 | ENA
Project description:Propionibacterium freudenreichii subsp. freudenreichii NBRC 12424 genome sequencing project
| PRJDB365 | ENA
Project description:Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The aim of this study was to investigate the adaptation of P. freudenreichii at cold temperature by means of the first global gene expression profile for this species. The temporal transcriptomic response of P. freudenreichii was analyzed at five times of growth, during growth at 30°C then for 9 days at 4°C, in the constant presence of lactate as the main carbon source. P. freudenreichii response was also investigated by RT-qPCR for 30 genes, by proteomics and metabolomics (main metabolites quantified in culture supernatant). Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from warm to cold temperature (P < 0.05 and |fold change| > 1). Most of the down-expressed genes were involved in cell machinery (cell division, protein turnover, translation, transcription and DNA replication). During incubation at cold temperature, P. freudenreichii accumulated carbon supplies by up-regulating genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis and in glycogen synthesis. Interestingly, some genes involved in the formation of important flavor compounds of cheese, coding for an extracellular lipolytic esterases and enzymes of the pathways of formation of branched-chain compounds, were not significantly affected by cold. In conclusion, P. freudenreichii is metabolically active at cold temperature and induces pathways to maintain its long-term viability, which could explain its contribution to cheese ripening even at low temperature. Gene expression was measured in the middle of exponential growth phase at 30°C (20 h, OD650 ≈ 0.5), at the end of exponential growth phase (40 h, OD650 ≈ 2), and after 3, 6 and 9 days of incubation at 4°C. Three independent biological experiments were performed at each time (20h, 40h, 3, 6 and 9 days) and labelled A, B, C. One technical repetition was performed using the RNA of the 20HA sample ; This technical repetition was labelled 20HAbis.
2011-12-01 | E-GEOD-30841 | biostudies-arrayexpress
Project description:Propionibacterium freudenreichii CIRM-BIA138 was grown for 11 days in YEL medium at 30°C without any addition of nutrients. RNA was extracted from bacteria harvested 24 H post-inoculation (exponential phase) and 72 H post-inoculation and was depleted from ribosmic sequences. RNA samples were sequenced on Hiseq 2000 generating single reads of 50 bp.
2016-12-07 | GSE75553 | GEO