Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae
- Department of Biomedical Sciences, City University of Hong Kong, China
- The University of Hong Kong, Pokfulam, China
- Shenzhen Research Institute, City University of Hong Kong, China
- Tung Biomedical Sciences Center, City University of Hong Kong, China
- Chengdu Research Institute, City University of Hong Kong, China
- Institute of Digital Medicine, City University of Hong Kong, China
Figures
Figure 1 with 2 supplements
Hierarchical height and collaboration of transcription factors (TFs) reveal the multiple regulatory patterns in Psph 1448A.
(a) Close-up representation of 262 TFs hierarchy in Psph 1448A (8 TFs showed no hierarchical characteristic). Nodes depict TFs. Colours of edges represent source-bases. (b) Enrichment of different …
Figure 1—figure supplement 1
Summary of chromatin immunoprecipitation sequencing (ChIP-seq) results in Psph 1448A.
(a) Locations of all the 301 annotated transcription factors (TFs) in Psph 1448A genome. Blue lines represent the TF loci. (b) ChIPed TFs are classified as respective family with different colours. …
Figure 1—figure supplement 2
Graph diagram of feedforward loop in Psph 1448A.
Transcription factor (TF) columns in feedforward loop (M13, n=696) are classified as families. TF-TF edges are distinguished with separate colours.
Figure 2 with 3 supplements
Bottom transcription factors (TFs) share the same binding sequences to coregulate in Psph 1448A.
(a) The co-association map for 170 TFs in Psph 1448A shows the co-associated scores of binding peaks of these TFs (rows) that overlap each TF peak (columns). The three-coloured rectangles represent …
Figure 2—figure supplement 1
Co-association and virulence-related functional category of transcription factors (TFs) at top level.
(a–b) The co-associated map and functional category of top TFs. The peak number of top TFs is shown at upper, corresponding to the TFs in the lower map. Functional enrichment analysis was performed …
Figure 2—figure supplement 2
Co-association and virulence-related functional category of transcription factors (TFs) at middle level.
(a–b) The co-associated map and functional category of middle TFs. The peak number of middle TFs is shown at upper, corresponding to the TFs in the lower map. Functional enrichment analysis was …
Figure 2—figure supplement 3
Co-association and virulence-related functional category of transcription factors (TFs) at bottom level.
(a–b) The co-associated map and functional category of bottom TFs. The peak number of bottom TFs is shown at upper, corresponding to the TFs in the lower map. Functional enrichment analysis was …
Figure 3 with 1 supplement
Virulence hierarchical regulatory network reveals 35 transcription factors (TFs) involved in virulence.
(a) Virulence hierarchical regulatory network shows the TF hierarchy and the large pool of target genes of multi-TF. Target genes are related with seven key virulence pathways, including biofilm …
-
Figure 3—source data 1
PDF file containing original electrophoretic mobility shift assay (EMSA), motility, biofilm, and extracellular polysaccharides (EPS) detection for Figure 3b–d, indicating the relevant binding and phenotypes.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig3-data1-v1.zip
-
Figure 3—source data 2
Original electrophoretic mobility shift assay (EMSA) gels and photos for EMSA, motility, biofilm, and extracellular polysaccharides (EPS) detection displayed in Figure 3b–d.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig3-data2-v1.zip
Figure 3—figure supplement 1
The validation of the binding sites of virulence-related transcription factors (TFs) in Psph 1448A.
(a–c) The promoter of rpoD is the negative control of PSPPH1951 and PSPPH2193. The promoter of PSPPH3658 is the negative control of PSPPH3268. (d) Growth curve of three TF mutants. (e) The …
-
Figure 3—figure supplement 1—source data 1
PDF file containing original electrophoretic mobility shift assay (EMSA) for Figure 3-figure supplement 1a–c, e, and g.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig3-figsupp1-data1-v1.zip
-
Figure 3—figure supplement 1—source data 2
Original electrophoretic mobility shift assay (EMSA) gels corresponding to Figure 3-figure supplement 1a–c, e, and g.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig3-figsupp1-data2-v1.zip
Figure 4 with 2 supplements
Hundreds of transcription factors (TFs) are identified to participate in metabolic pathways.
(a) Metabolic hierarchical regulatory network shows the TF hierarchy and the large pool of target genes of multi-TF. Target genes are related with eight key metabolic pathways, including …
Figure 4—figure supplement 1
Metabolic functional category of transcription factors (TFs) at three different levels.
(a–c) Functional category according to different metabolic pathways of top (a), middle (b), and bottom (c) TFs.
Figure 4—figure supplement 2
Key transcription factors (TFs) in different metabolic pathways.
(a) Radar plots show the putative key regulators identified in two different metabolic pathways, including DNA replication, and phosphonate and phosphonate metabolism. Each radiation line represents …
-
Figure 4—figure supplement 2—source data 1
PDF file containing original electrophoretic mobility shift assay (EMSA) for Figure 4-figure supplement 2b–d.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig4-figsupp2-data1-v1.zip
-
Figure 4—figure supplement 2—source data 2
Original electrophoretic mobility shift assay (EMSA) gels corresponding to Figure 4-figure supplement 2b–d.
- https://cdn.elifesciences.org/articles/96172/elife-96172-fig4-figsupp2-data2-v1.zip
Figure 5 with 2 supplements
Various conservations are observed in transcription factors (TFs) between different P. syringae pathovars.
(a) Proportion of the TF-target genes detected in one, two, three, or four tested genomes. C1–C4 represent the conservation of targets in one, two, three, and four strains. (b–c) Repartition of the …
Figure 5—figure supplement 1
Motif and functional enrichment analysis of PSPPH3122 in Psph 1448A, Pss B728a, and Pst DC3000 strains.
Motifs of PSPPH3122 in Psph 1448A (a) and Pst DC3000 (b) strains. (c) Gene Ontology (GO) analysis by hypergeometric test (BH-adjusted p<0.05) of PSPPH3122 in Psph 1448A, Pst DC3000, and Pss B728a …
Figure 5—figure supplement 2
Motif and functional enrichment analysis of PSPPH4127 in Psph 1448A, Pss B728a, Pst DC3000, and Psa C48 strains.
Motifs of PSPPH4127 in Psph 1448A (a), Pss B728a (b), Pst DC3000 (c), and Psa C48 (d) strains. (e) Gene Ontology (GO) analysis by hypergeometric test (BH-adjusted p<0.05) of PSPPH4127 in Psph 1448A, …
Figure 6
Functional modularised regulatory network in P. syringae exhibits the specific functions of both transcription factors (TFs) and their target genes.
(a) The functional categorical regulation network in Psph 1448A analysed by Gephi (resolution 0.9). The 16 modules (both TFs and their target genes) are labelled in different colours. TF nodes are …
Figure 7
Global transcriptional regulatory network in Psph 1448A.
The integrated transcriptional regulatory network reflects the interactions between all transcription factors (TFs) classified into 39 families from different DNA-binding domain types and target …
Additional files
-
Supplementary file 1
Hierarchical height and direct interaction of transcription factors (TFs).
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp1-v1.xlsx
-
Supplementary file 2
Functional category and peak numbers of top transcription factors (TFs), functional category of middle and bottom TFs.
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp2-v1.xlsx
-
Supplementary file 3
Hierarchical network of transcription factors (TFs).
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp3-v1.xlsx
-
Supplementary file 4
Homologous proteins in three strains (DC3000, B728a, and C48) with 1448A and binding peaks of five TFs (Irp, X2193, X2193, X4127, and OmpR).
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp4-v1.xlsx
-
Supplementary file 5
List of orthologous genes of 1448A transcription factors (TFs) in the other tested P. syringae strains (DC3000, B728a, and C48).
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp5-v1.xlsx
-
Supplementary file 6
Strains and primers used in this study.
- https://cdn.elifesciences.org/articles/96172/elife-96172-supp6-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/96172/elife-96172-mdarchecklist1-v1.docx
