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. 2022 Sep 15;12:15541. doi: 10.1038/s41598-022-19897-9

Table 1.

Expression of S. equorum KM1031-specific genes (identified by comparative genomic analysis) following treatment with chloramphenicol, erythromycin or lincomycin.

Gene locus Product Log2 (fold-change)a COG Localization
CHL ERY LIN
AWC34_RS00560 Melibiose:sodium transporter MelB 0.88 − 0.78 − 1.37 G Chromosome
AWC34_RS00565 Alpha-glucosidase/alpha-galactosidase 1.78 0.13 − 1.28 G Chromosome
AWC34_RS00570 AraC family transcriptional regulator − 1.03 − 0.92 − 1.59 K Chromosome
AWC34_RS01535 UDP-glucose 4-epimerase − 0.13 − 2.01 0.16 M Chromosome
AWC34_RS01540 Capsular biosynthesis protein 0.44 − 1.69 − 0.32 M Chromosome
AWC34_RS01545 UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing) 0.92 − 2.09 0.12 M Chromosome
AWC34_RS01550 Acetyltransferase − 0.70 − 1.86 0.46 R Chromosome
AWC34_RS01555 Capsular biosynthesis protein − 0.29 − 2.59 0.07 M Chromosome
AWC34_RS01560 O-antigen ligase family protein − 0.88 − 1.91 − 1.86 M Chromosome
AWC34_RS01565 Capsular biosynthesis protein − 1.68 − 2.31 − 1.33 M Chromosome
AWC34_RS01570 Nucleotide sugar dehydrogenase − 0.07 − 2.14 − 0.51 M Chromosome
AWC34_RS01575 Glycosyltransferase WbuB − 0.01 − 1.13 − 0.44 M Chromosome
AWC34_RS01585 Hypothetical protein − 0.75 − 2.84 − 1.01 M Chromosome
AWC34_RS01595 LytR family transcriptional regulator − 0.23 − 0.10 − 0.22 K Chromosome
AWC34_RS01660 Hypothetical protein − 3.09 − 0.64 − 1.06 G Chromosome
AWC34_RS01800 IS6-like element IS257 family transposase 0.28 0.69 − 0.89 L Chromosome
AWC34_RS01805 Antibiotic biosynthesis monooxygenase 0.62 − 0.06 − 0.39 S Chromosome
AWC34_RS01870 HTH domain-containing protein − 1.25 − 0.93 − 0.03 L Chromosome
AWC34_RS01875 Hypothetical protein − 1.10 − 0.44 − 0.64 PR Chromosome
AWC34_RS01880 Hypothetical protein − 1.63 0.30 0.52 SPO Chromosome
AWC34_RS01885 Metal-sensitive transcriptional regulator − 3.18 − 2.78 0.74 S Chromosome
AWC34_RS01890 Sulfite exporter TauE/SafE family protein − 3.39 − 0.62 − 0.40 S Chromosome
AWC34_RS01965 ABC transporter ATP-binding protein − 0.08 − 0.22 − 1.02 Q Chromosome
AWC34_RS01970 ABC transporter permease − 0.85 − 1.83 − 1.45 V Chromosome
AWC34_RS01975 Formate dehydrogenase 0.17 − 0.75 2.62 C Chromosome
AWC34_RS02005 LLM class flavin-dependent oxidoreductase 0.78 1.86 − 0.54 C Chromosome
AWC34_RS02010 Ribosomal-processing cysteine protease Prp 0.22 0.12 − 0.07 J Chromosome
AWC34_RS03190 CHAP domain-containing protein − 0.21 1.80 1.34 S Chromosome
AWC34_RS03985 Arsenate reductase (thioredoxin) − 1.12 1.83 − 0.16 T Chromosome
AWC34_RS10815 Transcriptional regulator − 1.76 − 1.24 0.38 K Chromosome
AWC34_RS10880 Hypothetical protein − 0.56 − 1.95 1.02 G Chromosome
AWC34_RS11115 Msr family ABC-F type ribosomal protection protein − 0.38 4.88 0.33 R Chromosome
AWC34_RS11790 Hypothetical protein 0.88 2.20 0.42 S Chromosome
AWC34_RS12575 Type I restriction endonuclease subunit R 1.01 − 0.38 − 0.76 V Chromosome
AWC34_RS12585 Restriction endonuclease subunit S − 0.13 − 1.48 − 0.93 V Chromosome
AWC34_RS12605 Site-specific DNA-methyltransferase 0.32 − 0.95 − 0.02 SL Chromosome
AWC34_RS12610 ApaLI family restriction endonuclease 0.28 − 0.90 − 0.30 V Chromosome
AWC34_RS12660 Hypothetical protein 1.28 − 1.79 − 1.72 V Chromosome
AWC34_RS12665 DUF2357 domain-containing protein − 0.93 − 2.09 − 1.03 S Chromosome
AWC34_RS13330 50S Ribosomal protein L33 − 0.12 0.75 0.09 S Chromosome
AWC34_RS13395 Hypothetical protein 1.03 − 0.02 0.44 S Chromosome
AWC34_RS12845 Recombinase family protein − 2.18 − 0.54 0.17 L Plasmid1
AWC34_RS12865 Putative sulfate exporter family transporter − 0.26 1.82 0.37 S Plasmid1
AWC34_RS12925 Hypothetical protein 0.22 1.06 − 1.01 S Plasmid1
AWC34_RS12980 Hypothetical protein − 1.60 − 0.90 − 0.01 L Plasmid1
AWC34_RS12985 Crp/Fnr family transcriptional regulator − 0.15 0.12 0.28 T Plasmid1
AWC34_RS12990 DNA starvation/stationary phase protection protein 0.05 0.06 0.19 P Plasmid1
AWC34_RS12995 Copper chaperone − 0.08 − 0.97 − 0.02 P Plasmid1
AWC34_RS13000 Heavy metal translocating P-type ATPase 0.74 1.50 − 0.60 P Plasmid1
AWC34_RS13035 Hypothetical protein 1.40 0.37 − 1.55 S Plasmid1
AWC34_RS13115 XRE family transcriptional regulator 0.06 1.04 1.17 K Plasmid2
AWC34_RS13160 MurR/RpiR family transcriptional regulator − 0.13 − 0.83 − 0.33 K Plasmid2
AWC34_RS13165 Betaine-aldehyde dehydrogenase − 1.64 − 2.65 − 0.86 KC Plasmid2
AWC34_RS13170 4-Hydroxy-tetrahydrodipicolinate synthase − 0.97 − 1.68 − 0.91 E Plasmid2
AWC34_RS13175 FAD-dependent oxidoreductase − 0.67 − 0.58 − 0.70 H Plasmid2
AWC34_RS13180 Hypothetical protein − 1.29 − 1.48 − 1.08 S Plasmid2
AWC34_RS13185 SDR family NAD(P)-dependent oxidoreductase 0.31 − 0.27 − 0.42 R Plasmid2
AWC34_RS13190 LysR family transcriptional regulator − 0.10 − 1.07 − 0.17 K Plasmid2
AWC34_RS13195 Acetylornithine deacetylase 0.45 1.79 0.07 E Plasmid2
AWC34_RS13215 LysE family translocator − 1.69 − 1.67 − 1.85 E Plasmid2
AWC34_RS13220 Recombinase family protein − 0.68 0.61 − 0.23 L Plasmid2
AWC34_RS13280 Threonine/serine exporter 0.14 1.05 − 0.58 S Plasmid2
AWC34_RS13285 Threonine/serine exporter − 0.25 − 0.66 0.03 S Plasmid2
AWC34_RS13295 Protein rep − 2.60 − 0.86 − 1.10 L pSELNU1
AWC34_RS13300 Lincosamide nucleotidyltransferase Lnu(A)' 0.02 − 1.16 0.54 S pSELNU1

Control indicates strain KM1031 cultured without antibiotics.

CHL chloramphenicol, ERY erythromycin, LIN lincomycin, COG clusters of orthologous groups.

a[Fold-change] was defined as [TMMantibiotic/TMMcontrol]. Values are means from duplicate experiments.