1. Microbiology and Infectious Disease

A chemically induced attenuated strain of Candida albicans generates robust protective immune responses and prevents systemic candidiasis development

  1. Swagata Bose
  2. Satya Ranjan Sahu
  3. Abinash Dutta
  4. Narottam Acharya  Is a corresponding author
  1. Department of Infectious Disease Biology, Institute of Life Sciences, India
https://doi.org/10.7554/eLife.93760.3
Share this article
Cite this article
  1. Swagata Bose
  2. Satya Ranjan Sahu
  3. Abinash Dutta
  4. Narottam Acharya
(2024)
A chemically induced attenuated strain of Candida albicans generates robust protective immune responses and prevents systemic candidiasis development
eLife 13:RP93760.
https://doi.org/10.7554/eLife.93760.3
  2. Download BibTeX
  3. Download .RIS
9 figures, 3 tables and 7 additional files

Figures

Figure 1 with 3 supplements
Download asset Open asset
Effect of metal chelators on the growth and biofilm of C. albicans.

(A) C. albicans cells were cultured in YPD media at 30 °C for 24 hr without (cyan blue) and with the indicated concentration of EDTA (purple), MgSO4 (Green), ZnCl2 (Grey), FeCl2 (Brown), and MnCl2 (Black), EDTA+MgSO4 (Lime green), EDTA+MgSO4@6 hr (dark blue), EDTA+ZnCl2 (Maroon), EDTA+FeCl2 (Orange), and EDTA+MnCl2 (Pink). Optimal absorbance was measured at 600 nm in different intervals of incubation. (B) The cultures from the above-mentioned experiment was diluted and plated on YPD plate. Colonies were counted and plotted to determine the CFU efficiency. (C) Pre-formed C. albicans biofilm was treated with EDTA and divalent metals as mentioned. Their effect on biofilm was observed post-24 hr treatment by crystal violet staining and estimating at 570 nm. (D) Effect of EDTA and divalent metals on C. albicans biofilm was again observed by acridine orange staining and visualization under a ×40 magnification using a CLSM. Similarly, the effect of other metal chelators like DTPA (Lime green), Aprotinin (blue), TPEN (orange) and CE (grey) on the growth (E), CFU (F), and biofilm formation of C. albicans analyzed by crystal violet staining (G) and CLSM (H). Mean values from three independent experiments considered and error bar represents SEM. p values *<0.05, **<0.01 and ****<0.0001 were significant as determine by one-way ANOVA.

Figure 1—source data 1

Effect of metal chelators on the growth, CFU, and biofilm of C. albicans.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig1-data1-v1.zip
Figure 1—figure supplement 1
Download asset Open asset
Identification of a fungistatic concentration of EDTA.

(A) Various concentrations of EDTA ranging from 0.9 µM to 500 µM was added to the C. albicans culture with a total volume of 150 µL in a 96-well plate and allowed to grow overnight at 30 °C under static condition. YPD media alone and without EDTA treatment culture as controls were also taken. After 24 hr, the image of the 96-well polystyrene plate was taken. (B) After 24 hr, the absorbance was measured at OD600 nm using a Perkin-Elmer plate reader and plotted using GraphPad Prism software version 8.0. p value as indicated ****<0.0001 was determined by one-way ANOVA. (C) C. albicans cells treated without and with 62.5 µM, 125 µM, and 250 µM concentration of EDTA for 24 hr and indicated dilutions were spotted on YPD-agar plate. The plate was incubated at 30 °C for 24 hr and imaged using a Chemidoc imaging system.

Figure 1—figure supplement 2
Download asset Open asset
Effect of 250 μM EDTA on cell viability.

C. albicans pre-culture was diluted to an OD600nm=0.5 and allowed to grow in the absence and presence of 250 μM EDTA at 30 °C and 200 rpm up to 12 hr. (A) At mentioned time points (0–12 hr), cells were harvested, stained with SYTOX Green and analyzed by flow cytometry (blue laser; excitation at 488 nm). The data acquisition was performed using the BD LSR Fortessa Flow cytometer and analysis was carried out by FlowJo version 8.1 software. Analysed data exported in JPEG format. Acquisition profile of unstained cells was also shown. (B) The percentage of dead cells population from two technical replicates was plotted using GraphPad Prism software version 8.0. No statistical significance difference was found between treated and untreated data. (C) Similarly, the harvested cells were stained with PI and images were captured using a fluorescence microscope (EVOS imaging system; Thermo Fisher Scientific) at ×40 magnification and the red dots indicated the dead cells. (D) The population of dead cells was determined from 15 microscopy frames for each time interval and plotted using GraphPad Prism. p value that was non-significant as determined by two-way ANOVA.

Figure 1—figure supplement 3
Download asset Open asset
Effect of EDTA on C.albicans morphology.

C. albicans pre-culture was diluted to an OD600nm=0.5 and allowed to grow in the absence and presence of 250 μM EDTA at 30 °C and 200 rpm up to 12 hr. Similar experiment was also carried with 10% serum and morphological transition was induced at 37 °C. (A) At various time intervals, cell morphology was observed using a ×40 Leica DM500 microscope (scale bar of 2 µm). (B) The percentages of singlet, doublet, pseudohyphae, and hyphae cells were quantified without (i) and with serum (ii). (C) The length of serum-induced germ tubes (n=60) in µm was measured using ImageJ software. p value as indicated **<0.01 or non-significance as determined by two-way ANOVA.

Figure 2 with 1 supplement
Download asset Open asset
Transcriptomics analyses C.albicans cells upon EDTA treatment.

(A) A Volcano plot depicting differentially expressed genes (DEGs) in CAET cells. The red dots indicate upregulated genes (411) and blue dots indicates the downregulated genes (388). (B) Heat map showing relative abundance of top 25 significantly upregulated and downregulated genes in Ca and CAET. RNA sequencing was carried out in triplicates. Red colour indicates upregulation and blue indicates downregulation as denoted by the Z score. (C) Double donut chart indicates top 100 significantly upregulated genes categorized into four main groups that is, metal transporters (light green), cell wall- and membrane-associated genes other than metal transporters (blue), others (includes drugs resistance-associated, morphology-associated, biosynthetic and catalytic processes; represented in grey), and uncharacterized genes (cream). Inner donut depicts the number of DEGs from the above categories associated with virulence and pathogenesis in C. albicans as reported by published literatures. (D) Double donut chart depicting top 100 significant downregulated gene categorized as metabolic pathways (green), cell-wall associated (blue), ribosomal (grey), others (includes morphology-associated, resistance-associated; represented in yellow), and uncharacterized (cream). Outer circle represents the total number of genes in each category and inner circle indicates the virulence-related genes out of the total number of genes in that specific category. (E) Gene ontology enrichment analysis for 411 upregulated DEGs. (F) Gene ontology enrichment analysis for 388 downregulated DEGs were plotted. Both in (E) and (F), x-axis represents the number of DEGs and y-axis represents various processes like BP (biological processes), MF (molecular functions), and CC (cellular components) indicated in maroon, blue, and grey colors, respectively. (G) STRING analyses showing relationship between DEGs. Interaction amongst 15 connected out of 31 upregulated DEGs involved in metal transport and homeostasis is shown. (H) STRING analysis shows 9 connected out of 33 upregulated DEGs involved in pathogenesis. (I) Among the down-regulated DEGs, 70 connected out of 74 DEGs belonging to cytosolic ribosomal genes as determined by STRING. (J) 38 connected out of 56 DEGs belonging to mitochondrial ribosomal components were connected by as determined STRING.

Figure 2—source data 1

Transcriptomic analyses of CAET.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig2-data1-v1.zip
Figure 2—figure supplement 1
Download asset Open asset
Transcriptomic analyses of CAET and validation.

(A) Principal Component Analyses (PCA) was performed for proper grouping of three biological replicates represented as MT523, MT524, and MT525 as one cluster for Ca and MT526, MT527, and MT528 for CAET for another. The plot scores indicate the principal component 1 vs. principal component 2 signifying the largest variable vs. second largest variable. (B) Gene expression was performed using qRT-PCR and semi-quantitative assay for selected upregulated genes obtained from the heat map that is, (i) metal ion associated gene ZRT1, (ii) cell wall associated gene CHT4 (chitin-specific gene), and (iii) host-pathogen interaction-related gene PGA13. Similarly, the downregulated genes selected are (iv) aconitase ACO2, (v) virulence-associated gene PLB1, and (vi) thiamine synthesis-associated gene THI13 expression were analysed. GAPDH considered as control. p values *<0.05 and ****<0.0001 were as determined by unpaired t test. (C) STRING analysis showing only the clusters related to 40 S (i), 60 S subunits (ii) and one-carbon metabolism (iii). An interaction score of 0.7 was considered for all the networks. (D) Gating strategy of unstained RAW cells alone was shown.

Figure 3
Download asset Open asset
ffect of EDTA on the cell wall and polysome of C. albicans.

(A) Showing TEM images of ultrathin sections of untreated (Ca) and EDTA-treated (CAET) C. albicans at different resolution. Samples visualized at ×14,000 magnification, arrow indicates the marked cell, and box indicates the focus area where thickness was measured. Scale bar = 2 µm for intact cells (i); scale bar = 1 µm for a single cell (ii); scale bar = 500 nm for zoomed in image of an individual cell wall (iii). (B) C. albicans cells were stained with Con A and analyzed by flow cytometry (i) and mean fluorescence intensity was measured to estimate the mannan level (ii). (C) C. albicans cells were stained with aniline blue and analyzed by flow cytometry (i) and mean fluorescence intensity was measured to estimate the β-glucan level (ii). (D) C. albicans cells were stained with calcofluor white and analyzed by flow cytometry (i) and mean fluorescence intensity was measured to estimate the chitin level (ii). Mean average of three independent biological replicates with error bars is shown. p values *<0.05 and ***<0.001 as determined by unpaired t-test. (E) Cell-free total ribosomes were isolated by taking two different concentrations (pellet size of 200 µL and 400 µL) of C. albicans cells (Ca and CAET) and fractionated using sucrose gradient centrifugation. Fractions were analysed and plotted. The position and transition of ribosome subunits, monosome and polysome peaks were as shown.

Figure 3—source data 1

Ultrastructure of C. albicans cells upon EDTA treatment and estimation of cell wall thickness, various components of cell wall, and ribosome levels.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig3-data1-v1.zip
Figure 4
Download asset Open asset
C.albicans-Macrophage interaction.

(A) Deep red-stained RAW 264.7 murine macrophage cells were co-cultured with C. albicans (Ca and CAET) in 1:1 ratio. After each time point (1 hr, 2 hrs and 3 hrs) cells were pooled down and double positive cells (CFSE-FITC channel and deep red-APC channel; Q2, P3) were analysed by flow cytometry (i). Mean florescence intensity of three independent biological replicates were plotted using the GraphPad Prism software (ii). (B) From a similar co-culture experiment, C. albicans cells (Ca and CAET) were retrieved from macrophage cells and plated on YPD/Chloramphenicol plate by taking appropriate dilutions. The plates were incubated at 30 °C for 48 hr. The plates were imaged (i) and colony-forming unit (CFU) was determined (ii). (C) A similar co-culture of macrophage and C. albicans (Ca and CAET) were carried out for 2.5 hr and the dying macrophages were observed by propidium iodide staining (Red dots). Images were captured with fluorescence microscope (EVOS imaging system; Thermo Fisher Scientific) at ×20 and ×40 magnifications (i) and the population of dead macrophages were determined (ii). p values *<0.05, **<0.01, and ***<0.01 as determined by two-way ANOVA.

Figure 4—source data 1

Estimation of phagocytosis, fungal cells clearance and macrophage killing.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig4-data1-v1.zip
Figure 5 with 2 supplements
Download asset Open asset
Systemic candidiasis development and progression in C. albicans challenged mice.

(A) Mice (n=6/category) were injected intravenously with 5x105 C. albicans cells (Ca: cyan blue and CAET: purple) and saline as control (grey) and their survivability was monitored for 30 days. In a similar set of experiment, mice (n=6/category) were first immunized with CAET (represented in brown) or sham vaccinated with saline (represented in orange), and after 30 days, they were further re-challenged with C. albicans. Their survivability was monitored for another 30 days and a survival curve was plotted. The number of sacrificed mice were mentioned on the particular days in the survival plot. 1° and 2° suggest primary and secondary challenges, respectively. Statistical significance of the survival curve was determined using Mantel-Cox test. p values were as mentioned, otherwise they were non-significant. Y-axis was represented in Log rank scale. (B) Fungal load in the kidney, liver, and spleen of sacrificed mice in Log10 scale was determined by CFU analyses. No statistical significant difference was observed between these groups. (C) PAS-staining for one of the kidneys carried out to visualize the fungal burden in the cortex and medulla regions under ×40 magnification. (D) To check the disease progression, a kinetic experiment was planned as indicated in the schematic diagram. A group of mice were injected intravenously with 5x105 C. albicans cells (Ca: cyan blue, CAET: purple, and 1° CAET 2°Ca: brown) and saline controls (grey and green) at 0 day, and five mice from each group were sacrificed on each day mentioned (3d, 7th, 10th, 20thh, and 30th day). Approximately 20 µl blood was drawn from the lateral tail vein of the mice prior to sacrifice. (E) Fungal load in the brain, liver, kidney, and spleen in Log scale was determined by CFU analyses. (F) Blood parameters such as WBC, Granulocytes, Platelets, and Monocytes levels were analyzed on the above-mentioned days and graphs were plotted using the GraphPad Prism software. The statistical analyses between saline and fungal infected mice groups of same day sacrificed were carried out. p values **<0.01, **<0.01, ***<0.00, and ****<0.0001 as determined by two-way ANOVA.

Figure 5—source data 1

Virulence and vaccine potentials of Ca Vs CAET.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig5-data1-v1.zip
Figure 5—figure supplement 1
Download asset Open asset
Systemic candidiasis development in C.albicans challenged mice.

Mice (n=6/category) were injected intravenously with 5x105 C. albicans cells (untreated Ca: cyan blue and CAET: purple) and saline as control (grey) and their survivability was monitored for 30 days. In a similar set of experiment, mice (n=6/category) were first immunized with CAET (represented in brown) or sham vaccinated with saline (represented in orange), and after 30 days, they were further re-challenged with C. albicans. Their survivability was monitored for another 30 days and a survival curve was plotted. 1° and 2° suggest primary and secondary challenges, respectively. Mice suffered due to severe infections were euthanized and fungal load in vital organs were determined by CFU analyses. Statistical significance of the survival curve was determined using Mantel-Cox test. p values were as mentioned and others were non-significant. Y-axis was represented in Log rank scale. Two repeat studies were shown.

Figure 5—figure supplement 2
Download asset Open asset
Kinetic analyses of fungal cells load and blood profiles of mice challenged with Ca and CAET.

(A) PAS-stained kidney sections of different mice groups (saline, Ca, CAET and 1°CAET 2°Ca) from the experiment in Fig.Figure 5D showing fungal burden at different times of sacrifice post inoculation. (B) Lymphocytes, RBC, MCHC, MCH, and MCV (fl) present in total blood of various mice groups sacrificed on various days from the experiment in Figure 5D was estimated. p values *<0.05, **<0.01, ***<0.001, and ****<0.0001 as determined by two-way ANOVA.

Figure 6
Download asset Open asset
Cytokine and chemokine estimation in infected mice.

The mice (n=3/category) were inoculated with Ca or CAET or saline and sacrificed on various days as indicated and cytokine and chemokine levels in the blood serum were quantified by using Bio-plex Pro cytokine multiplex kit. (A) A panel of Th-1 cytokines, that is IL-1α, IL-1β, IL2, IL-10, IL-12(p40), IL-12(p70), IFN-γ, TNF-α, and GM-CSF, (B) Th-2/Th-17 cytokines, that is IL-3, IL-4, IL-5, IL-6, IL-9, IL-13, and IL-17, and (C) Chemokines that is RANTES, MCP-1, MIP-1α, MIP-1β, KC, and EOTAXIN. The statistical analyses between saline and fungal infected mice groups of same day sacrificed were carried out. p values **<0.01, **<0.01, ***<0.00, and ****<0.0001 as determined by two-way ANOVA.

Figure 6—source data 1

Cytokines and chemokines estimation in fungal infected mice.

https://cdn.elifesciences.org/articles/93760/elife-93760-fig6-data1-v1.zip
Figure 7
Download asset Open asset
Model depicting the attributes of CAET cells.

EDTA alters the cell wall thickness by altering its composition. Metal transporters and several cell wall and membrane associated genes get upregulated. To mitigate the essential metal scarcity, genes involved in ribosome biogenesis and one-carbon metabolism were down-regulated. CAET cells get phagocytosed efficiently and eliminated faster by macrophages. CAET-infected mice survived and induced robust host immune responses to protect the lethal rechallenge. Thus, CAET is a potential live whole-cell vaccine candidate.

Author response image 1
Download asset Open asset
Author response image 2
Download asset Open asset

Tables

Table 1
A brief summary of RNA sequencing reads obtained from Illumina Novaseq.
Sample Name (Sequencing ID)Read Length (bp)Total raw readsReads after rRNA removalAverage Length after trimRead after trimming% known mRNA% Unknown mRNA
Wild type (MT523)151×221,937,41619,222,356 (87.62%)143.2219,221,72898.061.94
Wild type (MT524)151×220,794,99218,475,070 (88.84%)141.7118,474,42898.361.68
Wild type (MT525)151×220,564,21817,699,794 (86.07%)140.8917,699,18098.31.7
CAET (MT526)151×222,376,46620,284,442 (90.65%)140.7920,283,77698.151.85
CAET (MT527)151×221,412,80420.073,926 (97.49%)142.1420,073,23098.721.28
CAET (MT528)151×220,435,93819,391,726 (94.89%)142.2519,391,14298.851.5
Table 2
List of top 100 upregulated genes in EDTA treated C. albicans cell (CAET).
Metal Transporters
No. of DEGsName of DEGs (13)Fold ChangeFDR p-valueFunction
1ZRT15644.99425.20999E-82Zinc ion transporter; Hyphal inducer
2PRA11829.34671.3833E-282Zinc sequester; pH regulated antigen
3CFL5151.12914.16014E-13Ferric reductase
4CFL294.24811.5889E-282Ferric reductase; Virulence
5PHO8790.30671.0754E-176Phosphate transporter; Virulence
6ZRT268.17202.5856E-297Zinc uptake; Biofilm inducer
7CSA226.66470.000886698Hyphal inducer; Heme utilization protein; Biofilm inducer
8CSR123.22542.0725E-222zinc homeostasis, Filamentation inducer;
9CSA122.50383.4486E-166Hyphal inducer; Iron homeostasis; Biofilm inducer;
10HAP318.45115.412E-13Iron homeostasis;
11CFL48.46633.22997E-11Uptake of iron metal ion
12FRE97.50521.41623E-45Ion transport, Ferric reductase
13ARH25.75891.18159E-60Involved in heme biosynthesis
Cell-wall and -membrane associated
Name of the DEGs (15)Fold ChangeFDR p-valueFunction
1SCW428.99470.000794714Glucanase activity
2PGA1326.33478.3797E-163Cell wall integrity; Morphogenesis, Virulence
3PGA3122.09691.25365E-18Cell wall integrity
4CHT420.71214.5927E-126Chitin synthesis and degradation
5RIM912.41584.4708E-121Promote growth under alkaline condition
6ALS410.02181.4683E-110Enhance cell surface adhesion
7CSH19.53871.2788E-107Maintain cell integrity; Virulence
8MRV88.75260.007934383Biofilm inducer; Caspofungin tolerance
9HGT57.54332.42539E-86Glucose transporter
10CDA27.26641.39323E-07Chitin deacetylase
11PRN46.20375.00644E-35Protein with similarity to pirins
12GLX35.98903.73497E-61Binds human IgE; Induce biofilm
13PGA75.62472.14119E-46GPI-linked hyphal surface antigen; Induce spider biofilm
14RBT55.54147.36268E-45GPI-linked cell wall protein; utilize haemin and haemoglobin; biofilm induced
15JEN15.19304.63735E-06Localized on plasma membrane and induced by lactic acid
Others
Name of the DEGs (15)Fold ChangeFDR p-valueFunction
1LAP320.76486.7063E-221Aminopeptidase; Bleomycin resistance
2IFD618.47362.2359E-181Azole resistance; Biofilm-inducer
3ATO113.31996.23932E-08pH neutralizer in macrophage phagolysosome
4NOP610.52233.90346E-07Ribosome biosynthesis
5RAS210.26678.69395E-36Filamentous growth enhancer; cAMP pathway regulator
6HST68.69606.13855E-09Transport lipid; antifungal drugs resistance; Encode ABC transporters
7STE238.30303.41151E-92Involved in processing of mating pheromones
8FGR467.44821.72544E-07Filamentous Growth Regulator
9POL937.02911.77132E-69Encode reverse transcriptase, protease and integrase; Induce biofilm
10HPD15.99266.53346E-22Involved in degradation of toxic propionyl-CoA; Induce spider biofilm
11AOX25.69367.2209E-114Induce biofilm formation
12SOU25.57460.006421918L-sorbose utilization; biofilm induced
13GPD15.48052.01281E-74Involved in glycerol biosynthesis
14CAG15.30232.20049E-05Role in mating pheromone response
15FDH15.27752.01281E-74xidization of formate to CO2
Uncharacterized
Name (57 DEGs)Fold ChangeFDR p-valueFunction
1CAALFM_C200860CA1600.23014.4708E-121Uncharacterized
2CAALFM_C401340WA583.60990.000537249Uncharacterized
3CAALFM_CR08740WA64.84210.035751787Uncharacterized
4CAALFM_CR02340WA53.56093.38443E-05Uncharacterized
5CAALFM_CR07740WA42.20941.62356E-12Uncharacterized
6CAALFM_C602100WA32.17620.000435707Uncharacterized
7CAALFM_C104010CA21.98804.8225E-124Uncharacterized
8CAALFM_C604230WA19.14981.67518E-34Uncharacterized
9CAALFM_C110050WA18.13200.000124176Uncharacterized
10CAALFM_CR06510WA17.40476.21185E-37Uncharacterized
11CAALFM_CR06500CA13.60552.25687E-88Uncharacterized
12CAALFM_CR08310CA10.65934.21036E-20Uncharacterized
13CAALFM_CR06570CA10.62846.6067E-77Uncharacterized
14CAALFM_C204430WA9.92530.003875235Uncharacterized
15CAALFM_C303570CA9.61115.27224E-07Uncharacterized
16CAALFM_C306040WA9.46631.09545E-56Uncharacterized
17CAALFM_C106860WA9.40730.000100814Uncharacterized
18CAALFM_C602480WA9.38771.58803E-89Uncharacterized
19CAALFM_C302790WA9.12722.43382E-06Uncharacterized
20CAALFM_C503430WA8.69040.000101716Uncharacterized
21CAALFM_C402930WA8.64632.18312E-11Uncharacterized
22CAALFM_C403340CA8.62940.000183681Uncharacterized
23CAALFM_C701010WA8.47913.30179E-61Uncharacterized
24CAALFM_C202580WA8.41630.001492629Uncharacterized
25CAALFM_C405830WA8.35183.67121E-05Uncharacterized
26CAALFM_C304210WA8.10653.03712E-07Uncharacterized
27CAALFM_C406150CA7.97040.014291503Uncharacterized
28CAALFM_C303370CA7.97041.1929E-135Uncharacterized
29CAALFM_C204450WA7.84626.43154E-11Uncharacterized
30CAALFM_C202180WA (ZRT3)7.72723.31888E-71Uncharacterized
31CAALFM_C100270WA7.13984.2578E-73Uncharacterized
32CAALFM_C401860CA7.07431.14226E-09Uncharacterized
32CAALFM_C302360CA6.79695.99145E-37Uncharacterized
34CAALFM_C600980CA6.68967.44423E-52Uncharacterized
35CAALFM_CR06310WA6.65350.00233344Uncharacterized
36CAALFM_C202750CA6.57930.000307212Uncharacterized
37CAALFM_C200760CA6.47691.48506E-85Uncharacterized
38CAALFM_C104690CA6.29001.03644E-05Uncharacterized
39CAALFM_C304350CA6.22891.2123E-25Uncharacterized
40CAALFM_C207620WA6.16616.18529E-06Uncharacterized
41CAALFM_CR01910CA6.01670.000328533Uncharacterized
42CAALFM_C702280WA6.01400.037653707Uncharacterized
43CAALFM_C307070CA5.92262.70125E-54Uncharacterized
44CAALFM_C405900CA5.91681.1249E-116Uncharacterized
45CAALFM_CR07260CA5.87790.013967914Uncharacterized
46CAALFM_C106620CA5.87750.016118237Uncharacterized
47CAALFM_C109300CA5.83202.75478E-11Uncharacterized
48CAALFM_CR09530CA5.78852.74225E-78Uncharacterized
49CAALFM_C209850CA5.77403.08818E-07Uncharacterized
50CAALFM_C601940WA5.59260.006011195Uncharacterized
51CAALFM_C100310WA5.57296.50774E-57Uncharacterized
52CAALFM_C601810WA5.56371.97617E-12Uncharacterized
52CAALFM_C110060CA5.41344.01975E-08Uncharacterized
54CAALFM_CR07300WA5.22727.10193E-05Uncharacterized
55CAALFM_C402330CA5.21376.40082E-05Uncharacterized
56CAALFM_C603240WA5.21059.75776E-08Uncharacterized
57CAALFM_C305840WA (FMO1)5.17770.000145963Uncharacterized
Table 3
List of top 100 downregulated genes in EDTA treated C. albicans cell (CAET).
Metabolic pathways
No. of DEGsName (44 DEGs)Fold ChangeFDR p-valueFunction
1PHO100100.35869581.7869E-210encode an enzyme phosphomonoesterase
2PLB175.165623613.7897E-221Virulence; Phospholipase activity; Lipid metabolism
3THI448.258035242.1564E-130Involved in thiamine biosynthesis
4THI1325.459196578.2924E-175Regulate IL-10 and IL-12 production
5GIT122.71360053.2311E-112functions as proton symporter
6HSP3118.096392.39778E-23Involved in diauxic shift reprogramming
7PHO8417.261037314.3071E-163High-affinity inorganic phosphate/H+symporter
8PUT114.487498017.5039E-99Involved in amino acid metabolism
9INO110.743845311.5532E-128Encodes inositol-1-phosphate synthase
10OPT110.462183781.83956E-90Involved in peptide transportation
11PUT28.1329482151.989E-99Amino acid metabolism regulator
12LYS227.8950867632.77628E-95Homocitrate synthase activity and lysine auxotrophy
13ACO27.3330203322.21018E-91Putative aconitate hydratase 2
14SNZ17.2250247262.98178E-78Involved in pyridoxine (vitamin B6) synthesis
15BTA17.2014438932.2825E-11Encodes the betaine lipid synthase
16LYS46.8460205581.77724E-70Involve amino acid metabolism
17CAN26.0215609733.95846E-54Import arginine
18FCY245.9862769054.80688E-58Recruit vitamin B6 transport
19THI65.8919988713.5842E-104Thiamine biosynthesis
20LEU15.7759570215.4161E-99Catalyzes leucine biosynthesis pathway
21GIS25.7266577852.59522E-83Encodes the homologue of mammalian CNBP
22LYS125.6829282271.2519E-72Involved in dehydrogenation of homoisocitrate
23CHA15.5160834044.36052E-27Involved in nutrient acquisition/metabolism
24FET995.1714734944.85608E-18Involved in p-phenylenediamine oxidase; Iron transporter
25GCV25.1242448728.8508E-108Catabolises glycine; Induction in elevated CO2
26GIT34.7053219821.43209E-52Transport glycerophosphodiester metabolites into cells
27CYC14.5331203197.41108E-12Encode cytochrome c
28HXT54.3704449463.87863E-30Uptake fructose, glucose and mannose
29ILV34.3268557782.72309E-49Amino acid metabolism regulator
30OPT34.0854757491.8761E-38Transport of sulfur-containing compounds
31GAL14.0157489216.75558E-71Executes metabolic functions in carbon source uptake
32GCY13.9860279684.12996E-66Confers hypersensitivity to toxic ergosterol analog
33GAL103.8188937451.55917E-65Induce biofilm; Utilize the source of galactose
34GDH23.7690494018.49692E-47Catalyzes deamination of glutamate to alpha-ketoglutarate
35GCV13.7372544512.09928E-39Catabolises glycine; Induction in elevated CO2
36DFR13.4987166993.23053E-05Catalyses of 7,8-dihydrofolate to 5,4,7,8-tetrahydrofolate
37GDH33.4758525929.07648E-30Encode NADP+-dependent glutamate dehydrogenases
38CTP13.4561859922.97824E-16Involved in transportion of citrate
39TPO43.3510321694.97048E-29Bcr1- associated repression in RPMI a/alpha biofilms
40OPI33.3275638711.89288E-15Biosynthesis of phosphatidylcholine
41EGD23.2903896972.54237E-30GlcNAc-induced protein
42LYS23.2282011443.15144E-40lysine biosynthesis; biofilm induced
43NUP3.1378259017.10193E-05Involved in transportion of purine nucleosides and thymidine
44ARO33.044355091.66463E-45aromatic amino acid synthesis;
Cell-wall associated
Name (7 DEGs)Fold ChangeFDR p-valueFunction
1HGT222.872509321.9154E-170Encode cell- wall associated proteins
2PGA109.8177187992.80343E-96Involved in Iron acquisition
3TRY68.9367090025.07311E-24Transcriptional regulator in biofilm
4HSP306.4010661758.86109E-17Stress-protective function on plasma membrane
5ECM3313.9008220945.76083E-24Involved in cell wall biogenesis
6ACS23.0979218443.19601E-24antigenic during human and murine infection
7STB33.0382702945.50968E-41caspofungin induced
Ribosomal
Name (13 DEGs)Fold ChangeFDR p-valueFunction
1RPS28B5.0905707671.40419E-10Autoregulates the decapping of its own mRNA machinery
2RPS424.3477309891.02472E-32Enhance tolerance to fluconazole
3RDN184.0479754791.9867E-13component of the small (40 S) ribosomal subunit;
4RPS123.9442662661.51774E-29pre-rRNA processing and polysome content
5RPP1B3.6069499122.33237E-25Involved in regulation of translation elongation
6RPS21B3.5884390981.10333E-29Regulated by Nrg1, Tup1
7RPS133.4972332953.88662E-35_
8ASC13.3852911533.46635E-25Required for virulence in mice
9RPL183.2348522751.52941E-28repressed upon phagocytosis by murine macrophage
10RPL9B3.1931591553.27531E-29repressed upon phagocytosis by murine macrophages
11RPL53.1027324012.25382E-30repressed upon phagocytosis by murine macrophages
12RPP2B3.0839566045.93521E-16possibly involved in regulation of translation elongation
13RPS273.030192452.15647E-21repressed upon phagocytosis by murine macrophage
Others
Name (11 DEGs)Fold ChangeFDR p-valueFunction
1PGA455.5909172566.40747E-43Putative GPI-anchored protein of unknown function
2RBT74.2269494651.5772E-09Encode secreted RNase T2
3PEX43.9725087181.24715E-12Spider biofilm induction
4RME13.6976816057.1604E-68Development of fluconazole resistance
5THI203.2714943975.58989E-53Spider biofilm induced
6ASM33.2359033281.59858E-31Possible Kex2 substrate
7BFR13.2260663371.87417E-16Protein involved in the maintenance of normal ploidy
8TUF13.2242542827.29461E-36Encodes GTPase mitochondrial elongation factor Tu
9GAL73.2074674227.9819E-49downregulated by hypoxia
10SSP963.2030242841.12259E-06F-12/CO2 early biofilm induced
11CYB53.1791338121.7903E-06induced in high iron
Uncharacterized
Name (25 DEGs)Fold ChangeFDR p-valueFunction
1CAALFM_C400530CA25.2517153.77714E-07Uncharacterized
2CAALFM_CR08830WA13.1601073.7788E-05Uncharacterized
3CAALFM_CR06430WA6.7465080.002469228Uncharacterized
4CAALFM_CR09350CA6.1895991.40099E-55Uncharacterized
5CAALFM_C112940CA6.0613420.037846274Uncharacterized
6CAALFM_C404230WA5.5634652.28386E-82Uncharacterized
7CAALFM_C106870CA5.02020.017180492Uncharacterized
8CAALFM_C306240CA (MRPL39)4.9703670.002579226Uncharacterized
9CAALFM_C500130CA (YML34)4.7868795.51407E-07Uncharacterized
10CAALFM_C204770WA4.557910.001066926Uncharacterized
11CAALFM_C103620CA4.1617084.50987E-09Uncharacterized
12CAALFM_C501540WA (RPS11A)3.9097993.0519E-17Uncharacterized
13CAALFM_C503290CA (MRP10)3.9075681.74642E-10Uncharacterized
14CAALFM_C503480CA3.8716421.41077E-32Uncharacterized
15CAALFM_C208180CA3.7826140.001381795Uncharacterized
16CAALFM_C400990WA3.66193350.000850431Uncharacterized
17CAALFM_C403500CA3.656320.012820924Uncharacterized
18CAALFM_C204110WA3.4384881.6049E-10Uncharacterized
19CAALFM_C703560WA3.371043.35062E-18Uncharacterized
20CAALFM_C108770WA3.2435231.51784E-29Uncharacterized
21CAALFM_CR03110WA (MSE1)3.1721826.38954E-14Uncharacterized
22CAALFM_CR03470WA3.1621782.39698E-48Uncharacterized
23CAALFM_CR08480CA (RPS29A)3.1428552.18259E-06Uncharacterized
24CAALFM_CR02380CA3.0939990.000634778Uncharacterized
25CAALFM_C400230WA3.04579468.36614E-08Uncharacterized

Additional files

Supplementary file 1

List of top 100 upregulated genes in EDTA treated C. albicans cell (CAET) with detailed information.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp1-v1.xlsx
Supplementary file 2

GO annotation analyses of upregulated genes and downregulated genes.

(A) GO annotation analysis for 411 upregulated genes and (B) 388 downregulated genes.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp2-v1.xlsx
Supplementary file 3

STRING cluster analyses of DEGs.

(A) STRING cluster analysis for 411 upregulated genes, (B) 388 downregulated genes, and (C) 74 downregulated genes out of 388 DEGs specific to 40 S and 60 S ribosomal subunits.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp3-v1.xlsx
Supplementary file 4

STRING cluster analysis for 33 DEGs specific to pathogenesis.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp4-v1.xlsx
Supplementary file 5

List of top 100 downregulated genes in EDTA treated C. albicans cell (CAET) with detailed information.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp5-v1.xlsx
Supplementary file 6

Oligonucleotides and PCR conditions.

https://cdn.elifesciences.org/articles/93760/elife-93760-supp6-v1.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/93760/elife-93760-mdarchecklist1-v1.docx

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Swagata Bose
  2. Satya Ranjan Sahu
  3. Abinash Dutta
  4. Narottam Acharya
(2024)
A chemically induced attenuated strain of Candida albicans generates robust protective immune responses and prevents systemic candidiasis development
eLife 13:RP93760.
https://doi.org/10.7554/eLife.93760.3