title: A genomic and transcriptomic approach to investigate the blue pigment phenotype in Pseudomonas fluorescens.
abstract: Pseudomonas fluorescens is a well-known food spoiler, able to cause serious economic losses in the food industry due to its ability to produce many extracellular, and often thermostable, compounds. The most outstanding spoilage events involving P. fluorescens were blue discoloration of several food stuffs, mainly dairy products. The bacteria involved in such high-profile cases have been identified as belonging to a clearly distinct phylogenetic cluster of the P. fluorescens group. Although the blue pigment has recently been investigated in several studies, the biosynthetic pathway leading to the pigment formation, as well as its chemical nature, remain challenging and unsolved points. In the present paper, genomic and transcriptomic data of 4 P. fluorescens strains (2 blue-pigmenting strains and 2 non-pigmenting strains) were analyzed to evaluate the presence and the expression of blue strain-specific genes. In particular, the pangenome analysis showed the presence in the blue-pigmenting strains of two copies of genes involved in the tryptophan biosynthesis pathway (including trpABCDF). The global expression profiling of blue-pigmenting strains versus non-pigmenting strains showed a general up-regulation of genes involved in iron uptake and a down-regulation of genes involved in primary metabolism. Chromogenic reaction of the blue-pigmenting bacterial cells with Kovac's reagent indicated an indole-derivative as the precursor of the blue pigment. Finally, solubility tests and MALDI-TOF mass spectrometry analysis of the isolated pigment suggested that its molecular structure is very probably a hydrophobic indigo analog.
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy.
authors.forename: Nadia Andrea
authors.initials: NA
authors.lastname: Andreani
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy.
authors.forename: Lisa
authors.initials: L
authors.lastname: Carraro
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy; Institute of Functional Genomics (IGFL), 34-35 Avenue Tony Garnier, 69007 Lyon, France.
authors.forename: Maria Elena
authors.initials: ME
authors.lastname: Martino
authors.affiliation: Florence Computational Biology Group (ComBo), Department of Biology, University of Florence, Via Madonna del Piano, 6 Sesto Fiorentino, 50019 Florence, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Fasolato
authors.affiliation: Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Miotto
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 17. Listopadu 1192/12, 771 46 Olomouc, Czech Republic.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Magro
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 17. Listopadu 1192/12, 771 46 Olomouc, Czech Republic.
authors.forename: Fabio
authors.initials: F
authors.lastname: Vianello
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16 Legnaro, 35020 Padova, Italy. Electronic address: barbara.cardazzo@unipd.it.
authors.forename: Barbara
authors.initials: B
authors.lastname: Cardazzo
mesh_terms: D003611:Dairy Products / Q000382:microbiology*; D015536:Down-Regulation; D004734:Energy Metabolism / Q000235:genetics; D005516:Food Microbiology; D020869:Gene Expression Profiling; D023281:Genomics; D010088:Oxidoreductases / Q000235:genetics; D010101:Oxygen Consumption / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D010860:Pigments, Biological / Q000235:genetics*; D011551:Pseudomonas fluorescens / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics; D014364:Tryptophan / Q000096:biosynthesis; D015854:Up-Regulation
chemical_list: D010860:Pigments, Biological; D014364:Tryptophan; D010088:Oxidoreductases
keywords: Blue mozzarella; Comparative genomics and transcriptomics; Pseudomonas fluorescens