Table 3.
Non-ribosomal common highly expressed (CHX) genes in three pathogenic S. Enteritidis strains cultured under distinct environmental conditions (n = 34).
| Locus1 | Gene | Product | COG2 specific functional category | Localization3 | E(g)4 | Hybridization energy (ΔG) in kcal/mol5 | Protein abundance in S. Typhimurium6 |
|---|---|---|---|---|---|---|---|
| SEN_RS19340 | rho | Transcription termination factor Rho | Transcription | Cytoplasmic | 1.42 | -1.56 | Top 10 to 25% |
| SEN_RS18060 | cspA | Cold-shock protein | Transcription | Cytoplasmic | 1.72 | -3.34 | Top 30 to 40% |
| SEN_RS03055 | cspE | Cold-shock protein | Transcription | Cytoplasmic | 1.70 | -3.50 | Top 5 to 10% |
| SEN_RS06220 | cspC | Cold-shock protein CspC | Transcription | Cytoplasmic | 1.82 | -6.00 | Top 5 to 10% |
| SEN_RS20610 | hupA | DNA-binding protein HU-alpha CDS | Replication, recombination, and repair | Cytoplasmic | 2.05 | -5.70 | Top 5% |
| SEN_RS02220 | hupB | DNA-binding protein HU-beta | Replication, recombination, and repair | Cytoplasmic | 1.45 | -6.88 | Top 5% |
| SEN_RS21340 | groEL | Molecular chaperone GroEL | Post-translational modification, protein turnover, and chaperones | Cytoplasmic | 2.38 | -6.07 | Top 5% |
| SEN_RS21335 | groES | molecular chaperone groES | Post-translational modification, protein turnover, and chaperones | Cytoplasmic | 1.65 | -5.12 | Top 5% |
| SEN_RS01975 | Peroxiredoxin | Peroxiredoxin | Post-translational modification, protein turnover, and chaperones | Cytoplasmic | 1.67 | -7.45 | Top 5 to 10% |
| SEN_RS17750 | uspA | Universal stress protein A | Signal transduction mechanisms | Cytoplasmic | 1.54 | -7.89 | Top 5% |
| SEN_RS03070 | tatE | tatE | Intracellular trafficking, secretion, and vesicular transport | Cytoplasmic membrane | 1.12 | -4.30 | 25 to 75% |
| SEN_RS04830 | ompA | Outer membrane protein A | Cell wall/membrane/envelope biogenesis | Outer membrane | 3.03 | -5.59 | Top 5% |
| SEN_RS11705 | ompC | Phosphoporin PhoE | Cell wall/membrane/envelope biogenesis | Outer membrane | 1.63 | -5.44 | Top 5% |
| SEN_RS07685 | nmpC | Phosphoporin PhoE (ompD) | Cell wall/membrane/envelope biogenesis | Outer membrane | 2.99 | -6.09 | Top 5 to 25% |
| SEN_RS04025 | ompX | ompX | Cell wall/membrane/envelope biogenesis | Outer membrane | 2.65 | -5.24 | Top 10% |
| SEN_RS08655 | lpp | Major outer membrane lipoprotein | Cell wall/membrane/envelope biogenesis | Outer membrane | 2.43 | -5.81 | Top 5% |
| SEN_RS03605 | pal | Peptidoglycan-associated lipoprotein Pal | Cell wall/membrane/envelope biogenesis | Outer membrane | 2.49 | -5.71 | Top 5 to 10% |
| SEN_RS01165 | hlpA | Chaperone protein Skp | Cell wall/membrane/envelope biogenesis | Periplasmic | 1.58 | -8.42 | Top 5% |
| SEN_RS09130 | gapA | Aldehyde dehydrogenase | Carbohydrate transport and metabolism | Cytoplasmic | 2.58 | -4.83 | Top 5% |
| SEN_RS14530 | eno | Enolase | Carbohydrate transport and metabolism | Cytoplasmic | 2.57 | -5.07 | Top 5% |
| SEN_RS15150 | fba | Class II fructose-bisphosphate aldolase | Carbohydrate transport and metabolism | Cytoplasmic | 2.89 | -4.13 | Top 5 to 10% |
| SEN_RS12575 | ptsI | Phosphoenolpyruvate–protein phosphotransferase | Carbohydrate transport and metabolism | Cytoplasmic | 1.25 | -8.63 | Top 10 to 25% |
| SEN_RS12570 | ptsH | Phosphocarrier protein HPr | Carbohydrate transport and metabolism | Cytoplasmic | 1.29 | -5.81 | Top 5% |
| SEN_RS12580 | crr | Glucose-specific phosphotransferase enzyme IIA component | Carbohydrate transport and metabolism | Cytoplasmic | 1.94 | -6.87 | Top 5% |
| SEN_RS19120 | atpE | ATP synthase subunit C | Energy production and conversion | Cytoplasmic membrane | 1.61 | -6.07 | NA7 |
| SEN_RS19115 | atpF | ATP synthase subunit B | Energy production and conversion | Cytoplasmic membrane | 1.45 | -3.44 | Top 5 to 10% |
| SEN_RS04545 | pflB | Formate C-acetyltransferase | Energy production and conversion | Cytoplasmic | 3.36 | -7.11 | Top 10% |
| SEN_RS21315 | aspA | Aspartate ammonia-lyase | Amino acid transport and metabolism | Cytoplasmic | 1.61 | -3.26 | Top 10% |
| SEN_RS09630 | acpP | Acyl carrier protein | Secondary metabolites biosynthesis, transport and catabolism | Cytoplasmic | 1.60 | -4.26 | Top 10 to 25% |
| SEN_RS10710 | yeeX | DUF496 domain-containing protein | Unknown | Cytoplasmic | 1.27 | -4.56 | Top 5% |
| SEN_RS20875 | yjbJ | CsbD family protein—stress response | Unknown | Unknown | 1.50 | -6.09 | Top 5% |
| SEN_RS21370 | ecnB | Entericidin B lipoprotein | Unknown | Cytoplasmic membrane | 1.31 | -6.00 | Top 10 to 25% |
| SEN_RS06655 | hns | DNA-binding protein H-NS | General function prediction only | Cytoplasmic | 1.42 | -2.73 | Top 5% |
| SEN_RS13375 | yfiD | Autonomous glycil radical cofactor GrcA | General function prediction only | Cytoplasmic | 1.49 | -3.76 | Top 5 to 10% |
1Locus in reference sequence S. Enteritidis P125109 (NCBI Accession NC_011294).
2COG, cluster of orthologous groups.
3Localization according to PSORTb v3.0 (Yu et al., 2010).
4E(g), predicted general expression level ≥ 1.05 indicates predicted highly expressed gene (PHX) based on codon usage similar to reference highly expressed gene classes.
5Hybridization energy (ΔG) according to RNAcofold V2.4.9 with default parameters (Lorenz et al., 2011).
6Protein abundance averaged by PaxDb protein abundance database version 4.1 (https://pax-db.org/) based on S. Typhimurium strain LT2 cultured under nutrient rich media (LB) at log and stationary phase, and low-magnesium/low-pH media (Adkins et al., 2006; Wang et al., 2015).
7NA, Data Not Available.