Front Plant Sci Mar 14

Transcription

1 Case Study

2 Front Plant Sci Mar 14 30

3 33 Study Background Cryptochromes (CRY) are blue-light photoreceptors that mediate various light responses in plants and animals. It is known that CRY1 and CRY2 regulate a variety of physiological processes, including seedling photomorphogenesis and photoperiodic flowering, respectively. Trends in Plant Science, Volume 17, Issue 10, p , October 2012

4 34 About Cryptochromes 1 (CRY1) functional domains The C-termini of CRY1 (CCT1) is known to mediate CRY1 signaling. It has long been demonstrated that Arabidopsis CRY (CRY1 and CRY2) C-termini (CCT1 and CCT2) mediate light signaling through direct interaction with COP1. It is demonstrated that the N-termini of CRY1 (CNT1) are not only responsible for chromophores binding and blue light perception, but also mediation of their dimerization, which is essential for light activation of their photoreceptor activity.

5 35 Aimed Given that CNT1 and CCT1 are both involved in mediating CRY1 signaling, it is worth investigating how they are involved in regulating phytohormone-responsive gene expression at the transcriptomic level. In this study, we performed RNA-seq assay using transgenic plants expressing CCT1 fused to b-glucuronidase(gus) (GUS-CCT1, abbreviated as CCT1),and compared with the RNA-Seq results we obtained from cry1cry2 and CNT1 seedlings previously. Main findings CCT1 mediates CRY1 inhibition of GA promoted degradation of HY5 protein. The CCT1-mediated CRY1 regulation of GA response may be mediated through CCT1 regulation of COP1.

6 Register and Login to Pathway Studio 36

7 37 Questions risen from transcriptome analytical study What are all the known associations with CRY1 in the plant database? CRY1 is related with cryptochrome, phototropin, auxin signaling pathways. CRY1 mediates light signaling through direct inhibition with COP1. In Cryptochrome signaling pathway, COP1 plays an important role to regulate plant photoperiodism, hypocotyl growth, photomorphogenesis, phototropism through inhibiting HY5, CO, HFR1, MYB18. Focus on specific interactions: How does CRY1 regulates the phytohormone-response? CRY1 may affects phytohormone response through regulating the activation of COP1 and the synthesis of Auxin and GA.

8 38 CRY1 in Pathway Studio CRY1 is involved in 6 existing pathways, 61 group, and highly associated with Cryptochrome, Phototropin, Auxin signaling pathways

9 40 Cryptochrome Signaling Pathway CRY1 mediates light signaling through direct inhibition with COP1 In Cryptochrome signaling pathway, COP1 plays an important role to regulate plant photoperiodism, hypocotyl growth, photomorphogenesis, phototropism through inhibiting HY5, CO, HFR1, MYB18.

10 ENTITY DEFINITIONS Cell Process * biological processes, most coincide with Gene Ontology Clinical Parameter measured parameters of the human body used in clinical practice Complex * several polypeptides that form a complex via physical interactions Disease health conditions and disease terms from MeSH Functional Class * most functional classes coincide with Gene Ontology Protein defined by Entrez Gene - represents both genes and the gene products, including proteins and mirnas. Small Molecule in Mammal, naturally occurring metabolites and small molecules found in mammalian cells; ChemEffect adds drugs and non-naturally occurring small molecules to the mammal database. In Plant, naturally occurring metabolites and small molecules and other plant related chemicals (ex. herbicides or research related chemicals). The category small molecule may contain some biologically active polypeptides and proteins that work as drugs, such as monoclonal antibodies. Treatment non-chemical treatments and environmental conditions, such as cold shock. * Container Entities these are valid entities but also can have proteins mapped to them. You can see the proteins for the container entities in the child concepts in the property records for the specific entity. 41

11 RELATIONS DEFINITIONS Relation Types for the database: Binding direct physical interaction between two molecules. ChemicalReaction enzyme catalyzed reaction involving small molecules. DirectRegulation influences target activity by direct physical interaction (excluding promoter binding interactions). Expression regulator changes protein abundance by affecting levels of transcript or protein stability. mirnaeffect the inhibitory effect of a mirna on its mrna target. Regulation changes the activity of the target by an unknown mechanism (may be direct or indirect). This is a less specific relation type than others provided. MolSynthesis regulator changes the concentrations of the target (usually a small molecule target). MolTransport a regulator that changes the localization of the target (molecular translocation, export, import etc.) PromoterBinding a regulator that binds to the promoter of a gene. ProtModification a regulator that changes the modification of the target molecule, usually by a direct interaction such as phosphorylation, glycosylation, acetylation etc. 42

12 44 Questions risen from transcriptome analytical study What are all the known associations with CRY1 in the plant database? CRY1 is related with cryptochrome, phototropin, auxin signaling pathways. CRY1 mediates light signaling through direct interaction with COP1. In Cryptochrome signaling pathway, COP1 plays an important role to regulate plant photoperiodism, hypocotyl growth, photomorphogenesis, phototropism through inhibiting HY5, CO, HFR1, MYB18. Focus on specific interactions: How does CRY1 regulates the phytohormone-response? CRY1 may affects phytohormone response through regulating the activation of COP1 and the synthesis of Auxin and GA.

13 45 How does CRY1 regulates the phytohormone-response? CRY1 may affects phytohormone response through regulating the activation of COP1 and the synthesis of Auxin and Gibberellin (GA) 22 Proteins and Chemicals related to Phytohormone response

14 57 Questions risen from transcriptome analytical study What genes are regulated by CRY1, CCT1, CNT1, respectively? Genes with differential expression were identified with a p value < 0.01 and fold change (FC) > Genes are common regulated in group CRY1 and CCT Genes are common regulated in group CRY1 and CNT Genes are common regulated in group CCT1 and CNT Genes are common regulated in 3 groups What functions/pathway are associated with CCT1, CNT1 regulated genes? Both CCT1 and CNT1 regulated Genes are associated with 9 GO functions such as defense response, response to UV-B, gibberellin biosynthetic process and 1 Cold-stress signaling pathway CCT1 regulated Genes are associated with photosynthesis, response to light CNT1 regulated Genes are associated protein ubiquitination, defense response, Gibberellin Signaling, Salicylic Acid Signaling

15 58 What genes are regulated by CRY1, CCT1, CNT1, respectively? Three RNA-seq datasets CRY1, CCT1, and CNT1 CCT CRY1 CNT Genes are common regulated in group CRY1 and CCT Genes are common regulated in group CRY1 and CNT Genes are common regulated in group CCT1 and CNT Genes are common regulated in 3 groups

16 64 Questions risen from transcriptome analytical study What genes are regulated by CRY1, CCT1, CNT1, respectively? Genes with differential expression were identified with a p value < 0.01 and fold change (FC) > Genes are common regulated in group CRY1 and CCT Genes are common regulated in group CRY1 and CNT Genes are common regulated in group CCT1 and CNT Genes are common regulated in 3 groups What functions/pathway are associated with CCT1, CNT1 regulated genes? Both CCT1 and CNT1 regulated Genes are associated with 9 GO functions such as defense response, response to UV-B, gibberellin biosynthetic process and 1 Cold-stress signaling pathway CCT1 regulated Genes are associated with photosynthesis, response to light CNT1 regulated Genes are associated protein ubiquitination, defense response, Gibberellin Signaling, Salicylic Acid Signaling

17 65 What functions/pathway are associated with CCT1, CNT1 regulated genes? Common associated functions/pathway Name Cold stress signaling # of Measured p-value in # of Measured p-value in # of Entities terpenoid biosynthetic process Entities in CCT1 CCT1 Entities in CNT1 CNT1 Biological Process anthocyanin-containing compound response to UV-B E biosynthetic process plant-type cell wall modification cellular response to hypoxia defense response lipid storage CNT defense response, incompatible interaction E CCT gibberellin biosynthetic process gibberellin biosynthetic process # of Entities lipid storage defense response, incompatible interaction plant-type cell wall modification response to UV-B defense response E terpenoid biosynthetic cellular process response to hypoxia Pathway anthocyanin-containing Cold-Stress Signaling compound biosynthetic process Both CCT1 and CNT1 regulated Genes are associated with 9 GO functions such as defense response, response to UV-B, gibberellin biosynthetic process and 1 Cold-stress signaling pathway

18 66 What functions/pathway are associated with CCT1, CNT1 regulated genes? Unique associated functions/pathway with CCT1 regulated genes Name # of Entities # of Measured Entities p-value cell differentiation cell fate specification cellulose catabolic process cysteine biosynthetic process detection of biotic stimulus divalent metal ion transport epidermal cell differentiation flavonoid biosynthetic process glucosinolate biosynthetic process leaf morphogenesis leaf senescence myo-inositol hexakisphosphate biosynthetic process E-05 oxidation-reduction process E-05 pentose-phosphate shunt E-08 photosynthesis E-08 photosynthesis, light harvesting photosynthesis, light reaction E-06 photosynthetic electron transport in photosystem I E-05 photosystem II assembly E-06 plastid organization E-07 protein-chromophore linkage E-05 reductive pentose-phosphate cycle regulation of multi-organism process response to blue light E-06 response to far red light E-07 response to karrikin response to red light E-07 response to sucrose E-08 rrna processing secondary metabolite biosynthetic process starch CCT1 biosynthetic regulated process Genes are associated with trichoblast differentiation E-06 unsaturated fatty acid biosynthetic process photosynthesis, response to light 33 unique associated function from Sub Network enrichment Analysis (SNEA) with GO biological categories

19 67 Name What functions/pathway are associated with CCT1, CNT1 regulated genes? Unique associated functions/pathway with CNT1 regulated genes # of Entities # of Measured Entities p-value abscisic acid-activated signaling pathway actin filament-based movement copper ion transport defense response by callose deposition defense response to fungus E-06 defense response to insect endoplasmic reticulum unfolded protein response ethylene biosynthetic process E-08 ethylene-activated signaling pathway E-05 hyperosmotic salinity response intracellular signal transduction jasmonic acid mediated signaling pathway killing of cells of other organism MAPK cascade meristem development meristem structural organization negative regulation of defense response negative regulation of programmed cell death photomorphogenesis pollen germination pollen tube growth protein ubiquitination purine nucleobase transport regulation of flower development regulation of hydrogen peroxide metabolic process Name # of Entitie # of Measure p-value s d Entities regulation of immune response regulation of innate immune response E-05 regulation of timing of transition from vegetative to reproductive phase respiratory burst involved in defense response response to bacterium response to chitin E-09 response to endoplasmic reticulum stress response to ethylene E-05 response to freezing response to fungus response to hypoxia response to jasmonic acid response to mechanical stimulus E-06 response to molecule of bacterial origin response to ozone response to red or far red light response to salicylic acid response to water deprivation response to wounding E-06 salicylic acid mediated signaling pathway sexual reproduction signal transduction stamen development stamen filament development systemic acquired resistance systemic acquired resistance, salicylic acid mediated signaling pathway vasculature development CRY1 and CRY2 interact with COP1 s E3 ubiquitin ligase enhancer, SPA1 (SUPPRESSOR OFPHYTOCHROME A 1), through their C and N termini, respectively (Lian et al., 2011; Liu et al., 2011; Zuo et al., 2011). COP1 has E3 ubiquitin ligase activity, and physically interacts with various substrates, such as HY5/HYH, HFR1, LAF1, and CONSTANS, to promote their ubiquitination and Defense response and immune response degradation to regulate photomorphogenesis and flowering (Holm et al., 2002; Seo et al., 2003; Yang et al., 2005; Liu et al., 2008).

20 68 What functions/pathway are associated with CCT1, CNT1 regulated genes? Unique associated functions/pathway with CNT1 regulated genes Gibberellin Signaling P-value: # of entities: 51 # of measured entities: 8 Gibberellins (GAs) are plant hormones that regulate growth and influence various developmental processes, including stem elongation, germination, dormancy, flowering, sex expression, enzyme induction, and leaf and fruit senescence

21 73 Conclusion What are all the known associations with CRY1 in the plant database? CRY1 is related with cryptochrome, phototropin, auxin signaling pathways. CRY1 mediates light signaling through direct inhibition with COP1. In Cryptochrome signaling pathway, COP1 plays an important role to regulate plant photoperiodism, hypocotyl growth, photomorphogenesis, phototropism through inhibiting HY5, CO, HFR1, MYB18. Focus on specific interactions: How does CRY1 regulates the phytohormone-response? CRY1 may affects phytohormone response through regulating the activation of COP1 and the synthesis of Auxin and GA.

22 74 Conclusion What genes are regulated by CRY1, CCT1, CNT1, respectively? Genes with differential expression were identified with a p value < 0.01 and fold change (FC) > Genes are common regulated in group CRY1 and CCT Genes are common regulated in group CRY1 and CNT Genes are common regulated in group CCT1 and CNT Genes are common regulated in 3 groups What functions/pathway are associated with CCT1, CNT1 regulated genes? Both CCT1 and CNT1 regulated Genes are associated with 9 GO functions such as defense response, response to UV-B, gibberellin biosynthetic process and 1 Cold-stress signaling pathway CCT1 regulated Genes are associated with photosynthesis, response to light CNT1 regulated Genes are associated protein ubiquitination, defense response, Gibberellin Signaling, Salicylic Acid Signaling

23 Thank you! Questions?

24 For more information please contact 台北市 114 內湖區新湖一路 36 巷 28 號 中華民國台灣 Ph: Fax: x1022