Journal List > J Bacteriol Virol > v.45(3) > 1034176

Lim, Han, Kim, and Seo: Transcriptional Profiling of an Attenuated Salmonella Typhimurium ptsI Mutant Strain Under Low-oxygen Conditions using Microarray Analysis

Abstract

Salmonella causes a wide variety of diseases ranging from mild diarrhea to severe systemic infections, such as like typhoid fever, in multiple organisms, ranging from mice to humans. A lack of ptsI, which encodes the first component of phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS), is known to cause Salmonella Typhimurium attenuation; however, the mechanisms behind this have not yet been elucidated. In this study, a DNA microarray was performed to determine why the virulence of ptsI mutants is attenuated under low-oxygen conditions in which the ptsI expression is enhanced. Of 106 down-regulated genes, the most repressed were pdu and tdc genes, which are required for propanediol utilization and threonine and serine metabolism, respectively. In addition, half the flagellar genes were down-regulated in the ptsI mutant strain. Because pdu genes are induced during infection and Tdc products and flagella-mediated motility are necessary for the invasion of S. Typhimurium, the invasive ability of ptsI mutants was examined. We found that ptsI mutation reduced the ability of S. Typhimurium to invade into host cells, suggesting that reduced expression of the pdu, tdc, and flagellar genes is involved in the attenuation of ptsI mutants.

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Figure 1.
Distribution of differentially expressed genes. The genes whose expression was changed in the ptsI mutant were grouped into COG functional categories. The bars (black, down-regulated; and white, up-regulated) represent the number of genes in each COG category.
jbv-45-200f1.tif
Figure 2.
mRNA levels of ulaC (STM2344) in mlc mutants. Bacterial cultures were grown statically to mid-log phase. After total RNA isolation, qRT-PCR analysis was performed to determine ptsG and ulaC transcript levels. mRNA levels of each gene in the wild type were arbitrarily set to 1 (white bars), and then the relative expression of each mlc mutant gene (black bars) was determined by normalizing the mRNA levels to this value. Error bars indicate the standard deviations obtained in three independent experiments performed in duplicate.
jbv-45-200f2.tif
Figure 3.
The fold change for the pdu and tdc genes. Bars represent the expression ratio (ptsI to wt) for each gene, which was derived from the log2-transformed microarray hybridization results.
jbv-45-200f3.tif
Figure 4.
The fold change for the flagella and chemotaxis genes. Bars represent the expression ratio (ptsI to wt) for each gene, which was derived from the log2-transformed microarray hybridization results.
jbv-45-200f4.tif
Figure 5.
Defects in flagella biosynthesis in ptsI mutants. In all bar graphs, white and black bars represent the wild-type (WT) and ptsI mutant (ptsI) mutant strains, respectively. (A) Validation of microarray results for five flagellar genes. mRNA levels were measured through qRT-PCR, and the mRNA levels of each gene in WT were set to 1. Error bars indicate the standard deviations (SD) obtained in three independent experiments performed in duplicate. (B) WT and ptsI were compared for motility. Bar graphs show the mean halo diameters (zones of motility) ± SDs obtained from a quantitative motility assay performed in triplicate. The zone of motility was measured at 7 and 14 h after inoculation. (C) Salmonella invasion into HEp-2 epithelial and RAW 264.7 macrophage cells. The mammalian cells infected by WT and ptsI were lysed 2 h after infection and dilutions of the suspension were plated on LB agar medium to determine CFU. Data are presented as percentages of CFU of WT. Values are the means ± SDs obtained in three independent experiments performed in duplicate.
jbv-45-200f5.tif
Table 1.
List of primers used in qRT-PCR
Gene Forward (5′ → 3′) Reverse (5′ → 3′)
ptsG GTCGGTTCCGCTAACTTCAG CCCGTATCAGCAAGGTGTTT
ulaC TGCTGGGAACCTGGTTATCT TTTGGTGCTGCTGAACAATC
flhD CAACGAAGAGATGGCAAACA GACGCGTTGAAAGCATGATA
fliA CCGCTGAAGGTGTAATGGAT CCGCATTTAATAACCCGATG
fliZ AAACATTTCCCACGATCTGC CGGTAAAGGGGGATTTCTGT
flgM CCTTTGAAACCCGTTAGCAC GCCGTTTTTAATGCTTCGAC
fliC AACGACGGTATCTCCATTGC TACACGGTCGATTTCGTTCA
rrsH CGGGGAGGAAGGTGTTGTG CAGCCCGGGGATTTCACATC
Table 2.
The genes induced by ptsI mutation
Locustag Gene name Ratio (ptsI/wt) p-value B-value Description
STM2342 ulaA 53.09 1.4E-09 12.49 Ascorbate-specific PTS system EIIC
STM2341   46.19 8.4E-10 12.92 Putative transketolase
STM2340   33.89 3.0E-09 11.80 Putative transketolase
STM2344 ulaC 26.92 6.7E-10 13.13 Putative PTS system EIIA component
STM3685 mtlA 26.79 5.3E-09 11.27 PTS family, mannitol-specific enzyme IIABC components
STM2343 ulaB 21.69 6.8E-11 14.99 PTS system EIIB component
STM3686 mtlD 15.80 1.7E-10 14.28 Mannitol-1-phosphate dehydrogenase
STM2339 yfcC 12.87 4.9E-09 11.34 Putative integral membrane protein
STM3687 mtlR 7.76 2.0E-09 12.14 Repressor for mtl
STM2458 eutB 6.00 1.7E-05 3.24 Ethanolamine ammonia-lyase, heavy chain
STM2462 eutJ 5.38 7.9E-05 1.63 Paral putative heatshock protein (Hsp70)
STM1203 ptsG 5.03 3.5E-07 7.20 Sugar Specific PTS family, glucose-specific IIBCcomponent
STM2456 eutL 4.55 2.2E-04 0.58 Putative carboxysome structural protein, ethanolamine utilization
STM2459 eutA 4.24 1.2E-06 5.96 CPPZ-55 prophage; chaperonin in ethanolamine utilization
STM4007 glnA 3.99 3.6E-07 7.19 Glutamine synthetase
STM0759 ybgS 3.98 1.6E-06 5.68 Putative homeobox protein
STM2457 eutC 3.93 1.4E-05 3.44 Ethanolamine ammonia-lyase, light chain
STM1493   3.40 4.3E-05 2.26 Putative periplasmic component, ABC transport system
STM1831 manY 3.07 2.1E-05 3.01 Sugar Specific PTS family, mannose-specific enzyme IIC
STM2455 eutK 3.06 1.7E-04 0.84 Putative carboxysome structural protein, ethanolamine utilization
STM2460 eutH 2.79 3.1E-05 2.61 Putative transport protein, ethanolamine utilization
STM1491   2.71 2.4E-05 2.85 ABC-type proline/glycine betaine transport systems, ATPase component
STM1844 htpX 2.69 1.7E-04 0.85 Heat shock protein, integral membrane protein
STM1070 ompA 2.68 1.0E-05 3.77 Putative hydrogenase, membrane component
STM3384 yhdG 2.64 3.3E-05 2.54 Putative TIM-barrel enzyme, possibly dehydrogenase
STM1212 ycfJ 2.54 2.5E-04 0.42 Putative outer membrane lipoprotein
STM1929 otsB 2.52 5.2E-05 2.07 Trehalose-6-phosphate phophatase, biosynthetic
STM0833 ompX 2.48 2.0E-06 5.43 Outer membrane protease, receptor for phage OX2
STM0852 yliG 2.47 7.7E-06 4.04 Putative Fe-S oxidoreductases family 1
STM1731   2.43 1.1E-04 1.25 Putative catalase
STM0853 yliH 2.40 1.4E-04 1.02 Putative cytoplasmic protein
STM0838 ybiT 2.39 3.3E-04 0.14 Putative ATPase component of ABC transporter with duplicated ATPase domain
STM0870   2.36 6.4E-06 4.23 Putative transport protein
STM2781 virK 2.36 1.9E-04 0.74 Virulence gene; homologous sequence to virK in Shigella
STM1890 yebA 2.35 2.5E-04 0.45 Putative peptidase
STM0834 ybiP 2.32 5.4E-06 4.41 Putative Integral membrane protein
STM1242 envE 2.30 3.5E-05 2.48 Putative envelope protein
STM1730 yciE 2.21 4.7E-05 2.18 Putative cytoplasmic protein
STM2795 ygaU 2.16 2.7E-04 0.36 Putative LysM domain
STM2780 pipB2 2.14 9.3E-06 3.85 Homologue of pipB, putative pentapeptide repeats (8 copies)
STM0478 aefA 2.14 1.1E-05 3.66 Putative small-conductance mechanosensitive channel
STM4231 lamB 2.09 2.0E-04 0.64 Phage lambda receptor protein; maltose high-affinity receptor
STM1849   2.07 2.2E-04 0.54 Putative inner membrane protein
STM1285 yeaG 2.07 1.9E-04 0.69 putative Ser protein kinase
STM1234 trmU 2.06 2.0E-05 3.08 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase
STM2116 wzc 2.06 3.4E-04 0.12 Putative tyrosine-protein kinase in colanic acid export
STM1827   2.05 1.3E-04 1.14 Putative diguanylate cyclase/phosphodiesterase
STM2924 rpoS 2.05 3.1E-05 2.60 Sigma S (sigma 38) factor of RNA polymerase, major sigmafactor during stationary phase
STM3506 feoB 2.02 6.4E-05 1.84 FeoB family, ferrous iron transport protein B
STM1843   2.02 6.2E-05 1.88 Putative transport protein
STM4240 yjbJ 2.01 1.9E-04 0.69 Putative cytoplasmic protein
STM2925 nlpD 2.01 2.8E-05 2.71 Lipoprotein
Table 3.
List of the highly induced genes in ptsI mutants
Locus tag Gene name Ratio (ptsI/wt) p-value B-value Description
STM2041 pduD 0.06 3.2E-10 13.74 Propanediol utilization: dehydratase, medium subunit
STM2039 pudB 0.07 1.4E-10 14.45 Propanediol utilization: polyhedral bodies
STM2044 pduH 0.08 6.1E-10 13.20 Propanediol utilization: diol dehydratase reactivation
STM2042 pduE 0.09 1.1E-09 12.68 Propanediol utilization: dehydratase, small subunit
STM2040 pduC 0.09 3.4E-07 7.23 Propanediol utilization: dehydratase, large subunit
STM3244 tdcB 0.12 2.6E-07 7.52 Threonine dehydratase, catabolic
STM3241 tdcE 0.13 9.1E-07 6.24 Pyruvate formate-lyase 4/ 2-ketobutyrate formate-lyase
STM2045 pduJ 0.13 2.9E-09 11.84 Propanediol utilization: polyhedral bodies
STM3240 tdcG 0.15 9.0E-08 8.56 L-serine deaminase
STM2046 pduK 0.15 7.5E-08 8.74 Propanediol utilization: polyhedral bodies
STM4540   0.16 3.0E-05 2.63 Putative glucosamine-fructose-6-phosphate aminotransferase
STM2867 hilC 0.17 3.0E-06 5.04 Bacterial regulatory helix-turn-helix proteins, araC family
STM2043 pduG 0.17 2.4E-05 2.85 Propanediol utilization: diol dehydratase reactivation
STM3242 tdcD 0.17 5.8E-05 1.95 Propionate kinase/acetate kinase II, anaerobic
STM3243 tdcC 0.18 9.2E-08 8.54 HAAAP family, L-threonine/ L-serine permease, anaerobically inducible
STM1175 flgC 0.18 6.0E-07 6.65 Flagellar biosynthesis, cell-proximal portion of basal-body rod
STM1962 fliT 0.19 2.6E-07 7.51 Flagellar biosynthesis; possible export chaperone for FliD
STM1955 fliZ 0.19 2.4E-06 5.24 Putative regulator of FliA
STM3339 nanA 0.19 1.8E-06 5.54 N-acetylneuraminate lyase (aldolase)
STM3106 ansB 0.20 2.4E-04 0.45 Periplasmic L-asparaginase II
STM2051 pduP 0.21 1.2E-07 8.24 Propanediol utilization: CoA-dependent propionaldehyde dehydrogenase
STM1961 fliS 0.23 1.1E-05 3.71 Flagellar biosynthesis; repressor of class 3a and 3b operons (RflA activity)
STM1959 fliC 0.23 1.4E-07 8.14 Flagellar biosynthesis; flagellin, filament structural protein
STM2433 crr 0.23 3.3E-07 7.25 PTS family, glucose-specific IIA component
STM4124 oxyS 0.25 1.4E-07 8.13 Stable RNA induced by oxidative stress
STM1916 cheY 0.25 5.4E-07 6.76 Chemotaxis regulator, transmits chemoreceptor signals to flagelllar motor components
STM2055 pduU 0.34 4.4E-05 2.24 Propanediol utilization: polyhedral bodies
STM2049 pduN 0.35 4.3E-07 7.01 Propanediol utilization: polyhedral bodies
STM1973 fliJ 0.36 5.6E-05 1.99 Flagellar fliJ protein
STM4315 rtsA 0.37 7.4E-06 4.09 Putative AraC-type DNA-binding domain-containing protein
STM2900 invH 0.39 1.1E-06 6.06 Invasion protein
STM1183 flgK 0.39 2.1E-06 5.39 Flagellar biosynthesis, hook-filament junction protein 1
STM4539   0.39 3.0E-05 2.63 Putative glucosamine-fructose-6-phosphate aminotransferase
STM4458 yjgF 0.39 5.5E-06 4.39 Putative translation initiation inhibitor
STM0701 speF 0.40 3.3E-06 4.91 Ornithine decarboxylase isozyme, inducible
STM4538   0.40 1.8E-05 3.14 Putative PTS permease
STM1300   0.40 2.8E-06 5.09 Putative periplasmic protein
STM2063 phsC 0.40 4.2E-06 4.68 Hydrogen sulfide production: membrane anchoring protein
STM4106 katG 0.40 2.0E-05 3.08 Catalase; hydroperoxidase HPI(I)
STM2649 trxC 0.40 1.7E-05 3.21 Thioredoxin 2, redox factor
STM1971 fliH 0.41 2.5E-05 2.83 Flagellar biosynthesis; possible export of flagellar proteins
STM2865 avrA 0.41 1.2E-05 3.60 Putative inner membrane protein
STM3054 gcvH 0.42 9.6E-05 1.43 Glycine cleavage complex protein H, carrier of aminomethyl moiety via covalently bound lipoyl cofactor
STM4170 hupA 0.42 2.0E-04 0.66 DNA-binding protein HU-alpha (HU-2)
STM2893 invI 0.42 4.2E-05 2.30 Surface presentation of antigens; secretory proteins
STM1917 cheB 0.42 5.0E-06 4.50 Methyl esterase, response regulator for chemotaxis (cheA sensor)
STM1172 flgM 0.42 7.6E-06 4.06 Anti-FliA (anti-sigma) factor; also known as RflB protein
STM3156   0.43 6.9E-05 1.77 Putative cytoplasmic protein
STM0451 hupB 0.43 3.7E-05 2.41 DNA-binding protein HU-beta, NS1 (HU-1)
STM1301   0.43 1.8E-04 0.76 Putative mutator MutT protein
STM1976 fliM 0.43 9.0E-05 1.49 Flagellar biosynthesis, component of motor switch and energizing
STM4314 rtsB 0.44 1.4E-04 1.02 Putative bacterial regulatory proteins, luxR family
STM1838 yobF 0.44 4.9E-05 2.13 Putative cytoplasmic protein
STM4285 fdhF 0.44 7.6E-06 4.07 Formate dehydrogenase
STM2064 phsB 0.44 2.4E-05 2.89 Hydrogen sulfide production: ironsulfur subunit; electron transfer
STM2056 pduV 0.34 1.5E-06 5.73 Propanediol utilization
STM2055 pduU 0.34 4.4E-05 2.24 Propanediol utilization: polyhedral bodies
STM2049 pduN 0.35 4.3E-07 7.01 Propanediol utilization: polyhedral bodies
STM1973 fliJ 0.36 5.6E-05 1.99 Flagellar fliJ protein
STM4315 rtsA 0.37 7.4E-06 4.09 Putative AraC-type DNA-binding domain-containing protein
STM2900 invH 0.39 1.1E-06 6.06 Invasion protein
STM1183 flgK 0.39 2.1E-06 5.39 Flagellar biosynthesis, hook-filament junction protein 1
STM4539   0.39 3.0E-05 2.63 Putative glucosamine-fructose-6-phosphate aminotransferase
STM4458 yjgF 0.39 5.5E-06 4.39 Putative translation initiation inhibitor
STM0701 speF 0.40 3.3E-06 4.91 Ornithine decarboxylase isozyme, inducible
STM4538   0.40 1.8E-05 3.14 Putative PTS permease
STM1300   0.40 2.8E-06 5.09 Putative periplasmic protein
STM2063 phsC 0.40 4.2E-06 4.68 Hydrogen sulfide production: membrane anchoring protein
STM4106 katG 0.40 2.0E-05 3.08 Catalase; hydroperoxidase HPI (I)
STM2649 trxC 0.40 1.7E-05 3.21 Thioredoxin 2, redox factor
STM1971 fliH 0.41 2.5E-05 2.83 Flagellar biosynthesis; possible export of flagellar proteins
STM2865 avrA 0.41 1.2E-05 3.60 Putative inner membrane protein
STM3054 gcvH 0.42 9.6E-05 1.43 Glycine cleavage complex protein H, carrier of aminomethyl moiety via covalently bound lipoyl cofactor
STM4170 hupA 0.42 2.0E-04 0.66 DNA-binding protein HU-alpha (HU-2)
STM2893 invI 0.42 4.2E-05 2.30 Surface presentation of antigens; secretory proteins
STM1917 cheB 0.42 5.0E-06 4.50 Methyl esterase, response regulator for chemotaxis (cheA sensor)
STM1172 flgM 0.42 7.6E-06 4.06 Anti-FliA (anti-sigma) factor; also known as RflB protein
STM3156   0.43 6.9E-05 1.77 Putative cytoplasmic protein
STM0451 hupB 0.43 3.7E-05 2.41 DNA-binding protein HU-beta, NS1 (HU-1)
STM1301   0.43 1.8E-04 0.76 Putative mutator MutT protein
STM1976 fliM 0.43 9.0E-05 1.49 Flagellar biosynthesis, component of motor switch and energizing
STM4314 rtsB 0.44 1.4E-04 1.02 Putative bacterial regulatory proteins, luxR family
STM1838 yobF 0.44 4.9E-05 2.13 Putative cytoplasmic protein
STM4285 fdhF 0.44 7.6E-06 4.07 Formate dehydrogenase
STM2064 phsB 0.44 2.4E-05 2.89 Hydrogen sulfide production: ironsulfur subunit; electron transfer
STM1969 fliF 0.45 1.1E-04 1.26 Flagellar biosynthesis; basal-body MS (membrane and supramembrane)-ring and collar protein
STM2877 iagB 0.45 4.1E-05 2.30 Cell invasion protein
STM1130   0.45 1.8E-04 0.78 Putative inner membrane protein
STM0871 ybjM 0.45 1.8E-05 3.15 Putative inner membrane protein
STM1924 flhC 0.46 2.0E-05 3.08 Regulator of flagellar biosynthesis, acts on class 2 operons
STM4340 frdD 0.46 2.5E-04 0.43 Fumarate reductase, anaerobic, membrane anchor polypeptide
STM4535   0.46 1.8E-04 0.79 Putative PTS permease
STM1171 flgN 0.47 2.5E-05 2.82 Flagellar biosynthesis: belived to be export chaperone for FlgK and FlgL
STM2876 hilA 0.47 2.6E-05 2.79 Invasion genes transcription activator
STM2153 yehE 0.48 1.3E-05 3.53 Putative outer membrane protein
STM0327   0.48 3.2E-05 2.56 Putative cytoplasmic protein
STM2868   0.48 1.4E-05 3.43 Putative cytoplasmic protein
STM1925 flhD 0.49 4.6E-05 2.18 Regulator of flagellar biosynthesis, acts on class 2 operons
STM3611 yhjH 0.49 2.7E-05 2.73 Putative Diguanylate cyclase/phosphodiesterase domain 3
STM1977 fliN 0.49 7.9E-05 1.62 Flagellar biosynthesis, component of motor switch and energizing
STM1182 flgJ 0.49 4.3E-05 2.25 Flagellar biosynthesis
STM2238   0.49 1.6E-04 0.86 Putative phage protein
STM2413 yfeC 0.49 3.5E-05 2.48 Putative negative regulator
STM3850 yieF 0.49 2.9E-04 0.26 Putative oxidoreductase
STM1918 cheR 0.49 1.8E-05 3.16 Glutamate methyltransferase, response regulator for chemotaxis
STM2414 yfeD 0.49 1.1E-04 1.31 Putative negative regulator
Table 4.
List of the highly induced genes in ptsI mutants
Locus tag Gene Description Expression ratio
STM2342 ulaA Ascorbate-specific PTS system EIIC 53.09
STM2341   Putative transketolase 46.19
STM2340   Putative transketolase 33.89
STM2344 ulaC Putative PTS system EIIA component 26.92
STM3685 mtlA Mannitol-specific EIIABC components 26.79
STM2343 ulaB PTS system EIIB component 21.69
STM3686 mtlD Mannitol-1-phosphate dehydrogenase 15.80
STM2339 yfcC Putative integral membrane protein 12.87
STM3687 mtlR Repressor for mtl 7.76
STM2458 eutB Ethanolamine ammonia-lyase, heavy chain 6.00
STM2462 eutJ Paral putative heatshock protein (Hsp70) 5.38
STM1203 ptsG Glucose-specific EIIBC component 5.03
STM2456 eutL Ethanolamine utilization 4.55
STM2459 eutA Chaperonin in ethanolamine utilization 4.24
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