Article Figures & Data
Figures
- Fig. 1.
Expression of growth-phase-regulated genes during growth in the cecum. Relative expression of the genes described in Table 1 is shown. A white bar indicates expression in C. albicans cells grown in YPD for 5 h (exponential phase) relative to expression in cells grown in YPD for 3 days (post-exponential phase). A black bar indicates expression in C. albicans cells recovered from the cecum relative to expression in cells grown in YPD for 3 days. Genes 1 to 27 are expressed more highly in exponential phase than in post-exponential phase (white bar > 1.5). Genes 28 to 42 are expressed more highly in post-exponential phase (white bar < 0.67).
- Fig. 2.
Genes upregulated during growth in the cecum and in laboratory conditions. (A) Expected number of genes that would be upregulated during both growth in the cecum and growth in another condition, based on chance (gray bar). The value was calculated from the frequencies of upregulated genes that were observed in each data set. The black bar shows the number of genes that were observed to be upregulated in both conditions. E, expected; O, observed. **, P < 10−30; *, P < 10−10. (B) Percentage of genes in different classes. The white bar with thick lines indicates the percentage of hyphal genes (upregulated during hyphal growth in either the study of Kadosh and Johnson [25] or the study of Goyard et al. [19]). Genes that were not hyphal genes and were upregulated in at least one stress condition (oxidative stress [any of three time points] [15], osmotic shock [three time points] [15], temperature shift [three time points] [15], 3-AT [62], or starvation [carbon or nitrogen] [33]) were defined as stress genes (gray section). The percentage of genes that were neither hyphal nor stress genes and were upregulated in one of the other conditions is shown in the white section. The percentage of genes that were upregulated only in the indicated condition is shown in the black section.
- Fig. 3.
Gene expression in C. albicans cells lacking Cph2p or Tec1p. RNA was prepared from C. albicans cells grown in the murine cecum. Expression of the genes indicated at top of graph was measured by quantitative real time RT-PCR and normalized using the expression of ACT1. Expression is shown relative to expression in WT laboratory-grown exponential-phase cells. Each symbol represents the average of triplicate measurements from a different RNA sample. Strains were as follows: black circles, WT; open circles, cph2-null mutant; gray circles, cph2/CPH2+ reconstituted mutant; black squares, tec1-null mutant. Black bar indicates mean.
- Fig. 4.
Lack of Cph2p alters murine intestinal colonization. WT (DAY185 or SN100), cph2 deletion mutant, cph2UAU mutant, CPH2 reconstituted null mutant, or tec1UAU mutant were orally inoculated by gavage into Swiss Webster mice. At various days postinoculation, the amounts of C. albicans in fecal pellets were measured. The amounts of C. albicans in organs of the intestinal tract were measured after sacrifice. (A) CFU per gram of fecal pellet. Mice were sampled repeatedly, and each symbol represents a sample from a different mouse. Black triangles, WT C. albicans; black diamonds, cph2 mutant strain; gray diamonds, CPH2 reconstituted strain; bars, geometric means. (B) CFU per gram of organ or organ contents from mice sacrificed on day 21 postinoculation. Each symbol represents a sample from a different mouse. For the stomach and cecum, the colonization in the contents is shown. For the ileum, the contents plus wall were homogenized. Organs are indicated at the top of the graph. Black triangles, WT C. albicans; black diamonds, cph2 mutant strain; open diamonds indicate CFU/g below the limit of detection; gray diamonds, CPH2 reconstituted strain; bars, geometric means. (C) CFU per gram of fecal pellet. Mice were sampled repeatedly, and each symbol represents a sample from a different mouse. Black triangles, WT C. albicans; black diamonds, tec1UAU mutant strain; bars, geometric means.
Tables
- Table 1.
Distinct physiological state of C. albicans cells recovered from the murine cecume
a Gene numbering corresponds to the genes whose expression is shown in Fig. 1.
b Expo indicates fold up- or downregulation in exponential-phase cells compared to that in post-exponential-phase cells.
c Cecum indicates fold up- or downregulation in C. albicans cells from the cecum compared to that in post-exponential-phase cells.
d Cecum/expo indicates the ratio of up- or downregulation in the cecum to that in exponential-phase cells.
↵e P values were determined by using the Student t test. Black-shaded values, >1.5; gray-shaded values, <0.67.
- Table 2.
Comparison of C. albicans gene expression during growth in the cecum and growth under laboratory conditions
Gene type and condition No. of genes No. of genes P c No. of filtered upregulated genesd Filtered overlap (no. of genes)f Filtered P valued Overlap expecteda Overlap observedb Expected Observed Upregulated genes Cecum 408 358 Alkaline pHe 247 16 49 4 × 10−16 204 12 35 2 × 10−10 Hypoxiaf 46 3 17 3 × 10−15 36 2 10 6 × 10−7 Galactoseg 82 5 30 8 × 10−27 71 4 25 7 × 10−24 Biofilmh 479 31 104 1 × 10−42 444 26 91 1 × 10−39 37°C, 10 mini 81 4 26 7 × 10−19 71 4 24 1 × 10−21 Osmotic shock, 10 mini 106 7 28 4 × 10−15 94 6 23 6 × 10−13 3-ATj 336 22 76 9 × 10−33 303 18 60 7 × 10−24 C starvationk 102 7 25 5 × 10−12 95 6 21 7 × 10−10 Downregulated genes Cecum 467 Alkaline pHe 221 16 12 NS Hypoxiaf 20 1 2 NS Biofilmh 457 34 107 9 × 10−40 37°C, 10 mini 154 11 8 NS Osmotic shock, 10 mini 105 8 8 NS Oxidative stress, 60 mini 39 3 9 3 × 10−3 C starvationk 31 2 8 2 × 10−3 3-ATj 313 23 143 6 × 10−153 ↵a Calculated as: (total genes) × (frequency upregulated in cecum) × (frequency upregulated under the indicated condition).
↵b That is, cecum upregulated genes that were also upregulated under the indicated condition.
↵c That is, the P value determined by the chi-square test. NS, not significant.
↵d Filtering to remove genes that were upregulated in hyphal cells was performed using the data of Goyard et al. (19) or Kadosh et al. (25).
↵e According to Bensen et al. (6).
↵f According to Setiadi et al. (50).
↵g According to Martchenko et al. (36).
↵h According to Nett et al. (40).
↵i According to Enjalbert et al. (15).
↵j According to Tournu et al. (62).
↵k According to Lorenz et al. (33).
- Table 3.
Comparison of C. albicans gene expression during commensal colonization of the cecum and during candidiasis
Gene type and condition No. of genes No. of genes P c No. of filtered upregulated genesd Filtered overlap (no. of genes)d Filtered P valued Overlap expecteda Overlap observedb Expected Observed Upregulated genes Cecum 408 358 Kidneye 35 2 26 1 × 10−56 31 2 20 3 × 10−42 Liver, 5 hf 167 11 24 6 × 10−4 145 9 15 NS Thrushg 49 3 15 4 × 10−10 37 2 8 1 × 10−3 Downregulated genes Cecum 467 Kidneye 37 3 9 1 × 10−3 Liver, 5 hf 92 8 20 2 × 10−4 Thrushg none ↵a Calculated as: (total genes) × (frequency upregulated in cecum) × (frequency upregulated under the indicated condition).
↵b That is, cecum upregulated genes that were also upregulated under the indicated condition.
↵c That is, the P value determined by the chi-square test.
↵d Filtering to remove genes that were upregulated in hyphal cells was performed using the data of Goyard et al. (19) or Kadosh et al. (25). NS, not significant.
↵e According to Walker et al. (65).
↵f According to Thewes et al. (60).
↵g According to Zakikhany et al. (67).
- Table 4.
C. albicans genes upregulated during colonization of the cecum and invasion of host tissue
Function or location Genesa Adhesion ALS10 , ALS1, SUN41, ECE1 Response to chemical stimuli PHR1 , TOS1, GAL10, SOD5 Transporter HGT1 , ENA2, COR1, PHO84, PHO89, FRP2, FRP3, CDR1, CAN2,DIP5, ORF19.1172, ORF19.2292 Cell surface IHD1 , PLB4, PGA7, PGA54 Metabolic activity ADH5, MLS1, ENO1, PCK1, IDP2, CTN3, FAA4 Miscellaneous GAC1, PPQ1, AFG3, MRK1 (RIM11), POL93, ADR1, PRB2, VPS21 Unknown ORF19.2659, ORF19.3902, ORF19.5848, ORF19.2515, ORF19.6688, ORF19.6169, ORF19.3713 ↵a Underlined genes are upregulated in laboratory-grown hyphae (19, 25) and as presented in the Candida Genome Database (www.candidagenome.org ).
Supplemental material
Files in this Data Supplement:
- Supplemental file 1
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List of genes up- or downregulated in C. albicans cells from the cecum versus C. albicans cells in post-exponential phase.
Zipped MS Excel document, 50K. - Supplemental file 2
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List of genes up- or downregulated in exponential-phase C. albicans cells versus C. albicans cells in post-exponential phase.
Zipped MS Excel document, 107K. - Supplemental file 3
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List of genes upregulated in C. albicans cells from the cecum versus C. albicans cells in exponential phase.
Zipped MS Excel document, 47K. - Supplemental file 4
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List of genes downregulated in C. albicans cells from the cecum versus C. albicans cells in exponential phase.
Zipped MS Excel document, 51K. - Supplemental file 5
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List of genes upregulated in C. albicans cells from the cecum and under other conditions.
Zipped MS Excel document, 21K. - Supplemental file 6
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List of genes downregulated in C. albicans cells from the cecum and under other conditions.
Zipped MS Excel document, 21K. - Supplemental file 7
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List of C. albicans strains used.
Zipped MS Word document,12K. - Supplemental file 8
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List of primers used.
MS Word document, 40K.
- Supplemental file 1
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List of genes up- or downregulated in C. albicans cells from the cecum versus C. albicans cells in post-exponential phase.
