The genome sequence of Melampsora larici-populina the causal agent of the poplar rust disease...
-
Upload
joan-bowerman -
Category
Documents
-
view
219 -
download
3
Transcript of The genome sequence of Melampsora larici-populina the causal agent of the poplar rust disease...
The genome sequence of Melampsora larici-populinathe causal agent of the poplar rust disease
Inventory and annotation of Mlp Signaling genes
Mlp Summer workshop – INRA Nancy, August 20-21 2008
Duplessis Sébastien (INRA Nancy)
Tree/Microbe Interactions Joint Unit, INRA/University Nancy, UMR 1136 IAM
Nutrient changes
Biotic interactions(mating, plant infection)
Environmental stress (T°, water, light, …)
RESPONSE
nucleus
Adjustment
Mlp signaling genes
Nutrient changes
Biotic interactions
Environmental stress (T°, water, light…)
RESPONSE
nucleus
Adjustment
RTF
Transduction
Protein activity& protein expression
regulation
Gene expression regulation
Mlp signaling genes
G-
G- G-
PLC Ras
GPCR GPCR
RTK
GDP
PKC
MAPKKK
AC
PKA
cAMP
Ca2+ store IP3-R
CaM
Ca2+
Ca2+
CDPKs
nucleus
GTP
PIP2
IP3 DAG
PLC
TF
TF
TF
TF
PPases
MAPKKK MAPKKK
MAPKK MAPKK MAPKK
MAPK MAPK MAPK
G-
G- G-
Fungal signaling pathways
Sensing plant surface
Stomata (cuticle)penetration
Matthias Hahn, 2000
Why studying Mlp signaling genes?
Sporulation signal
Establishing the host-fungus interfaceFormation of haustorial structureDealing with plant defenses (oxidative, osmotic stress)Nutrient sensing
Selection of signaling genes based on litterature with a focus on plant/fungal interactions
=> large number of publications on transduction pathways involved in plant-pathogen interactions (deletion mutants, role in virulence, mating, filamentation…)
=> extensive studies in Saccharomyces cerevisiae
Since…
Complete inventory of signaling genes in Neurospora crassa (Borkovich et al, 2004)
Focus on transduction pathways in Magnaporthe grisea genome paper (Dean et al, 2005)
Comparative analyses of several genes families in Aspergilli sp (Lafon et al, FGB, 2006)
Recent review on fungal G-a protein related signaling (Li et al, 2007; Ann Rev Microbiol )
U. Maydis signaling gene overview (Garcia-Pedrajas et al, 2008)
Complete inventory in L. bicolor and 4 basidiomycetes (Martin et al, 2008; Duplessis et al, unpubl.)
Inventory of Mlp signaling genes
G-protein mediated signaling in N. crassa
Extensive catalog of signaling genes in N. crassa
Role of G-protein mediated signaling in M. grisea
Zhao et al, 2007 – Eukaryotic Cell
Role of MAPK-related signaling in pathogenic fungi
Mgrisea
Umaydis
Cneoformans
G-protein mediated signaling in fungi
Li et al, 2007 – Annual Review Microbiology
Compilation of sequences listed in N. crassa and fungal signaling reviews
About 30 classes of proteins were investigated =>
— histidine kinases, p21-activated kinases, germinal center kinases, oananiche cAMP dependent-protein kinase (PKA), protein kinase C (PKC), mitogen-activated protein kinases (MAPK, MAPKK, MAPKKK),
— G-protein coupled receptors (GPCR: glucose sensor, cAMP, PTH11, PheR, Stm1, …), heterotrimeric ( su) and monomeric (ras) G-proteins, Regulator of G-proteins (RGS)
— adenylate cyclase (AC), phosphodiesterase (PDE), phospholipase C (PLC)
— protein phosphatases (PP1, PP2A-2B-2C, PP5)
— Calcium-related signaling proteins (Ca2+-ATPases, Calmoduline (CaM), Ca2+ and/or CaM-binding protein, Ca2+ exchanger, Ca2+ permeable channel)
A large catalog of MANUALLY VALIDATED or CURATED GENE MODELS was established in L. bicolor and homologs (blastp/tblastn) were found in C. cinereus, P. chrysosporium, U. maydis and C. neoformans
Mlp signaling genes inventory - I
— Best blastp hits for all target proteins (asco- /basidio-mycetes)
— Core set of putative signaling proteins in Mlp
— Inspection of protein/gene sequence (JGI website)
— Alignment with closest homologs => missing N & C terminal regions— Typical polypeptidic domains in DB (Pfam, ProDom, Interpro, et al.)— Validation of structural domains and/or active sites
— Alignment with ESTs— Alignment with CDS of closest fungal homologs—Mlp introns, 5’ and 3’ ends inspection
— Enlarging the initial set by blastp & tblastn against best gene models (aa) / genome
— Curation -when needed- is performed in Artemis— Validation of models directly performed on JGI website after inspection of entire class
— Phylogenetic analysis, closest homologs, class/subclass attribution
— Annotation form on JGI Mlp website
Mlp signaling genes inventory - II
— Best blastp hits for all target proteins (asco- /basidio-mycetes)
— Core set of putative signaling proteins in Mlp
— Inspection of protein/gene sequence (JGI website)
— Alignment with closest homologs => missing N & C terminal regions— Typical polypeptidic domains in DB (Pfam, ProDom, Interpro, et al.)— Validation of structural domains and/or active sites
— Alignment with ESTs— Alignment with CDS of closest fungal homologs—Mlp introns, 5’ and 3’ ends inspection
— Enlarging the initial set by blastp & tblastn against best gene models (aa) / genome
— Curation -when needed- is performed in Artemis— Validation of models directly performed on JGI website after inspection of entire class
— Phylogenetic analysis, closest homologs, class/subclass attribution
— Annotation form on JGI Mlp website
Mlp signaling genes inventory - III
A total of 216 genes inspected
Validation/Annotation of Gabg proteins
Mlp signaling genes - of Gabg proteins
Mlp signaling genes – Summary of first inventory
M. larici-populina
41 genesSimilar number to U. Maydis &C. neoformans
Mlp signaling genes – Summary of first inventory
95 genes Calcium relatedCaM and CaM binding proteins, CDPKs, Calcineurine, Calcium channels, Calcium ATPases
16 GPCRs (3+ 1 Ste3, cAMP GPCRs, opsin-related GPCRs, mPR-GPCRs)
10+2 Histidine kinases
48 PPases (+ 32 extra sequences)
4 PLC
Mlp signaling genes – Example of Signaling genes
Mlp signaling genes
Mlp signaling genes
Emilie Tisserant & Benoît Hilselberger (INRA Nancy) Mlp Bioinfo
Mlp 98AG31
the 'bad guy' genomic team at INRA
UMR 1136 IAM Duplessis Sébastien & Francis Martin