Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops
Abstract
:1. Introduction
2. Results
2.1. CRP-Mediated FFLs in E. coli
2.2. CRP-FFLs Characterized by Distinct cAMP Dose–Responses
2.3. GO Enrichment Analysis of FFLs in CRP Regulatory Network
3. Discussion
3.1. Integration of Different FFL Types Diversifies the Output Response
3.2. Functional Analysis of FFLs in CRP-Regulated Networks
4. Application of FFLs
5. Materials and Methods
5.1. Construction of CRP-FFLs
5.2. Identification of CRP-Regulated Genes Using cAMP Dose–Response Microarray
5.3. Analysis of Microarray Data
5.4. Hierarchical Clustering and Functional Analysis
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Type | Number of CRP-FFLs | Number of TF | Number of Gene | Genes |
---|---|---|---|---|
Coh1 | 49 | 13 | 49 | araF, araG, dctA, fecA, fecB, fecC, fecD, fecE, fucA, fucI, fucK, fucO, fucP, fucR, fumC, hyfH, idnD, idnK, idnO, lamB, malE, malF, malG, malK, malM, malS, marB, ompF, prpB, prpC, prpD, prpE, rhaR, sdhA, sdhB, sdhC, sdhD, srlA, srlB, srlD, srlE, sucA, sucB, sucC, sucD, xylA, xylF, xylG, xylH |
Coh2 | 15 | 3 | 10 | gadA, gadB, gadB, gadC, gadC, gadE, gadE, gadX, gltD, gltF, mdtE, mdtE, mdtF, mdtF, proP |
Coh3 | 2 | 1 | 2 | gltD, gltF |
Coh4 | 26 | 3 | 26 | acs, actP, aldB, fadL, flhC, flhD, glcC, guaA, guaB, hlyE, hupB, mglA, mglC, mtlA, mtlD, mtlR, nanA, nanE, nanK, nanT, nmpC, xylF, xylG, xylH, yiaK, yjcH |
InCoh1 | 87 | 22 | 73 | cdd, chbB, cirA, cyoD, cyoD, cyoE, cyoE, cytR, entD, entH, fecA, fecB, fecC, fecD, fecE, fepA, fiu, flhC, flhD, fumC, galK, galK, galP, galP, galS, glcC, glpD, glpF, glpK, glpT, gntK, gntP, gntP, gntU, grcA, grcA, lsrA, lsrB, lsrC, lsrD, lsrF, lsrG, lsrK, lsrR, malI, malX, manX, manY, manZ, marB, mglA, mglA, mglA, mglB, mglB, mglB, mglC, mglC, mglC, mtlA, mtlD, mtlR, nagB, nagE, nupC, nupG, prpR, rbsA, rbsB, rbsC, rbsD, rbsK, rbsR, srlA, srlB, srlD, srlE, tsx, udp, uidA, uidB, uidC, uxuA, uxuA, uxuB, uxuB, xylA |
InCoh2 | 8 | 3 | 8 | bhsA, gadA, gadB, gadC, gadX, nirB, osmY, yiaJ |
InCoh3 | 1 | 1 | 1 | araJ |
InCoh4 | 14 | 4 | 14 | csgD, csgE, csgF, csgG, cyoD, cyoE, exuT, glpB, grcA, malE, malF, malG, marB, nrdB |
Functional Group ID | Group ID | GO Term | p-Value | Number of Gene | Summary of Function |
---|---|---|---|---|---|
FG1 | SG1 | GO:0006099 tricarboxylic acid cycle | 5.02 × 10−12 | 8 |
|
GO:0009060 aerobic respiration | 8.00 × 10−11 | 8 | |||
GO:0045333 cellular respiration | 3.13 × 10−9 | 8 | |||
GO:0015980 energy derivation by oxidation of organic compounds | 2.18 × 10−8 | 8 | |||
GO:0006091 generation of precursor metabolites and energy | 2.25 × 10−7 | 8 | |||
GO:0055114 oxidation-reduction process | 7.12 × 10−3 | 8 | |||
FG2 | SG2 MG6 | GO:0008643 carbohydrate transport | 3.84 × 10−26 | 37 |
|
GO:0034219 carbohydrate transmembrane transport | 6.99 × 10−18 | 27 | |||
GO:0071702 organic substance transport | 4.69 × 10−12 | 44 | |||
GO:0006810 transport | 2.93 × 10−8 | 49 | |||
GO:0051234 establishment of localization | 3.75 × 10−8 | 49 | |||
GO:0015749 monosaccharide transport | 5.37 × 10−8 | 14 | |||
GO:0044765 single-organism transport | 2.23 × 10−7 | 46 | |||
GO:0051179 localization | 4.36 × 10−7 | 49 | |||
GO:0015768 maltose transport | 4.45 × 10−5 | 6 | |||
GO:0009401phosphoenolpyruvate-dependent sugar phosphotransferase system | 1.03 × 10−4 | 10 | |||
GO:0055085 transmembrane transport | 1.20 × 10−4 | 36 | |||
GO:0015750 pentose transport | 2.71 × 10−4 | 7 | |||
GO:0044724 single-organism carbohydrate catabolic process | 6.79 × 10−4 | 21 | |||
GO:0015766 disaccharide transport | 7.07 × 10−4 | 7 | |||
GO:0042956 maltodextrin transport | 7.40 × 10−4 | 5 | |||
GO:0015772 oligosaccharide transport | 1.61 × 10−3 | 7 | |||
GO:0016052 carbohydrate catabolic process | 2.08 × 10−3 | 21 | |||
GO:0006004 fucose metabolic process | 3.19 × 10−3 | 6 | |||
GO:0019521 D-gluconate metabolic process | 7.58 × 10−3 | 6 | |||
GO:0044275 cellular carbohydrate catabolic process | 8.56 × 10−3 | 11 | |||
FG3 | SG3 MG2 MG4 | GO:0055080 cation homeostasis | 7.34 × 10−6 | 8 |
|
GO:0050801 ion homeostasis | 9.10 × 10−6 | 8 | |||
GO:0048878 chemical homeostasis | 1.37 × 10−5 | 8 | |||
GO:0042592 homeostatic process | 3.33 × 10−4 | 8 | |||
GO:0055072 iron ion homeostasis | 7.44 × 10−3 | 5 | |||
GO:0045852 pH elevation | 9.50 × 10−3 | 3 | |||
GO:0051454 intracellular pH elevation | 9.50 × 10−3 | 3 | |||
FG4 | SG4 MG1 MG5 | No significant GO term |
| ||
FG5 | SG5 MG3 | No significant GO term |
|
Functional Group ID | Type | Group ID | Number of CRP-FFLs (Gene) | Coh1 | Coh2 | Coh3 | Coh4 | InCoh1 | InCoh2 | InCoh3 | InCoh4 |
---|---|---|---|---|---|---|---|---|---|---|---|
FG1 | CRP-sFFLs | SG1 | 10 (10) | V | V | ||||||
FG2 | SG2 | 78 (78) | V | V | V | V | |||||
FG3 | SG3 | 10 (10) | V | V | V | V | V | V | |||
FG4 | SG4 | 2 (2) | V | ||||||||
FG5 | SG5 | 1 (1) | V | ||||||||
FG4 | CRP-mFFLs | MG1 | 4 (2) | V | V | ||||||
FG3 | MG2 | 15 (7) | V | V | V | ||||||
FG5 | MG3 | 2 (1) | V | V | |||||||
FG3 | MG4 | 14 (6) | V | V | |||||||
FG4 | MG5 | 6 (2) | V | V | |||||||
FG2 | MG6 | 60 (27) | V | V | V | V |
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Yang, C.-D.; Huang, H.-Y.; Shrestha, S.; Chen, Y.-H.; Huang, H.-D.; Tseng, C.-P. Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. Int. J. Mol. Sci. 2018, 19, 2335. https://doi.org/10.3390/ijms19082335
Yang C-D, Huang H-Y, Shrestha S, Chen Y-H, Huang H-D, Tseng C-P. Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. International Journal of Molecular Sciences. 2018; 19(8):2335. https://doi.org/10.3390/ijms19082335
Chicago/Turabian StyleYang, Chi-Dung, Hsi-Yuan Huang, Sirjana Shrestha, Yen-Hua Chen, Hsien-Da Huang, and Ching-Ping Tseng. 2018. "Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops" International Journal of Molecular Sciences 19, no. 8: 2335. https://doi.org/10.3390/ijms19082335