Enzyme-specific profiles for genome annotation: PRIAM

Abstract

The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes.

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

“…Protein motifs and domains were documented using the InterPro databank. In parallel, genes coding for enzymes were classified using the PRIAM software 41 . TMHMM vs2.0 was used to identify transmembrane domains 42 , and SignalP 3.0 was used to predict signal peptide regions 43 .…”

Human Cytomegalovirus Carries a Cell-Derived Phospholipase A2 Required for Infectivity

“…Here, we will briefly sketch the bioinformatic method PRIAM described in more detail elsewhere (11), for the detection of potential enzymatic activities, here PLA2, in a fully sequenced genome, here HCMV. Protein sequences belonging to the cytosolic PLA2 family, as indicated by the ENZYME database (6), were downloaded from SWISSPROT and used to construct profile position-specific scoring matrices in the following manner: a multiple alignment is constructed for the cytosolic PLA2 protein sequences, and the associated profile is a scoring scheme that takes into account the distribution of amino acids at each alignment position (4).…”

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

“…PRI enzyme functions were assigned using PRIAM (Enzyme rel. of 6 March 2013) (Claudel-Renard et al 2003). Targeting and transmembrane signals were obtained from SignalP4.1 (Petersen et al 2011), NetNES1.1 (la Cour et al 2004), TargetP1.1 (Emanuelsson et al 2000) and SecretomeP2.0 (Bendtsen et al 2004).…”