Table 2.
Known ASR-related gene mapping from literature in response to pH change. Literature-supported ASR-related genes found in close species or other Lactococcus lactis strains. The template transporters and genes were first identified in published studies from the NCBI and UniProt databases. Lactococcus lactis Il1403 was used as the organism which is very close to MG1363 if template gene existed. Only 36 templates that successfully mapped to the MG1363 genome were listed, which resulted in 33 genes. All mapped genes and corresponding templated were organized by their regulated pathways which were further used as functional modules. Mapped genes were searched in 51 regulons to build the connections between functional modules and regulons.
| Template Organisms | MG1363 | |||
|---|---|---|---|---|
| Organisms | Transporters | Functions/Pathways | Mapped Genes (Locus Tag) | Regulons |
| Lactococcus lactis | ldh | LDH | ldh (llmg_1120) | NHP6A, llrA |
| ldhB | ldhB (llmg_0392, llmg_0475) | |||
| ldhX | ldhX (llmg_1429) | |||
| Lactococcus lactis | gadB | GAD | gadB (llmg_1179) | N/A |
| gadC | gadC (llmg_1178) | |||
| L actococcus lactis | arcA | ADI pathway | arcA (llmg_2313) | NHP6A, llrA, llrC, hllA |
| arcB | arcB (llmg_2312) | |||
| arcC1 | arcC1 (llmg_2310) | |||
| arcC2 | arcC2 (llmg_2309) | |||
| argF | argF (llmg_1754) | |||
| Bacteria | ureA/B/C $ | Urea degradation | pyrC (llmg_1508) | N/A |
| L actococcus lactis | atpEBFHAGDC $$ | F0/F1ATPase | llmg_1952, llmg_1951, llmg_1950, llmg_1949, llmg_1948, llmg_1947, llmg_1946, llmg_1945 |
llrA, (Regulon8, llmg_1803) $$$ |
| Lactococcus lactis | rcfB | Acid response | rcfB (llmg_2512) | (Regulon39, llrD) $$$ |
|
Lactococcus lactis, Escherichia coli K12 |
dnak | Chaperone, Protein repair and protease | dnaK (llmg_1574) | llrA |
| groEL | groEL2 (llmg_0411) | |||
| groES | groES (llmg_0410) | |||
| grpE | grpE (llmg_1575) | |||
| clpE | clpE (llmg_0528) | |||
| clpC | clpC (llmg_0615) | |||
| clpP | clpP (llmg_0638) | |||
|
Lactococcus lactis, Bacillus subtilis |
dltC, agK, SGP, ffh |
Envelope alterations | llmg_0878 | NHP6A, llrA |
| Lactococcus lactis | recA, uvr, smn | DNA repair | llmg_0374, llmg_0534, llmg_1718 llmg_1221 | (Regulon39, llrD) $$$ |
$ Three subunits of urease enzymes coded by ureABC operon found preserved in multiple bacteria. $$ Altogether eight genes. $$$ The homolog prediction or motif research results with low homolog similarity but have meaningful biological relevance. Abbreviations: LDH, L-lactate dehydrogenase; GAD, glutamate decarboxylases; ADI, arginine deiminase; N/A, not found.