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. 2020 Mar 31;11(2):e00445-20. doi: 10.1128/mBio.00445-20

TABLE 3.

Relative gene expression detected by microarray for genes showing statistically significant >1.5-fold differences in expression for the thick-capsule ΔadcAII AIIL strain compared to the WT D39 straina

Regulation status in hyperencapsulated strains and gene no. Gene name Predicted/known function Mutant strain and capsule phenotype
ΔadcAII (AIIL) thick ΔadcAII/phtD (AII+Pcl4) thick ΔadcAII (Cl44) none
Upregulated
    SPD_0104 LysM domain protein 1.80 1.93 1.20
    SPD_0389 accD Acetyl-CoA carboxylase subunit beta 1.55 1.59 −1.37
    SPD_0646 Hypothetical protein 1.74 2.05 −1.18
    SPD_0890 phtE Histidine triad protein 3.04 3.18 1.04
    SPD_0891 Truncated histidine triad protein 3.25 1.16 1.37
    SPD_0892 Truncated histidine triad protein 3.31 1.09 1.43
    SPD_0893 Hypothetical protein 3.39 1.04 1.59
    SPD_1038 phtA Histidine triad protein 1.98 1.52 −1.05
    SPD_1874 LysM domain-containing protein 2.53 2.90 1.19
    SPD_1997 adcA Zinc ABC transporter AdcA lipoprotein 1.52 1.41 1.03
    SPD_2000 adcR adc operon repressor AdcR 1.55 1.65 −1.06
Downregulated
    SPD_0052 purL Phosphoribosylformylglycinamidine synthase −2.45 −2.36 1.24
    SPD_0053 purF Amidophosphoribosyltransferase −2.27 −2.34 1.25
    SPD_0055 purN Phosphoribosylglycinamide formyltransferase −2.13 −2.18 1.36
    SPD_0090 ABC transporter lipoprotein −2.02 −2.19 2.04
    SPD_0166 ribH Riboflavin synthase, beta subunit −2.76 −3.44 1.56
    SPD_0167 ribB Riboflavin biosynthesis protein RibB −2.51 −3.34 1.71
    SPD_0168 ribE Riboflavin synthase subunit alpha −2.52 −3.30 1.66
    SPD_0169 ribD Riboflavin biosynthesis protein RibD −2.40 −3.30 1.67
    SPD_0224 pitD PitD iron ABC transporter permease −2.28 −2.11 1.46
    SPD_0226 pitA PitA iron ABC transporter lipoprotein −2.01 −1.37 1.72
    SPD_0265 adhP Alcohol dehydrogenase −1.80 −1.83 1.63
    SPD_0279 celB Cellobiose PTS system IIB component −2.28 −1.79 1.76
    SPD_0300 Oligohyaluronate lyase −2.49 −1.60 1.32
    SPD_0362 mtlF Mannitol PTS system IIA component −2.38 −2.40 1.40
    SPD_0364 Amino acid ABC transporter ATPase −3.00 −2.80 1.84
    SPD_0444 lytB Endo-beta-N-acetylglucosaminidase −1.55 −1.69 1.38
    SPD_0450 creX/psrA Type I restriction-modification system −3.39 −4.24 −1.43
    SPD_0452 hsdS′ (hsdS2) Type I restriction-modification system −3.62 −6.41 1.25
    SPD_0453 hsdS (hsdS1) Type I restriction-modification system −2.01 −2.36 1.15
    SPD_0466 blpT BlpT protein, fusion −1.79 −2.26 1.52
    SPD_0472 blpA ABC transporter, ATP-binding protein −2.21 −3.47 1.59
    SPD_0473 blpY Immunity protein BlpY −1.50 −2.17 1.44
    SPD_0553 Hypothetical protein −1.59 −1.44 1.26
    SPD_0595 Hypothetical protein −1.55 −1.72 −0.64
    SPD_0608 pyrF Orotidine 5′-phosphate decarboxylase −1.65 −1.60 1.02
    SPD_0609 pyrE Orotate phosphoribosyltransferase −1.77 −1.67 1.02
    SPD_0610 Hypothetical protein −2.18 −2.26 1.45
    SPD_0611 Hypothetical protein −1.76 −1.94 1.19
    SPD_0612 Hypothetical protein −2.07 −2.06 1.00
    SPD_0613 Hypothetical protein −1.70 −1.83 1.09
    SPD_0614 ABC transporter, ATP-binding protein −1.76 −1.77 1.11
    SPD_0615 ABC transporter substrate binding protein −1.51 −2.25 1.25
    SPD_0616 glnQ Amino acid ABC transporter ATPase −1.56 −2.38 1.13
    SPD_0617 glnP Amino acid ABC transporter permease −1.76 −2.64 1.25
    SPD_0618 glnP Amino acid ABC transporter permease −1.71 −2.51 1.20
    SPD_0851 pyrK Dihydroorotate dehydrogenase II −1.90 −1.90 1.16
    SPD_0852 pyrD Dihydroorotate dehydrogenase IB −2.32 −2.28 1.11
    SPD_0853 lytB Endo-beta-N-acetylglucosaminidase −1.71 −1.65 1.09
    SPD_0888 adcAII Zn2+ ABC transporter lipoprotein −3.87 −3.03 −5.95
    SPD_0889 phtD Hypothetical protein −1.78 −2.50 −4.2
    SPD_1009 serB Phosphoserine phosphatase −1.51 −1.24 1.60
    SPD_1011 glxK Glycerate kinase −1.63 −1.26 1.58
    SPD_1035 PTS system, IIA component −4.70 −4.83 −1.91
    SPD_1036 PTS system, IIA component −7.26 −5.84 −2.93
    SPD_1050 lacD Tagatose 1,6-diphosphate aldolase −1.61 −1.60 1.44
    SPD_1051 lacC Tagatose-6-phosphate kinase −1.62 −1.62 1.49
    SPD_1052 lacB Galactose-6-phosphate isomerase LacB −1.58 −1.56 1.46
    SPD_1053 lacA Galactose-6-phosphate isomerase LacA −1.61 −1.61 1.51
    SPD_1074 metY O-Acetylhomoserine sulfhydrylase −1.64 −1.92 1.51
    SPD_1131 carB Carbamoylphosphate synthase subunit −1.60 −1.37 1.06
    SPD_1133 pyrB Aspartate carbamoyltransferase subunit −1.51 −1.30 1.01
    SPD_1175 Putative membrane protein −1.68 −1.75 −1.43
    SPD_1176 ABC transporter, ATP-binding protein −1.69 −1.81 1.38
    SPD_1177 Drug efflux ABC transporter −1.73 −1.68 1.43
    SPD_1178 ptrB Prolyl oligopeptidase family protein −1.73 −1.78 −1.47
    SPD_1179 Hypothetical protein −1.74 −1.80 1.59
    SPD_1454 Hypothetical protein −1.56 −1.61 1.17
    SPD_1455 Hypothetical protein −1.84 −3.29 1.25
    SPD_1498 Oxidoreductase −2.21 −2.23 1.34
    SPD_1501 Sugar ABC transporter permease −3.73 −3.58 1.42
    SPD_1503 Hypothetical protein −3.25 −4.03 1.09
    SPD_1513 Hypothetical protein −1.77 −2.68 −1.40
    SPD_1568 GTP cyclohydrolase −1.80 −1.55 1.53
    SPD_1584 ABC transporter permease −2.30 −2.16 2.08
    SPD_1650 fatC Iron uptake ABC transporter permease −2.84 −2.23 1.30
    SPD_1793 Universal stress protein family −1.54 −1.74 2.00
    SPD_1865 adh Zinc-containing alcohol dehydrogenase −1.59 −1.28 1.48
    SPD_1972 Hypothetical protein −2.38 −2.96 1.75
    SPD_1985 adh2 Iron-containing alcohol dehydrogenase −2.05 −1.89 1.59
    SPD_1987 Fucolectin-related protein −3.12 −2.96 1.49
    SPD_1989 PTS system, IID component −2.19 −1.83 1.88
    SPD_1990 PTS system, IIC component −1.94 −1.74 1.60
    SPD_1991 PTS system, IIB component −1.83 −1.45 1.52
    SPD_1992 PTS system, IIA component −2.03 −1.79 1.68
    SPD_1993 fucU Fucose operon FucU protein −2.33 −2.10 1.83
    SPD_1994 fucA l-Fuculose phosphate aldolase −2.17 −2.33 1.63
    SPD_1995 fcsK l-Fuculose kinase FucK, putative −2.13 −2.07 2.12
    SPD_2013 glpK Glycerol kinase −2.76 −2.36 1.25
a

For comparison, the fold differences compared to WT D39 strain for the thick-capsule ΔadcAII/phtD strain (AII + Pcl14) and a normal-capsule-thickness ΔadcAII strain (Cl144) are provided alongside. The adcAII, phtD, and SpnD39III (ST5556II) type I restriction-modification system genes are indicated in bold, and gene expression profile differences in the ΔadcAII/phtD or the ΔadcAII (Cl144) compared to the ΔadcAII AIIL hyperencapsulated strain are indicated in italics. Abbreviations: CoA, coenzyme A; PTS, phosphotransferase.