Table 2.
The thirty genes showing the highest differential expression (up- or down-regulated) at the intercellular aggregation step during biofilm production by BCG.
| Gene_Name | Gene_ID | Log2fold | Avg_p value | Product |
|---|---|---|---|---|
| lppB | BCG_2567 | 2.7988 | 2.68E−08 | Probable conserved lipoprotein lppB |
| BCG_3184c | BCG_3184c | 2.5898 | 1.30E−15 | Possible transcriptional regulatory protein (probably tetR-family), orthologous to Rv3160c. Rv3160c was involved in response to thioridazine (PLoS One. 2010 Apr 8;5(4):e10069. 10.1371/journal.pone.0010069) |
| PE22 | BCG_2124 | 2.5607 | 5.75E−15 | PE family protein |
| BCG_2486c | BCG_2486c | 2.496 | 0.000174564 | Conserved hypothetical protein. Contains a Protein Disulfide Oxidoreductase domain (7.33e−35) |
| BCG_3185c | BCG_3185c | 2.4789 | 5.66E−19 | Possible dioxygenase |
| BCG_1115 | BCG_1115 | 2.4553 | 3.66E−16 | Conserved hypothetical protein. Contains a DNA-binding beta-propeller fold protein YncE. (1.79e−34) |
| BCG_2748c | BCG_2748c | 2.3981 | 3.53E−09 | Conserved hypothetical protein. Contains a S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I domain (8.96e−66) |
| sigE | BCG_1281 | 2.2979 | 1.16E−16 | Alternative RNA polymerase sigma factor sigE |
| BCG_0010c | BCG_0010c | 2.2359 | 5.18E−21 | Probable conserved membrane protein. It contains a 40 aa stretch (out of 111 aa) similar to bacterial plekstrin homology domain (2.65e−8) |
| BCG_0040c | BCG_0040c | 2.2296 | 8.44E−20 | Probable conserved membrane protein. It contains a 40 aa stretch (out of 111 aa) similar to bacterial plekstrin homology domain (2.65e−8) |
| lprR | BCG_2566 | 2.2247 | 1.51E−09 | Probable conserved lipoprotein lprR |
| fadD23 | BCG_3889 | 2.1317 | 3.07E−22 | Probable fatty-acid-CoA ligase fadD23, involved in sulfolipid production (Microbiology. 2007 Sep;153(Pt 9):3133-40.) |
| PPE70 | BCG_3183c | 2.1152 | 2.70E−20 | PPE family protein |
| hupB | BCG_3007c | 2.1028 | 5.22E−07 | Probable DNA-binding protein HU homolog hupB |
| BCG_0088 | BCG_0088 | 2.1007 | 9.08E−15 | Hypothetical protein |
| BCG_0221 | BCG_0221 | 2.0983 | 1.45E−11 | Conserved hypothetical protein |
| BCG_3929 | BCG_3929 | 2.0163 | 8.42E−20 | Conserved hypothetical protein. Orthologous Rv3866 (EspG). A deletion of espG in M. marinum reduced sliding motility and biofilm formation by M. marinum (Front Microbiol. 2018 May 30;9:1160. 10.3389/fmicb.2018.01160). |
| ppsC | BCG_2955 | 1.8996 | 9.31E−19 | Phenolpthiocerol synthesis type-I polyketide synthase ppsC |
| rplK | BCG_0689 | 1.8485 | 4.98E−10 | Probable 50S ribosomal protein l11 rplK |
| PPE53 | BCG_3182c | 1.848 | 9.55E−17 | PPE family protein |
| recX | BCG_2749c | 1.7905 | 5.94E−11 | Regulatory protein recX |
| BCG_0653 | BCG_0653 | 1.7809 | 3.40E−05 | Hypothetical protein |
| BCG_1191 | BCG_1191 | 1.7798 | 5.19E−05 | Conserved hypothetical protein. Orthologous to Rv1130, PrpD, 2-methylcitrate dehydratase. |
| BCG_2192c | BCG_2192c | 1.7692 | 7.07E−14 | Possible transposase |
| lpqK | BCG_0436c | 1.7462 | 6.92E−12 | Possible conserved lipoprotein lpqK |
| BCG_1053 | BCG_1053 | 1.7207 | 5.49E−09 | Hypothetical protein |
| parA_1 | BCG_3976c | 1.7153 | 6.49E−14 | Probable chromosome partitioning protein parA |
| BCG_0343 | BCG_0343 | 1.7095 | 6.09E−11 | Probable dehydrogenase/reductase |
| BCG_1826 | BCG_1826 | 1.7054 | 1.42E−09 | Conserved hypothetical protein. Orthologous to Rv1794, which is part of the ESX-5 secretion system (Mol Microbiol. 2012 Mar;83(6):1195-209. 10.1111/j.1365-2958.2012.08001.x.) |
| rpsK | BCG_3524c | 1.704 | 1.04E−09 | Probable 30S ribosomal protein S11 rpsK |
| tyrT | tyrT | -4.7515 | 0.00058183 | tRNA-Tyr |
| BCG_0115 | BCG_0115 | -4.6431 | 2.78E−17 | Probable oxidoreductase. Orthologous to Rv0082. |
| BCG_0112 | BCG_0112 | -4.1372 | 6.19E−31 | Hypothetical protein. Orthologous to Rv0079, part of the DosR-regulon. Contains a 46 aa region (out of 273 aa) with Sigma 54 modulation/S30EA ribosomal protein C-terminus (2.2e−11) |
| BCG_1838c | BCG_1838c | -3.8293 | 2.20E−18 | Hypothetical protein |
| BCG_3001 | BCG_3001 | -3.7853 | 9.73E−06 | Possible conserved secreted protein |
| BCG_0114 | BCG_0114 | -3.5825 | 4.44E−09 | Probable transcriptional regulatory protein. Orthologous to Rv0081. Part of the DosR-regulon. |
| hycD | BCG_0117 | -3.3564 | 1.98E−11 | Possible formate hydrogenlyase hycD (FHL) |
| BCG_0113 | BCG_0113 | -3.3198 | 1.60E−08 | Conserved hypothetical protein. Orthologous to Rv0080. Part of the DosR-regulon. Contains a Pyridoxine 5'-phosphate (PNP) oxidase-like and flavin reductase-like proteins domain (1.66e−19) |
| gluU | gluU | -3.2724 | 0.000581961 | tRNA-Glu |
| BCG_0410c | BCG_0410c | -3.1733 | 0.005478442 | Conserved hypothetical protein. Xanthine dehydrogenase accessory factor. Xanthine and CO dehydrogenase maturation factor (3.83e−57) |
| EBG00001157338 | EBG00001157338 | -3.1712 | 0.000181053 | tRNA |
| BCG_3454c | BCG_3454c | -3.165 | 1.60E−05 | Conserved hypothetical protein. Type II toxin-antitoxin (TA) system Phd/YefM family antitoxin similar to Mycobacterium tuberculosis VapB antitoxins Orthologous to Rv3385c. |
| BCG_1725c | BCG_1725c | -3.1551 | 1.92E−11 | Probable conserved ATP-binding protein ABC transporter |
| BCG_2178c | BCG_2178c | -3.1213 | 0.00184171 | Conserved hypothetical protein. Contains Flavin-utilizing monoxygenases (4.46e−58) |
| BCG_2265 | BCG_2265 | -3.1205 | 3.06E−08 | Conserved hypothetical protein |
| BCG_3157c | BCG_3157c | -3.1202 | 1.23E−14 | Conserved hypothetical protein. Orthologous to Rv3134c, in operon with dosR, part of the DosR-regulon. Universal stress protein family. |
| serX | serX | -3.1175 | 0.000416156 | tRNA-Ser |
| EBG00001157336 | EBG00001157336 | -3.081 | 0.000153611 | tRNA |
| lysU | lysU | -3.0572 | 0.000223606 | tRNA-Lys |
| serV | serV | -2.9977 | 0.000401639 | tRNA-Ser |
| TB31.7 | BCG_2650 | -2.9848 | 6.22E−10 | Conserved hypothetical protein TB31.7. Orthologous to Rv2623, part of DosR-regulon. Universal stress protein family. |
| EBG00001157351 | EBG00001157351 | -2.9789 | 5.40E−06 | tRNA |
| iniB | BCG_0380 | -2.9678 | 1.85E−17 | Isoniazid inductible gene protein iniB |
| BCG_1777 | BCG_1777 | -2.9632 | 2.44E−17 | Conserved hypothetical protein |
| argH | BCG_1698 | -2.9341 | 8.39E−07 | Probable Argininosuccinate lyase argH |
| BCG_2266 | BCG_2266 | -2.9043 | 7.57E−07 | Conserved hypothetical protein. Contains a C-terminal 71 aa stretch similar to Superfamily of nucleases (8.51e−3) |
| hspX | BCG_2050c | -2.8879 | 9.61E−07 | Heat shock protein hspX. Orthologous to Rv2031c, alpha crystalin, part of the DosR-regulon. |
| BCG_2049c | BCG_2049c | -2.8578 | 1.28E−07 | Conserved hypothetical protein. Orthologous to Rv2030c, part of the DosR-regulon. Contains N-terminal (aa 15-228) Phosphoribosyl transferase (PRT)-type I domain (4.14e−98) and another stretch (aa 223-663 out of 681) with Erythromycin esterase homolog domain (8e−155) |
| BCG_3154 | BCG_3154 | -2.8493 | 4.09E−09 | Conserved hypothetical protein. Orthologous to Rv3131, part of the DosR-regulon. |
| BCG_3287c | BCG_3287c | -2.8072 | 3.32E−07 | Conserved hypothetical protein |
| BCG_2624 | BCG_2624 | 4.1276 | 0.009472594 | Probable conserved integral membrane protein. 59 aa long. |
| BCG_0112 | BCG_0112 | 4.0751 | 3.50E−24 | Hypothetical protein. Orthologous to Rv0079, part of the DosR-regulon. Contains a 46 aa region (out of 273 aa) with Sigma 54 modulation/S30EA ribosomal protein C-terminus (2.2e−11) |
| BCG_2082 | BCG_2082 | 3.5644 | 0.006797916 | Conserved hypothetical protein |
| BCG_2051 | BCG_2051 | 3.4061 | 4.19E−17 | Conserved hypothetical protein Acg. Part of the DosR-regulon. |
| BCG_2653c | BCG_2653c | 3.3755 | 2.16E−12 | Conserved hypothetical protein. Orthologous to Rv2626c, part of the DosR-regulon. Contains CBS pair domain found in Hypoxic Response Protein 1 (HRP1) -like proteins (4.13e−50). |
| BCG_3157c | BCG_3157c | 3.357 | 8.15E−16 | Conserved hypothetical protein. Orthologous to Rv3134c, in operon with dosR, part of the DosR-regulon. Universal stress protein family. |
| BCG_1628 | BCG_1628 | 3.324 | 9.27E−06 | Conserved hypothetical protein |
| BCG_1777 | BCG_1777 | 3.2859 | 6.02E−21 | Conserved hypothetical protein. Orthologous to Rv1738, part of the DosR-regulon |
| BCG_1772c | BCG_1772c | 3.1827 | 1.13E−12 | Probable conserved transmembrane protein. Orthologous to Rv1733c, part of the DosR-regulon. |
| PE_PGRS42d | BCG_2505c | 3.1391 | 0.000695518 | PE-PGRS family protein [second part] |
| TB31.7 | BCG_2650 | 3.1235 | 2.72E−10 | Conserved hypothetical protein TB31.7. Orthologous to Rv2623, part of DosR-regulon. Universal stress protein family. |
| BCG_0115 | BCG_0115 | 3.1231 | 1.05E−05 | Probable oxidoreductase. Orthologous to Rv0082. |
| BCG_3454c | BCG_3454c | 3.0372 | 0.000216715 | Conserved hypothetical protein. Type II toxin-antitoxin (TA) system Phd/YefM family antitoxin similar to Mycobacterium tuberculosis VapB antitoxins |
| BCG_1838c | BCG_1838c | 3.0323 | 1.20E−09 | Hypothetical protein |
| BCG_2178c | BCG_2178c | 3.032 | 0.008749493 | Conserved hypothetical protein. Contains Flavin-utilizing monoxygenases (4.46e−58) |
| BCG_0614 | BCG_0614 | 3.0014 | 4.54E−15 | Conserved hypothetical protein. Orthologous to Rv0569, part of the DosR-regulon. |
| hspX | BCG_2050c | 2.8196 | 1.61E−09 | Heat shock protein hspX. Orthologous to Rv2031c, alpha crystalin, part of the DosR-regulon. |
| thiE | BCG_0453c | 2.8106 | 0.000357906 | Probable thiamine-phosphate pyrophosphorylase thiE |
| BCG_0113 | BCG_0113 | 2.7983 | 1.12E−06 | Conserved hypothetical protein. Orthologous to Rv0080. Part of the DosR-regulon. Contains a Pyridoxine 5'-phosphate (PNP) oxidase-like and flavin reductase-like proteins domain (1.66e−19) |
| PE_PGRS13 | BCG_0885 | 2.7947 | 3.02E−14 | PE-PGRS family protein |
| BCG_0114 | BCG_0114 | 2.7491 | 0.000116177 | Probable transcriptional regulatory protein. Orthologous to Rv0081. Part of the DosR-regulon. |
| BCG_0168 | BCG_0168 | 2.6959 | 3.97E−05 | Pseudogene |
| BCG_2563 | BCG_2563 | 2.6227 | 0.009558631 | Hypothetical alanine rich protein |
| BCG_3001 | BCG_3001 | 2.6148 | 0.009815904 | Possible conserved secreted protein |
| BCG_3287c | BCG_3287c | 2.6089 | 4.29E−05 | Conserved hypothetical protein |
| BCG_0662 | BCG_0662 | 2.592 | 1.93E−08 | Probable integral membrane protein |
| BCG_3154 | BCG_3154 | 2.5861 | 1.09E−07 | Conserved hypothetical protein. Orthologous to Rv3131, part of the DosR-regulon. |
| BCG_2049c | BCG_2049c | 2.5844 | 9.49E−08 | Conserved hypothetical protein. Orthologous to Rv2030c, part of the DosR-regulon. Contains N-terminal (aa 15-228) Phosphoribosyl transferase (PRT)-type I domain (4.14e−98) and another stretch (aa 223-663 out of 681) with Erythromycin esterase homolog domain (8e−155) |
| leuT | leuT | 2.5789 | 0.005156523 | tRNA-Leu |
| BCG_3716c | BCG_3716c | 2.5574 | 0.00164617 | Probable conserved transmembrane protein. Contains Flp pilus assembly protein TadB domain (3.29e−41) |
| BCG_0010c | BCG_0010c | -4.5012 | 4.50E−31 | Probable conserved membrane protein. It contains a 40 aa stretch (out of 111 aa) similar to bacterial plekstrin homology domain (2.65e−8) |
| BCG_0040c | BCG_0040c | -4.435 | 4.43E−17 | Probable conserved membrane protein. It contains a 40 aa stretch (out of 111 aa) similar to bacterial plekstrin homology domain (2.65e−8) |
| BCG_3494c | BCG_3494c | -4.2797 | 3.95E−16 | Hypothetical protein |
| lppU | BCG_2802c | -3.4282 | 1.19E−22 | Probable lipoprotein lppU |
| BCG_2159c | BCG_2159c | -3.4146 | 1.35E−24 | Hypothetical protein |
| BCG_2673c | BCG_2673c | -3.3701 | 2.34E−07 | Hypothetical protein |
| BCG_3307c | BCG_3307c | -3.312 | 1.66E−11 | Probable conserved transmembrane protein. It contains a 75 aa stretch (out of 111 aa) similar to bacterial plekstrin homology domain (4.36e−18) |
| BCG_0088 | BCG_0088 | -3.2898 | 6.03E−20 | Hypothetical protein |
| rho | BCG_1357 | -3.2069 | 1.45E−12 | Probable transcription termination factor rho homolog |
| BCG_1104c | BCG_1104c | -3.1715 | 3.72E−28 | Hypothetical protein |
| rpsM | BCG_3525c | -3.1288 | 2.36E−19 | Probable 30S ribosomal protein S13 rpsM |
| BCG_3139 | BCG_3139 | -3.09 | 7.74E−06 | Conserved hypothetical protein. tRNA(Arg) A34 adenosine deaminase TadA domain (1.47e−34) |
| BCG_1926c | BCG_1926c | -3.0538 | 0.000420994 | Conserved hypothetical protein. S-adenosylmethionine-dependent methyltransferases domain (6.49e−22) |
| BCG_1350 | BCG_1350 | -3.0417 | 2.98E−05 | Hypothetical protein |
| BCG_1001c | BCG_1001c | -3.039 | 0.000254116 | Probable mycolyl transferase. 76 aa, similar to FbpC. |
| BCG_2748c | BCG_2748c | -3.0182 | 6.70E−24 | Conserved hypothetical protein. Contains a three-Cys-motif partner protein domain (8.96e−66) |
| BCG_1115 | BCG_1115 | -2.9826 | 5.71E−10 | Conserved hypothetical protein. Contains a DNA-binding beta-propeller fold protein YncE (1.79e−34) |
| dnaA_2 | BCG_0031 | -2.9643 | 3.00E−24 | Chromosomal replication initiator protein dnaA |
| PPE70 | BCG_3183c | -2.9502 | 6.02E−20 | PPE family protein |
| BCG_3911 | BCG_3911 | -2.9473 | 1.83E−08 | Probable conserved transmembrane protein. Putative Ca2+/H+ antiporter (2.81e−61) |
| BCG_3929 | BCG_3929 | -2.9222 | 4.01E−22 | Conserved hypothetical protein. Orthologous Rv3866 (EspG). A deletion of espG in M. marinum reduced sliding motility and biofilm formation by M. marinum (Front Microbiol. 2018 May 30;9:1160. 10.3389/fmicb.2018.01160). |
| BCG_2192c | BCG_2192c | -2.9092 | 9.86E−14 | Possible transposase |
| lpqK | BCG_0436c | -2.9037 | 3.46E−08 | Possible conserved lipoprotein lpqK |
| rpsK | BCG_3524c | -2.8992 | 1.14E−17 | Probable 30S ribosomal protein S11 rpsK |
| dnaA_1 | BCG_0001 | -2.8632 | 5.63E−22 | chromosomal replication initiation protein dnaA |
| BCG_1987c | BCG_1987c | -2.8213 | 1.10E−10 | Hypothetical protein |
| BCG_0078c | BCG_0078c | -2.8174 | 1.00E−14 | Conserved hypothetical protein. N-terminal (74 aa) with Transcriptional regulator PadR-like family domain (3.67e−22) |
| rpoA | BCG_3522c | -2.7989 | 2.70E−08 | Probable DNA-directed RNA polymerase (alpha chain) rpoA |
| BCG_3899 | BCG_3899 | -2.7944 | 8.14E−08 | Conserved hypothetical protein. Contains Minimal MMP-like domain (6.69e−50) |
| lprR | BCG_2566 | -2.7685 | 1.32E−05 | Probable conserved lipoprotein lprR. Orhtologous to lppA |