Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid
- Biology Program, New York University Abu Dhabi, United Arab Emirates
- Max Planck Institute for Marine Microbiology, Germany
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Australia
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Australia
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, United Arab Emirates
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu Dhabi, United Arab Emirates
Figures
Figure 1 with 1 supplement
Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in Phycobacter and A. macleodii.
Left: Scatter plot of the log2 fold-change of differentially expressed (DE) genes present in KEGG pathways listed on the y-axis. Each circle represents the differential expression of a gene in the …
Figure 1—figure supplement 1
Effect of azelaic acid (Aze) on growth of Phycobacter.
(A) As a sole carbon source (1 mM) and (B) in comparison to a control. For (B) Aze was added at T=0 hr to treatments while controls received an equivalent volume of Milli-Q water. RNA samples were …
Figure 2 with 1 supplement
Proposed azelaic acid (Aze) catabolism in Phycobacter based on transcriptomics and isotope labeling.
Left: Log2 fold-change of differentially expressed (DE) genes is shown as circles at 0.5 (left circle) and 8 hr (right circle) after the addition of Aze to Phycobacter cells relative to controls. …
Figure 2—figure supplement 1
13C-Aze assimilation by Phycobacter and A. macleodii (reported as δ(13C) [‰, VPDB]) during a 2 hr incubation.
VPDB indicates Vienna Pee Dee Belemnite. Asterisks denote significant differences between the two bacteria (repeated-measure ANOVA, n=3, p<0.001). Error bars indicate the standard deviation of the …
Figure 3
Genomic neighborhood structure of azeR and azeTSL in Phycobacter and P. nitroreducens DSM9128.
Genes predicted in silico to belong to a single operon are marked by blue boxes. Bold-faced gene abbreviations in Phycobacter denote upregulated genes in response to azelaic acid (Aze). Operon …
Figure 4
Model of azelaic acid (Aze) catabolism in Phycobacter and toxic effects in A. macleodii.
Colored boxes and circles represent metabolic pathway expression ratios and differential gene expression (log2 fold-change), respectively, at 0.5 and 8 hr for (a) Phycobacter and at 0.5 hr for (b) A.…
Figure 5 with 1 supplement
Transcriptional coexpression networks of hub transcriptional factors (TFs) azeR and xre, and their putative target genes in Phycobacter and A. macleodii.
Nodes represent genes (circles) and TFs (triangles) connected by edges based on significant coexpression correlation (PCIT; r≥0.95) for (a) Phycobacter and (b) A. macleodii. Nodes are grouped based …
Figure 5—figure supplement 1
Transcriptional coexpression networks constructed using the partial correlation coefficient with information theory algorithm in Phycobacter and A. macleodii.
Initial networks (a, d) consisted of key transcriptional factors (TFs) (identified by regulatory impact factor analysis) and differentially expressed genes. Nodes are depicted either as circles for …
Figure 6 with 3 supplements
Bacterial and archaeal diversity in seawater treated with azelaic acid (Aze).
(a) Alpha-diversity indices of observed OTUs, Chao1, Shannon and Simpson across the Aze-treated and control samples. (b) Principal coordinate analysis (PCoA) of Bray-Curtis distances (permutational …
Figure 6—figure supplement 1
Effect of azelaic acid (Aze) treatment on the alpha- and beta-diversity of soil.
(a) Alpha-diversity indices of observed OTUs, Chao1, Shannon and Simpson across the Aze-treated and control samples. (b) Principal coordinate analysis (PCoA) of Bray-Curtis distances (permutational …
Figure 6—figure supplement 2
Effect of azelaic acid (Aze) treatment on the alpha- and beta-diversity of A. thaliana root microbiome.
(a) Alpha-diversity indices of observed OTUs, Chao1, Shannon and Simpson across the Aze-treated and control treatments. (b) Principal coordinate analysis (PCoA) of unweighted Unifrac distances …
Figure 6—figure supplement 3
Bacterial diversity in the roots of A. thaliana treated with azelaic acid (Aze).
(a) Relative abundance of the top 25 microbial families based on 16S rRNA gene amplicon sequencing of A. thaliana root microbiome following Aze infiltration. Plant-free control is untreated soil and …
Additional files
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Supplementary file 1
A summary of the differentially expressed (DE) genes in Phycobacter and A. macleodii.
The first worksheet summarizes the number of DE genes for Phycobacter at 0.5 and 8 hr and A. macleodii at 8 hr in response to azelaic acid. Percent values represent the ratio of genes in each category to the total number of genes in each genome. The second, third, and fourth sheets provide the DESeq output data (product ID, baseMean, log2FoldChange, pvalues, etc.) for Phycobacter at 0.5 and 8 hr and A. macleodii at 8 hr.
- https://cdn.elifesciences.org/articles/88525/elife-88525-supp1-v1.xlsx
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Supplementary file 2
List of selected differentially expressed (DE) genes by (A) Phycobacter and (B) A. macleodii in response to azelaic acid addition.
Genes with no values indicate no statistically significant differential expression compared to controls. Genes were considered significantly DE if they had a p-adjusted value of <0.05 and a log2 fold-change of ≥±0.50. Genes predicted to be in a single operon structure are listed in the direction of transcription within a single box, where relevant. Genes operon structures were predicted by OperonMapper. Genes common to more than one pathway are listed only once.
- https://cdn.elifesciences.org/articles/88525/elife-88525-supp2-v1.xlsx
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Supplementary file 3
List of all differentially expressed (DE) genes by (A) Phycobacter and (B) A. macleodii in response to azelaic acid addition.
Genes were considered significantly DE if they had a p-adjusted value of <0.05 and a log2 fold-change of ≥±0.50.
- https://cdn.elifesciences.org/articles/88525/elife-88525-supp3-v1.xlsx
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Supplementary file 4
Characteristics of 13C-Aze uptake by Phycobacter and A. macleodii.
(A) Carbon fractionation and uptake rate of bacteria exposed to 13C-Aze. (B) 13C-labeled metabolites detected in Phycobacter after incubation with 13C-Aze.
- https://cdn.elifesciences.org/articles/88525/elife-88525-supp4-v1.xlsx
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Supplementary file 5
Transcriptional factors (TFs) with significant regulatory impact factor (RIF) score and their differential gene expression in Phycobacter and A. macleodii.
- https://cdn.elifesciences.org/articles/88525/elife-88525-supp5-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/88525/elife-88525-mdarchecklist1-v1.docx
