Extracellular adenosine deamination primes tip organizer development in Dictyostelium
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology-Madras, India
Figures
Figure 1 with 1 supplement
adgf mutant validation.
(A) Schematic representation of adgf locus showing the relative positions of the primers (P1–P4) and the blasticidin resistance cassette (bsr). Primer P1 (adgf fwd) is at the start codon of adgf, and primer P4 (adgf rev) is 264 bp upstream of the stop codon, flanking the insertion site. Primers P2 (pGWD2) and P3 (pGWD1) are located within the bsr cassette. bsr insertion is in exon 2 of adgf. (B) PCR analyses using P1 and P4 primers. A 1.4-kb shift in the adgf mutant. PCR using P1 and P2 primers showed an amplicon from the mutant (M) and not from the wild-type (WT). PCR using P3 and P4 primers showed an amplicon with the adgf mutant while WT did not show any amplicon. (C) Semi-quantitative RT-PCR of the internal control, rnlA and adgf−. adgf expression during development in Dictyostelium. (D) Total RNA was isolated from Dictyostelium during vegetative growth and development using TRIzol method. To quantify adgf expression, qRT-PCR was carried out with rnlA as a control and the fold-change was calculated accordingly. Time points are shown in hours (bottom). Error bars represent the mean and SEM (n = 3).
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Figure 1—source data 1
PDF with original gel images for Figure 1B, C, showing the relevant bands.
- https://cdn.elifesciences.org/articles/104855/elife-104855-fig1-data1-v1.zip
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Figure 1—source data 2
Original files for gel images displayed in Figure 1B, C.
- https://cdn.elifesciences.org/articles/104855/elife-104855-fig1-data2-v1.zip
Figure 1—figure supplement 1
Bioinformatic analyses of ADGF.
(A) BLAST analysis of ADGF. (B) SMART analysis depicting different ADA domains within ADGF. ADGF has an ADA and an N-terminal deaminase domain similar to human ADA2. Multiple sequence alignment of Dictyostelium ADGF with ADGF from other organisms. (C) The shaded region depicts the N-terminal signal sequence characteristic of extracellular proteins. (D) The active site residue highlighted in red is conserved between D. discoideum and human ada2. (E) Phylogenetic analysis of ADGF across different organisms. The maximum likelihood method was used for constructing the tree using molecular evolutionary genetic analysis X (MEGAX). Structural comparison of human ADA2 and Dictyostelium ADGF. Identical tertiary structures of human ADA2 and Dictyostelium ADGF. (F) ADA2 (CECR1) Homo sapiens and (G) DdADGF. (H) Alignment of Dictyostelium ADGF with human ADA2 (CECR1).
Figure 2 with 2 supplements
Aggregates formed by adgf mutants were larger in size.
(A) The graph shows the mound size and the number of aggregates formed by WT and adgf−. A minimum of 20 aggregates were analyzed per experiment. The values represent mean ± SEM; n = 3 independent biological replicates. Significance level is indicated as ***p< 0.001 (Student’s t-test). (B) Expression levels of the genes, countin (ctn) and small aggregates (smlA) during aggregation in adgf− compared to WT. rnlA was used as the internal control. Data represent mean ± SEM (n=3). Significance level is indicated as *p< 0.05, **p< 0.01 (Student’s t-test). (C) WT and adgf− cells were developed on KK2 agar, and after 16 hr, the multicellular mounds/slugs were dissociated by vigorous vortexing in KK2 buffer. Individual cells were counted using a hemocytometer and resuspended in a phosphate buffer. Non-adherent single cells were counted 45 min after incubation. The percent cell–cell adhesion was plotted by normalizing the values to the non-adherent WT count to 100%. Error bars represent the mean ± SEM (n = 3). The level of significance is ****p< 0.0001 by Student’s t-test. (D) qRT-PCR analysis of cadherin (cadA) and contact site (csA) during aggregation. The fold-change in RNA transcript levels is relative to WT at the indicated time points. Error bar is mean and SEM (n = 3). Significance level is indicated as ****p < 0.0001 (Student’s t-test). (E) Under agarose chemotaxis assay. The average cell speed in response to 10 μM cAMP was recorded. A minimum of 25 cells were tracked for each experiment. The graph represents the mean ± SEM (n = 3). ns, non significant, by Student’s t-test. Developmental phenotype of adgf−. (F) WT and adgf− cells were washed, plated on 1% KK2 agar plates at a density of 5 × 105 cells/cm2, incubated in a dark, moist chamber and images were taken at different time intervals. (G) WT cells treated with 100 nM of DCF mimicked the mound arrest phenotype of the mutant. The time points are indicated in hours at the top of the figure. Scale bar: 2 mm (n = 3). (H) WT and adgf− cells after 36 hr of development. Scale bar: 0.5 mm (n=3). (I) Fruiting bodies of WT and adgf−. Scale bar: 2 mm. Atleast 30 fruiting bodies were analyzed for each experiment, n = 3 independent biological replicates.
Figure 2—video 1
Timelapse video of wild-type AX4 development.
Scale bar is 2 mm.
Figure 2—video 2
Timelapse video of adgf− development.
Scale bar is 2 mm.
Figure 3
adgf mounds have reduced ADA activity and high adenosine levels.
(A) ADA activity in WT and adgf− harvested at 12 and 16 hr. The enzymatic assay for ADA was performed in adgf− with the corresponding WT control. Error bars represent the mean and SEM (n = 3). Significance level is indicated as **p < 0.01 (Student’s t-test). (B) Quantification of adenosine levels in WT and adgf mutants at 12 and 16 h. Level of significance is indicated as *p < 0.05, **p < 0.01, ***p < 0.001 by Student’s t-test. Data represent mean and SEM (n = 3). (C) Expression profile of 5′ nucleotidase (5′nt) and phosphodiesterases (regA, pdsA) involved in cAMP-to-adenosine conversion. The fold-change in RNA transcript levels is relative to WT at the indicated time points. rnlA was used as an internal control. Error bars represent the mean and SEM (n = 3). Level of significance is indicated as *p< 0.05, **p< 0.01, ***p< 0.001.
Figure 4
Overexpression of adgf rescued the mound arrest phenotype.
(A) adgf− mounds were treated with 5 and 10 U ADA enzyme, and imaged at 16 hr. Scale bar: 2 mm (n = 3). (B) The full-length adgf gene was cloned in the vector pDXA-GFP2. The overexpression construct was verified by restriction digestion with HindIII and KpnI enzymes. (C) adgf overexpression in the mutant rescued the mound arrest. (D) Overexpression of adgf in WT background. Scale bar: 2 mm (n = 3). The time points in hours are shown at the top. WT cells mixed with adgf− rescued the adgf mutant phenotype. (E) Mixing of WT with adgf− in a 1:4 ratio showed a partial rescue, and a full rescue of the adgf− mound arrest phenotype in a 1:1 ratio with WT. Scale bar: 2 mm; (n=3). (F) Development of adgf mutants in the presence of adgf− CM and WT CM on KK2 agar plates. WT CM rescued the mound arrest. Scale bar: 2 mm; (n=3). (G) Development of WT in the presence of WT CM and adgf− CM on KK2 agar plates. adgf− CM induced mound arrest in WT cells. Scale bar: 2 mm (n = 3).
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Figure 4—source data 1
PDF with original gel images for Figure 4B, showing the relevant bands.
- https://cdn.elifesciences.org/articles/104855/elife-104855-fig4-data1-v1.zip
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Figure 4—source data 2
Original files for gel images displayed in Figure 4B.
- https://cdn.elifesciences.org/articles/104855/elife-104855-fig4-data2-v1.zip
Figure 5 with 3 supplements
Adenosine deamination reaction rescues the mound arrest of adgf.
(A) Quantification of ammonia using the ammonia assay kit. WT and adgf− mounds were harvested and lysed using a cell lysis buffer. Cell debris was removed by centrifugation, and the supernatant was used to quantify ammonia. Error bars represent mean and SEM (n=3). **p<0.01, by Student’s t-test. (B) Treatment of adgf− mounds with ammonia. Ammonia was generated by mixing 2 ml of NH4Cl and 2 ml of 1 N NaOH. The mixture was poured on top of the lid and the KK2 plates with the mounds were inverted and sealed thereafter. Images were taken 3.5 hr post treatment. Dose-dependent effect of ammonia on the rescue. Scale bar: 2 mm (n = 3). (C) WT and adgf− cells on either side of a compartmentalized Petri dish led to tip formation in adgf−. Scale bar: 2 mm; (n=3). (D) adgf− cells on one side and KK2 buffer containing adenosine and ADA on the other side of the compartmentalized dish, rescued the mound defect. Caffeine rescues the large mound size of adgf mutant. Scale bar: 2 mm; (n=3). (E) adgf− cells were treated with different concentrations of caffeine (100 nM, 1 µM) while plating, and images were taken during mound stage. Scale bar: 2 mm; n = 3. (F) Exposure to ammonia does not rescue the mound size of adgf mutant. adgf− mounds were exposed to 0.01 M ammonia and images were captured 3.5 hr post chemical treatment. Scale bar: 2 mm (n = 3).
Figure 5—figure supplement 1
Total protein and RNA levels during mound stage of development.
(A) Total protein levels were estimated using BCA assay. (B) Total RNA levels in the WT and adgf−. The error bars represent the mean ± SEM (n = 3). ns = not significant (Student’s t-test).
Figure 5—figure supplement 2
Volatiles released from K. pneumoniae rescue the mound arrest phenotype of adgf−.
Picture depicting K. pneumoniae and adgf− cells on either side of a compartmentalized Petri dish. Scale bar: 2 mm (n = 3). K. pneumoniae and adgf− cells were developed on either side of compartmentalized dish, and photographs were captured at 16 hr.
Figure 5—figure supplement 3
Treatment with adenosine and other purines does not induce mound arrest in WT.
(A) WT cells were treated with adenosine (10 µM) while plating, and imaged at different time intervals. Scale bar: 2 mm; n = 3. (B) WT cells were treated with 10 µM guanosine and 10 µM 2-deoxy adenosine, plated for development and images were taken after 16 hr. Scale bar: 2 mm; n = 3. (C) adgf− mounds were treated with inosine and images were captured 3.5 hr post chemical treatment. Scale bar: 2 mm; n = 3.
Figure 6 with 2 supplements
Impaired cAMP signalling in adgf−.
(A) Total cAMP levels in WT and adgf− mounds were quantified using cAMP-XP assay kit (Cell Signaling, USA). Level of significance is indicated as *p < 0.05, **p < 0.01, by Student’s t-test. Error bars are mean ± SEM (n = 3). (B) acaA expression was quantified using qRT-PCR. The error bars represent the mean ± SEM (n = 3). *p< 0.05, **p< 0.01 (Student’s t-test). (C) adgf− mounds. (D) Time course of adgf− mounds treated with 8-Br-cAMP and imaged at different intervals. Scale bar: 2 mm (n = 3). Treatment with cyclic di-GMP and caffeine rescues the mound arrest phenotype. (E) Addition of cyclic-di-GMP restored tip formation in adgf− 3.5 hr after the treatment. Scale bar: 1 mm (n = 3). (F) PDE inhibitor (IBMX) treatment failed to rescue the adgf− mound arrest. Scale bar 1 mm (n = 3). (G) adgf− mounds treated with caffeine formed tips 3.5 hr post treatment. Scale bar: 2 mm (n = 3). Altered cAMP wave pattern in adgf mutants. (H) Optical density waves depicting cAMP wave generating centres in WT and adgf−. WT shows spiral and adgf− exhibits circular wave propagation. Scale bar 1 mm; (n=3).
Figure 6—video 1
Timelapse video of cAMP wave propagation in AX4.
Scale bar: 0.5 mm.
Figure 6—video 2
Timelapse video of cAMP wave propagation in adgf−.
Scale bar: 0.5 mm.
Figure 7
Expression levels of adgf, acaA, and pde4 in response to adenosine and ammonia treatment.
(A) Expression levels of adgf, acaA, and pde4 in response to adenosine treatment (100 nM, 500 nM, and 1 µM). (B) And ammonia treatment (0.1, 1, and 10 mM). Data represent mean and SEM. Level of significance is indicated as *p < 0.05, **p < 0.01, and ***p < 0.001, ns-non significant (n = 3) by one way ANOVA analysis. (C) cAMP levels in adgf mutants rescued with ammonia. Level of significance is indicated as **p < 0.01 (n = 3, Student’s t-test). Expression levels of prestalk (pst), ecmA, ecmB and prespore (psp), pspA cell type markers in adgf−. The expression profile of (D) pst (ecmA, ecmB) and psp (pspA) specific markers in WT and adgf− was quantified using qRT-PCR. Error bars represent mean and SEM. Level of significance is indicated as **p < 0.01 and ****p < 0.0001 (n = 3) by Student’s t-test. The fold-change in RNA transcript levels is relative to WT at the indicated time points. rnlA was used as the internal control.
Figure 8 with 1 supplement
Mixing of WT cells with adgf− following DIL staining.
(A–C) DIL labelled cells were mixed with unlabelled cells and plated on KK2 agar. Images were captured during the migrating slug stage. The left panel shows bright field, and the right panel shows the corresponding fluorescence images. Scale bar: 0.5 mm (n = 3).
Figure 8—figure supplement 1
Neutral red staining of mounds and slugs.
(A) WT and adgf− cells were stained with NR, plated and images were captured at different time intervals. Scale bar: 2 mm (n = 3). Pst/psp marker expression in slugs after inhibitor treatment. (B) ecmA-GFP. (C) ecmO-GFP. (D) pspA-RFP expression in the slugs after DCF treatment. Scale bar: 2 mm, n=3.
Figure 9
Sorting of pst-GFP- and psp-GFP+ Dictyostelium cells by fluorescence activated cell sorter.
(A) Forward scatter (FSC) vs. side scatter (SSC) plot used to gate total cells. (B) Singlets were gated based on FSC-H vs. FSC-A to exclude doublets and aggregates. (C) GFP fluorescence profile of gated single cells reveals two populations: pst-GFP⁻ and psp-GFP+, corresponding to pst and psp cells, respectively. (D) GFP⁻ (pst) and (E) GFP+ (psp) fractions. (F) adgf expression in FACS sorted samples was quantified by quantitative real-time PCR (qRT-PCR). Error bars are mean ± SEM. Level of significance is indicated as **p < 0.01 (n = 3) by Student’s t-test.
Figure 10 with 2 supplements
adgf acts downstream of the histidine kinase dhkD.
(A) dhkD mutants on KK2 agar plates. Scale bar 1 mm; (n=3). (B) 5 and 10 U ADA rescued the mound arrest phenotype in a dose-dependent manner. Scale bar: 1 mm (n = 3). Images were taken 3.5 hr post treatment. (C) Addition of 20 U ADA led to formation of multiple tips. Scale bar: 2 mm (n = 3).
Figure 10—figure supplement 1
Treatment of mounds with ADA and DCF.
(A) ADA enzyme was directly added on top of the mound arrest mutants at 12 hr, and images were taken after 3.5 hr. Scale bar: 2 mm; n = 3. (B) Ammonia restores tip formation in dhkD -mounds. Scale bar: 2 mm; n = 3. (C) cAMP levels in dhkD mutants rescued with ammonia. Error bars are mean ± SEM. *p< 0.05, n=3 (Student’s t-test). (D) Multi-tipped mutants were treated with 1 mM DCF, plated for development and images were taken after 16 hr. Scale bar: 2 mm; n = 3.
Figure 10—figure supplement 2
Developmental phenotype of different deaminase gene knockouts.
(A) Deoxy-cytidine triphosphate deaminase, (B) N-acetyl glucosamine, (C) glucosamine-6-phosphate deaminase, (D) 2-amino muconate deaminase, (E) threonine deaminase, and (F) adenosine monophosphate deaminase. Scale bar: 2 mm; n = 3.
Figure 11
Model illustrating the role of adgf in development.
adgf suppresses the expression of genes involved in cell adhesion, cadA and csaA, and regulates the mound size and tip development by directly acting on adenosine, ammonia levels and cAMP signalling. Line ending in an arrow indicates that the previous gene/factor either directly or indirectly raises the activity or levels of the second; line ending in a cross-bar indicates inhibition. Dotted lines indicate ADGF interacting with APRA.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Dictyostelium discoideum) | adgf - (adenosine deaminase-related growth factor) | GWDI Bank, Dicty Stock Center, Northwestern University | DBS0237637 (GWDI_47_C_1) | Insertion in exon 2 of DDB_G0275179 |
| Strain, strain background (Dictyostelium discoideum) | AX4 (wild-type) | Dictybase (http://dictybase.org/) | DBS0235521 | Parent strain used for all experiments |
| Strain, strain background | Klebsiella pneumoniae | Dictybase | DBS0351098 | Used as a food source on SM/5 agar plates |
| Recombinant DNA reagent | pDXA-GFP2 (plasmid) | Dictybase | AF269235 | Dictyostelium expression vector with GFP |
| Recombinant DNA reagent | adgfOE; AX4/adgfOE | This paper | — | Full-length adgf (1.7 kb) cloned into pDXA-GFP2, and transformed into adgf- and WT-AX4 cells |
| Commercial assay or kit | ADA activity assay kit | Abcam | ab204695 | Used for adenosine deaminase activity |
| Commercial assay or kit | Adenosine quantification kit | Abcam | ab211094 | Used for total adenosine measurement |
| Commercial assay or kit | Ammonia assay kit | Sigma-Aldrich | AA0100 | Used for total ammonia estimation |
| Commercial assay or kit | cAMP-XP assay kit | Cell Signaling Technology | 4339 | For cAMP quantification |
| Software, algorithm | MEGA X | Kumar et al., 2018 | RRID:SCR_000667 | Used for phylogenetic tree construction |
| Software, algorithm | SMART | Letunic and Bork, 2018 | RRID:SCR_005026 | For domain analysis |
| Software, algorithm | BLAST | Altschul et al., 1990 | RRID:SCR_004870 | For sequence similarity search |
| Software, algorithm | HADDOCK 2.4 | Honorato et al., 2024 | RRID:SCR_014902 | For protein–protein docking |
| Software, algorithm | AlphaFold | Jumper et al., 2021 | RRID:SCR_023662 | For tertiary structure prediction |
| Software, algorithm | PyMOL | Schrödinger, LLC | RRID:SCR_000305 | For protein visualization |
| Software, algorithm | ImageJ | NIH | RRID:SCR_003070 | For image analysis |
| Software, algorithm | GraphPad Prism | GraphPad Software | RRID:SCR_002798 | For statistical analyses |
| Software, algorithm | NIS-Elements D | Nikon | RRID:SCR_000667 | For microscopy image processing |
| Other | Nikon Eclipse TE2000 microscope | Nikon, Japan | RRID:SCR_023161 | For fluorescence and live imaging |
| Other | FACS Discover S8 Image Sorter | BD Biosciences, USA | — | Used for sorting GFP-positive/negative cells |
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/104855/elife-104855-mdarchecklist1-v1.pdf
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Supplementary file 1
Compilation of supplementary tables (A–D) used in this study.
Table A: Various deaminases annotated in D. discoideum. Table B: Primers used for adgf semi-quantitative PCR. Primers used for adgf overexpression and vector construction. Table D: Primers used for real-time PCR.
- https://cdn.elifesciences.org/articles/104855/elife-104855-supp1-v1.pdf
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Extracellular adenosine deamination primes tip organizer development in Dictyostelium
eLife 14:RP104855.
https://doi.org/10.7554/eLife.104855.4
