Table 2.
DESeq2 results for genes associated with the metabolism of sulfur-containing amino acids in L. paracasei FAM18149.
| Gene (locus_tag)a | Functionb | Induction methionine-deficient vs. cysteine-deficient CDM (log2 fold change) | Adjustedp-value | Transcriptional unit (regulatory element) |
|---|---|---|---|---|
| metQ1 (00255) | MULTISPECIES: substrate-binding protein of an ABC superfamily methionine transporter | −0.1 | 1.0 | metQ1 (T-boxmet) |
| cysE (00525) | serine O-acteyltransferasec | −1.2 | 4.1E-08 | cysE-cysK (n. d.) |
| cysK (00530) | MULTISPECIES: cysteine synthase A | −1.1 | 1.5E-09 | cysE-cysK (n. d.) |
| metC (00830) | cystathionine gamma-lyased | 1.5 | 5.7E-07 | yckJ-yckK-metC (T-boxmet) |
| yckK (00835) | MULTISPECIES: amino acid ABC transporter substrate-binding protein | 1.3 | 2.6E-04 | yckJ-yckK-metC (T-boxmet) |
| yckJ (00840) | MULTISPECIES: cysteine ABC transporter permease | 0.7 | 3.3E-01 | yckJ-yckK-metC (T-boxmet) |
| metF (00930) | MULTISPECIES: 5,10-methylenetetrahydrofolate reductase | 2.2 | 5.5E-19 | metE-metF (T-boxmet) |
| metE (00935) | MULTISPECIES: 5-methyltetrahydropteroyltriglutamate–homocysteine S-methyltransferase | 2.5 | 4.0E-36 | metE-metF (T-boxmet) |
| yxjH (01620) | MULTISPECIES: vitamin-B12 independent methionine synthase | 1.3 | 3.9E-07 | yxjH-luxS (T-boxmet) |
| luxS (01625) | MULTISPECIES: S-ribosylhomocysteine lyase / autoinducer-2 production protein LuxS | 0.4 | 7.2E-01 | yxjH-luxS (T-boxmet)e |
| malY (02475) | MULTISPECIES: putative C-S lyase | 0.3 | 0.7 | malY (n. a.) |
| metK (02170) | MULTISPECIES: methionine adenoysltransferase | 0.2 | 1.0 | metK (SMK box) |
| metQ2 (04115) | MULTISPECIES: MetQ/NlpA family ABC transporter substrate-binding protein | 0.7 | 1.0 | metQ2 (T-boxmet) |
| metQ3 (04120) | MULTISPECIES: MetQ/NlpA family ABC transporter substrate-binding protein | 1.2 | 5.4E-08 | metQ3-metN-metP (T-boxmet) |
| metN (04125) | MULTISPECIES: ATP-binding protein of an ABC superfamily methionine transporter | 1.1 | 9.9E-08 | metQ3-metN-metP (T-boxmet) |
| metP (04130) | MULTISPECIES: ABC transporter permease | 1.0 | 7.9E-04 | metQ3-metN-metP (T-boxmet) |
| pfs (04610) | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | −0.3 | 0.9 | pfs (n. a.) |
| glnP2 (14340) | MULTISPECIES: polar amino acid ABC transporter inner membrane subunit | −2.5 | 1.6E-19 | glnP2-glnM2-artM2-glnH4 (T-boxcys) |
| glnM2 (14345) | MULTISPECIES: amino acid ABC transporter permease | −2.5 | 3.5E-17 | glnP2-glnM2-artM2-glnH4 (T-boxcys) |
| artM2 (14350) | MULTISPECIES: polar amino acid transport system ATP-binding protein | −2.6 | 1.5E-21 | glnP2-glnM2-artM2-glnH4 (T-boxcys) |
| glnH4 (14355) | MULTISPECIES: amino acid ABC transporter substrate-binding protein | −2.9 | 1.6E-33 | glnP2-glnM2-artM2-glnH4 (T-boxcys) |
| cysE2 (14655) | serine acetyltransferase | −2.9 | 2.0E-22 | cysE2-ctl1-cysK2 (RIT, antisense RNA) |
| ctl1 (14660) | cystathionine beta and gamma-lyase | −3.2 | 8.3E-42 | cysE2-ctl1-cysK2 (RIT, antisense RNA) |
| cysK2 (14665) | MULTISPECIES: cystathionine beta-synthase | −3.1 | 5.2E-34 | cysE2-ctl1-cysK2 (RIT, antisense RNA) |
n. d, not detected; n. a, not analyzed; RIT, rho-independent terminator.
Common gene names from Bacillus subtilis and Escherichia coli are used. Gene names for transporter are based on searches of the Transporter Classification Database (Saier et al., 2014). Numbers in brackets represent the locus_tag, of which the prefix FAM18149_ was omitted.
Functions assigned based on BLAST searches.
The gene name is designated as metA in L. paracasei ATCC 334. Since the gene in fact encodes a serine acetyltransferase (Bogicevic et al., 2016), the gene name cysE is used in this study.
The recombinant-produced protein also exhibited cystathionine gamma-synthase activity in vitro (Irmler et al., 2008).
The putative promoter 5′-TTAACA-N18-TATGAT-3′, which was identified in Lactobacillus rhamnosus GG (Lebeer et al., 2007), is also located upstream of luxS in L. paracasei FAM18149, indicating a T-box-independent expression of the respective gene.