# Differential Proteomic Analysis of _Listeria monocytogenes_ during High-Pressure Processing
## 3 Results
### GO and COGs Enrichment Analysis of HPP-Induced DEPs  
Functional classification was used to characterize terms enriched in gene ontology biological processes (GOBPs), molecular functions (GOMFs), and cellular components through GO analysis and string functional protein association networks. Considering treatment with low-pressure HPP (E2/C), there were 56 DEPs comprising 50 proteins annotated in 8 GOBPs, primarily cellular metabolic (49) and biosynthetic processes (45), followed by protein metabolic process (36 blue nodes), translation (34 red nodes), the nucleic acid metabolic process (12 green nodes), ribosome biogenesis (8 yellow nodes), biological regulation (6 dark green nodes), and DNA-templated transcription (4 pink nodes) (Figure 3a). Regarding GOMFs, 30 proteins showed structure molecule activity for ribosomes and 31 participated in nucleic acid binding, including 4 in DNA binding, and 19, 5, and 3 proteins in rRNA, tRNA, and mRNA binding, respectively. There were 45 proteins in the cytoplasm, with 30 ribosomal proteins. Under high pressure, H4/C treatment exhibited all 73 DEPs for 11 GOBPs, primarily cellular processes (65) and cellular metabolic processes (63), including 47 and 16 proteins for macromolecule and small-molecule metabolic processes, respectively. Among them, 37 DEPs were involved in the protein metabolic process (blue nodes) and 35 DEPs were involved in translation (red nodes). Other DEPs related to the nucleic acid metabolic process (15 green nodes), ribosome biogenesis (8 yellow nodes), biological regulation (8 dark green nodes), and DNA-templated transcription (6 pink nodes) were also indicated. The other 3 GOBPs specific for the H4/C group were the carbohydrate derivative biosynthetic process (8 light blue nodes), peptidoglycan-based cell wall biogenesis (3 orange nodes), and nucleotide-excision repair (2 purple nodes (Figure 3b). The abundant GOMFs involved 46 DEPs responsible for binding and 34 proteins for nucleic acid binding, including 6 for DNA binding and 28 for RNA binding (20, 5, and 3 proteins for rRNA, tRNA and mRNA binding, respectively). The 27 proteins exhibited catalytic activity. In total, 58 proteins were related to cellular components, mainly involved in the ribosome. Overall, H4/C exhibited similar but enhanced effects with H2/C on GOBPs, GOMFs and cellular components.  
According to the Database of Clusters of Orthologous Groups of proteins (COGs), most DEPs with strong interactions (64.3 and 52.1% for H2/C and H4/C, respectively) were related to translation, ribosomal structure and ribosome biogenesis (32 ribosomal proteins, ribosome-recycling factor, phenylalanine-tRNA ligase alpha subunit, translation initiation factor IF-3, D-alanyl carrier protein, elongation factor P, aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit C, ribosome-binding factor A, ribosome maturation factor RimM, ribonuclease Z and threonine-tRNA ligase) (Table S4). The remaining DEPs were mainly involved in nucleotide transport and metabolism (7.1 and 8.2% for H2/C and H4/C, respectively) and in transcription (7.1 and 8.2% for H2/C and H4/C, respectively) (Table S4).