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.

Department of Comparative Biomedicine and Food Science University of Padova Viale dell'Università 16 Legnaro 35020 Padova Italy

Department of Comparative Biomedicine and Food Science University of Padova Viale dell'Università 16 Legnaro 35020 Padova Italy; Institute of Functional Genomics 34 35 Avenue Tony Garnier 69007 Lyon France

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

Department of Molecular Medicine University of Padova Via Gabelli 63 35121 Padova Italy

Florence Computational Biology Group Department of Biology University of Florence Via Madonna del Piano 6 Sesto Fiorentino 50019 Florence Italy

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