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. 2022 May 16;204(6):e00121-22. doi: 10.1128/jb.00121-22

TABLE 2.

Genes affected by Wal-ON conditions

Gene, changed ≥4-fold Operona Gene name Annotationb Log2 fold change
 Cell wall associationd
WalR overexpression
 CRISPRi against walc
WalR WalRD54E
cd630_07390 07390 Hypothetical protein 5.26 5.70 −1.38 SPI
cd630_15220 15220 pgdA Peptidoglycan deacetylase 4.02 4.26 −1.09 SPI
cd630_05490 05490 Hypothetical protein 3.87 4.51 −1.84 SPI
17810 walA Lipoprotein NCe NC −2.76 SPII
cd630_17820 17820 walR TC response regulator 3.81 3.67 −2.51
17830 walK TC sensor histidine kinase NC NC −2.33 Membrane
17840 truA2 tRNA pseudouridine synthase A NC NC −2.34
cd630_07380 07380 Hypothetical protein 3.43 4.14 −1.22 SPI
cd630_08670 08670 Hypothetical protein 3.28 3.97 NC Membrane
cd630_07400 07400 PLP-dependent aminotransferase 3.21 2.38 NC
cd630_10880 10880 Hypothetical protein 2.88 3.14 −1.40 Membrane
cd630_01660 01660 Peptidase 2.76 2.95 NC
01650 Amino acid transporter NC NC NC Membrane
cd630_27940 27940 cwp12 Cell wall binding protein 2.69 2.82 NC SPI
cd630_33090 33090 ligA DNA ligase 2.64 2.62 NC
cd630_18250 18250 metY O-Acetylhomoserine sulfhydrylase 2.50 2.80 −0.57
cd630_18260 18260 metA Homoserine O-succinyltransferase 2.60 2.85 −0.88
cd630_14281 14281 Hypothetical protein 2.59 3.22 NC
cd630_27860 27860 cwp5 Cell wall binding protein 2.51 2.65 NC SPI
cd630_25380 25380 Lipoprotein 2.47 2.70 −0.70 SPII
cd630_03910 03910 asnB Asparagine synthetase 2.47 3.30 NC Membrane
cd630_14960 14960 Hypothetical protein 2.37 2.86 −0.74 SPI
cd630_25370 25370 5′-Nucleotidase/phosphoesterase 2.33 2.49 −0.59 SPI
cd630_27910 27910 cwp2 Cell wall binding protein 2.30 2.36 −0.59 SPI
27900 LmbE-like deacetylase 1.56 1.46 −0.55
27890 cwp66 Cell wall binding protein 1.41 1.42 −0.58 SPI
cd630_28620 28620 Peptidase 2.29 2.24 −2.53
cd630_34880 34880 gtaB1 UTP-G1P uridylyltransferase 2.23 2.34 −0.73
cd630_20580 20580 Hypothetical protein 2.22 2.43 −1.26 Membrane
cd630_07410 07410 glpK1 Glycerol kinase 2.21 0.63 NC
07420 eutH Ethanolamine utilization protein 1.46 NC NC Membrane
10350 cwp16 Amidase, cell wall binding protein 1.24 1.33 NC SPI
cd630_10360 10360 cwp17 Amidase, cell wall binding protein 2.15 2.35 NC SPI
cd630_21170 21170 trxB2 Thioredoxin reductase 2.12 2.18 NC
cd630_00210 00210 pycA Pyruvate carboxylase 2.10 2.16 −0.46
cd630_13890 13890 Chloromuconate cycloisomerase 2.09 2.18 −0.28
13900 Hypothetical protein 1.30 1.64 Membrane
cd630_22490 22490 ATPase 2.07 2.20 NC
cd630_22480 22480 Hypothetical protein 1.81 2.04 NC
cd630_10890 10890
10900		 rgbR
rgbS 		TC response regulator 2.04 2.24 −1.13
10900 rgbS TC sensor HK (fragment) NC 1.16 NC Membrane
cd630_30930 30930 Aminobutyrate hydrolase 2.15 2.35 NC
30920 Putative amino acid transporter 1.52 1.02 NC Membrane
cd630_26810 26810 Putative Ca-chelating protein 2.01 2.59 NC SPI
cd630_36010 36010 d-Alanyl–d-alanine carboxypeptidase 1.99 2.35 −1.38 SPI
cd630_00220 00220 Elongation factor G 1.97 2.09 NC
cd630_14290 14290 Acyl-CoA N-acyltransferase 1.92 2.47 −1.15
cd630_22280 22280 Hypothetical protein 1.83 2.05 −0.70 Membrane
cd630_01100 01100 Hypothetical protein 1.81 2.02 NC Membrane
01110 Hypothetical protein 1.51 1.73 NC SPI
01111 Hypothetical protein NC 1.14 NC
cd630_09940 09940 Serine-pyruvate aminotransferase 1.77 2.10 NC
cd630_19942 19942 Hypothetical protein 1.74 2.12 NC
cd630_05270 05270 Beta-lactamase-like hydrolase 1.73 2.13 −0.85
cd630_22270 22270 Radical SAM protein 1.67 2.02 −0.55 SPII
cd630_18070 18070 NADPH-dependent FMN reductase 1.49 2.07 −1.53 Membrane
cd630_03901 03901 Hypothetical protein 0.92 2.37 NC
cd630_10631 10631 Hypothetical protein −0.07 2.18 −0.62 Membrane
cd630_30360 30360 Major facilitator superfamily transporter −1.59 −2.13 1.11 Membrane
cd630_10540 10540 bcd2 Acyl-CoA dehydrogenase −1.93 −2.23 1.03
cd630_10550 10550 etfB Electron transfer flavoprotein beta −1.78 −2.11 1.07
cd630_10560 10560 etfA Electron transfer flavoprotein alpha −1.95 −2.18 1.10
cd630_10570 10570 crt2 3-Hydroxybutyryl-CoA dehydratase −1.96 −2.27 1.06
cd630_31000 31000 C4-dicarboxylate anaerobic carrier −1.88 −2.59 NC Membrane
cd630_30990 30990 Amidohydrolase −1.80 −2.47 NC Membrane
cd630_10580 10580 hbd 3-Hydroxybutyryl-CoA dehydrogenase −1.86 −2.05 0.89 SPII
cd630_10590 10590 thlA1 Acetyl-CoA acetyltransferase −1.96 −2.16 0.77
16820 queK Queuosine hydrolase monomer −1.31 −1.60 NC
16830 ECF transporter S-comp. −1.39 −1.65 NC Membrane
cd630_16840 16840 queL Radical SAM superfamily protein −1.90 −2.06 NC
23900 BlaI-like −1.47 −1.65 NC
cd630_23890 23890 BlaR-like −1.94 −2.26 0.80 Membrane
23880 Putative PG hydrolase −1.50 −1.77 NC SPI
36040 Hypothetical protein −0.86 −0.94 0.71
cd630_36030 36030 Phosphoesterase −1.97 −2.01 1.09 Membrane
cd630_14040 14040 Oligopeptide transporter −2.02 −2.03 NC Membrane
14041 Hypothetical protein −2.02 −1.88 NC
25120 PTS, subunit IIA −1.11 −1.47 NC
25110 PTS, antiterminator −1.45 −1.46 NC
cd630_25100 25100 PTS, subunit IIBC −2.04 −2.19 0.97 Membrane
cd630_25320 25320 Alanine-glyoxylate transaminase −2.05 −2.34 1.41
cd630_25310 25310 Hypothetical protein −2.67 −2.75 1.35 Membrane
cd630_27680 27680 Cell wall hydrolase −2.06 −2.29 NC SPI
cd630_29660 29660 adhE1 Acetaldehyde-CoA/alcohol dehydrogenase −2.08 −2.37 −1.09 Membrane
cd630_18120 18120 Response regulator −2.08 −2.28 NC
cd630_22600 22600 Major facilitator superfamily transporter −2.13 −2.32 NC Membrane
cd630_20160 20160 Hypothetical protein −2.19 −2.29 4.18
cd630_25090 25090 Glycoside hydrolase −2.22 −2.33 1.16
cd630_21070 21070 Permease family protein −2.23 −2.32 NC Membrane
cd630_10220 10220 YczE-like membrane protein −2.26 −2.73 0.93 Membrane
10230 Transcriptional regulator −1.70 −1.94 1.63
cd630_10240 10240 potA ABC transport ATP-binding protein −2.27 −2.36 1.77
cd630_10250 10250 potB ABC transport permease −2.47 −2.82 1.72 Membrane
cd630_10260 10260 potC ABC transport permease −2.53 −2.39 1.60 Membrane
cd630_10270 10270 potD ABC transport substrate binding protein −2.29 −2.37 1.55 SPII
cd630_26640 26640 murE UDP-N-acetylmuramoylalanyl-d-glutamate-2,6-diaminopimelate ligase −2.85 −3.07 0.93
cd630_26670 26670 ptsG-BC PTS, subunit IIBC −3.17 −3.52 NC SPI
cd630_26660 26660 ptsG-A PTS, subunit IIA −3.12 −3.51 NC
cd630_21510 21510 Hypothetical protein −3.56 −3.82 0.68 Membrane
a

Lists other operon members in order.

b

TC, two component; PTS, phosphoenolpyruvate-dependent sugar phosphotransferase system; CoA, coenzyme A.

c

CRISPRi against wal: fold change comparing sgRNA-neg to sgRNA-walA1 strain in the absence of xylose.

d

Reports predictions by SignalP (SPI, predicted to be a substrate of signal peptidase I; SPII, predicted to be a substrate of signal peptidase II) and by BUSCA (membrane). The BUSCA prediction is given only for those genes that were not already predicted to be SPI or SPII substrates by SignalP.

e

NC, no change, i.e., the fold change was close to 1 and the P value was >0.05.