Gene annotation: Nitrogen transporter families and N metabolism Annick Brun, Eva Lucic, Marc Buée,...

Gene annotation: Nitrogen

transporter families and N

metabolism

Annick Brun, Eva Lucic, Marc Buée, Barbara Montanini, Damien Blaudez , Francis Martin et Michel Chalot.

INRA-Nancy, 5 avril 2006

Unité Mixte de Recherche 1136INRA/Université Henri Poincaré

Interactions/Arbres Micro-OrganismesIFR "Génomique, Ecophysiologie et Ecologie fonctionnelle"

BP 239 - 54506 Vandoeuvre-lès-Nancy Cedex, France

Marmeisse, R., et al. (2005)

New Phytologist 163 (3), 481-498.

Laccaria bicolor proteases

Approximately 130 proteases in L. bicolor

0

10

20

30

40

50

60

CaspaseFungalysin

Calpain

Serine carboxypeptidase

Peptidase A4

Aspartyl peptidase

Laccaria

Phanerochaete

Caspase: involved in apoptosis

Fungalysin: membrane attachments, remodeling of cytoskeletal, apoptosis

Calpain: probably contributes to destruction of host tissues in infection (plant and animal infections)

Ascomycota cluster (Trichoderma, Aspergillus oryzae, A. nidulans)

Basidiomycota cluster 2 (Coprinus, Laccaria, Phanerochaete, Ustilago)

Potentially involved in the degradation of the OM

Basidiomycota (Hymenomycetes) cluster 1 (Coprinus, Laccaria, Phanerochaete, Coccidioides)

Basidiomycota cluster 3 (Coprinus, Laccaria, Phanerochaete, Ustilago)

HomosapiensAF188276trire12182616527

trire144471AN64872

AO090701000002AO090009000148

trire120934trire115265

AO090005001254AO090023000269

Lacbi5Lacbi15

Lacbi14Lacbi20

Lacbi1Phchr110202Phchr1138924128676

Lacbi10Phchr1135770

IrpexLacteus55670673Phchr1135608Phchr17287

Phchr1131827Phchr18656Phchr1140526

Phchr11404248663Phchr1138749

Phchr1127942Phchr1138081

Phchr1138453Phchr121562165

trire120738Phchr129558

AN68882AO090120000474

trire14184138410trire14577714530

AO090012000667AN21572AO090012000209

AN66862trire135965

AN81022AO090010000644

trire138078UM03860

AN29032AO090003000693

Coccidioidesimmitis6760077trire144744

Lacbi11Phchr1129956

UM04926AO090038000229

Lacbi8Cr00g034610

Lacbi12Cr00g042690


Lacbi21Lacbi22

Lacbi23Lacbi13Cr00g046680

Phchr1133748UM02043UM02178

Phchr1847084698468Phchr18471

Phchr1127295127228Phchr129984

Phchr14012579177929Amuscaria14494876

Phchr1130379UM00064AN44222AO090023000872

trire121534Lacbi18Phchr1126189

UM02597Lacbi3

Cr00g079010Lacbi9

Cr00g067990Phchr15147

Cr00g068000Phchr11952Phchr11966



Lacbi6Cr00g073510

Lacbi7Phchr12038

Phchr1302UM05736

Lacbi4Phchr18365

UM05205Lacbi16Lacbi17

Lacbi19Cr00g001290

Phchr16203Phchr19628Cr00g053780

UM05097trire120750

trire134765Lacbi2

Phchr1800880108011

100 changes

Number of gene models for the Oligopeptide Transporter (OPT) family

0

2

4

6

8

10

12

14

16

LaccariaCoprinus

Phanerochaete

UstilagoAspergillus

CryptococcusNeurospora

Lacbi eu2.Lbscf0020g01400

CC1G 12490.1


Phchr1fgenesh1 pg.C scaffold 1000108

Phchr 1gwh2.9.64.1

Phchr1 fgenesh1 pg.C scaffold 8000049

Phchr1fgenesh1 pm.C scaffold 5000008

Phchr1fgenesh1 pm.C scaffold 2000072

Phchr 1 e gww2.14.31.1

Phchr1 fgenesh1 pg.C scaffold 31000004


CC1G 11245.1

UM04347.1

CC1G 10290.1

CC1G 10984.1

Lacbie gww1.1.1077.1

Phchr1e gww2.11.74.1UM02387.1

CNAG 03013.1

Phchr1e gww2.12.45.1Lacbi e gww1.58.4.1CC1G 04679.1CC1G 04682.1

AN7597.3NC gi|28926364AN7188.3

NC gi|28923991

CNAG 01964.1SC Opt1pCNAG 04617.1

NC gi|28921107

SC Opt2pAN8374.3

NC gi|28924907NC gi|28923356

CNAG 05790.1

UM04574.1

NC gi|28921191

Phchr1 e gwh2.3.87.1Phchr1e gwh2.18.11.1Phchr1e gww2.3.99.1

Lacbi estExt GeneWisePlus worm.C 120102

AN6452.3

UM05968.1

Phchr1e gww2.1.135.1

Phchr1 e gww2.5.66.1Lacbi eu2.Lbscf0048g01450Phchr1e gww2.4.62.1

CC1G 10862.1

NC gi|28916765UM04028.1NC gi|28919713

Lacbi e gww1.12.26.1CC1G 11084.1

UM02763.1

NC gi|28920019

AN0700.3SC Ygl114wpUM02744.1

CNAG 05737.1Phchr1 gww2.3.118.1lacbi e gwh1.11.51.1CC1G 06323.1

0.2

Phanerochaete chrysosporium

Coprinus cinereusLaccaria bicolor

Cryptococcus neoformans

Ustilago maydis

Tetra / pentapeptide and glutathione transport

Marmeisse, R., et al. (2005)


Number of gene models for the Amino Acid -Polyamine - Organocation Transporter (APC)

family

0

10

20

30

40

50

LaccariaCoprinus

Phanerochaete

UstilagoAspergillus


HC gi|24210855



Lacbi e gww1.3.93.1


SC Put4pSC Agp2p

AF (Agp2) gi|66849835

Lacbi gww1.2.218.1

AM gi|4468097Lacbi eu2.Lbscf0001g02870

Lacbi estExt GeneWisePlus human.C 20647

AF (Dip5) gi|66852852

SC Dip5p

SC Lyp1p

Can1p

SC Alp1p

Lacbi eu2.Lbscf0117g00010Lacbi gww1.29.33.1

Lacbi gww1.37.8.1

NC AAP gi|2197048AF (Gap1) gi|66846710

PN (GAP)gi|41745538

SC Gap1p

SC Hip1p

SC Sam3pSC Tat2p

SC Bap2pSC Bap3pSC Tat1p

SC Agp1pSC Gnp1p

SC Agp3pLacbi eu2.Lbscf0001g14290

AF gi|21627813

Lbgwh1.35.18.1

SC Ssy1p

SC Tpo5pCN gi|57227536

Lacbi estExt GeneWisePlus human.C 250107Lacbi estExt GeneWisePlus human.C 24...Lacbi e gww1.25.34.1

SC Hnm1pSC Bio5p

NC (AAP-2) gi|38636415Lacbi e gwh1.9.72.1

Lacbi eu2.Lbscf0004g02440Lacbi estExt GeneWisePlus worm.C 400094

SC Uga4p

Lacbi e gww1.2.872.1

Lacbi gww1.50.6.1Lacbi e gww1.50.52.1


Lacbi eu2.Lbscf0054g00920CN gi|57223589Lacbi e gwh1.2.157.1

SC Mup3pLacbi e gww1.11.74.1



Lacbi e gww1.17.134.1Lacbi gwh1.15.75.1

AF (Mup) gi|66849555SC Mup1p

Lacbi gwh1.7.21.1

SC Avt1pLacbi gww1.11.44.1SC Avt3pSC Avt4p

Lacbi gww1.5.141.1SC Avt2p


SC Avt7pSC Avt6p

SC Avt5p

0.2

L-type Amino Acid Transporter

(LAT)

Yeast Amino Acid

Transporter (YAT)

Amino Acid/Choline Transporter

(ACT)

Amino Acid/Auxin Permease

(AAAP)

Number of gene models for the Ammonium Transporter (Amt) family

0

1

2

3

4

5

6

7

8

LaccariaCoprinus

Phanerochaete

UstilagoAspergillus


10 gene models

AMT expression by RT-PCR

Amino acids content

Glutamine content

AMT3.1

AMT1

AMT2.1

AMT13.2

AMT13.4

T0 -N48 +N24 Carpo

A

B

Comparison of relative gene numbers for each transporter family

0,00

1,00

2,00

3,00

4,00

5,00

6,00

AmmoniumTransporter

(Amt)

Nitrate/Nitriteporter (NNP)

Amino Acid-Polyamine-

Organocation(APC)

OligopeptideTransporter

(PTR)

OligopeptideTransporter

(OPT)

Ureatransporter

(DUR)

Cytosinepurine

permease

Ratio of number of genes

Lac/CopLac/PhaLac/UstLac/AspLac/CryLac/Neu

x2 - x4

Amino Acid Metabolism 494 Alanine and aspartate metabolism 25 Arginine and proline metabolism 34 Cysteine metabolism 9 Glutamate metabolism 32 Glycine, serine and threonine metabolism 46 Histidine metabolism 30 Lysine biosynthesis 22 Lysine degradation 46 Methionine metabolism 17 Phenylalanine metabolism 24 Phenylalanine, tyrosine and tryptophan biosynthesis 18 Tryptophan metabolism 92 Tyrosine metabolism 36 Urea cycle and metabolism of amino groups 20 Valine, leucine and isoleucine biosynthesis 12 Valine, leucine and isoleucine degradation 31

KEGG Metabolic Pathways

Energy Metabolism 130 ATP synthesis 17 Carbon fixation 19 Methane metabolism 3 Nitrogen metabolism 32 Oxidative phosphorylation 37 Photosynthesis 1 Reductive carboxylate cycle (CO2 fixation) 14 Sulfur m etabolism 7

GDH à NADPH

1,1,1

Glutamate synthase NADPH

1,1,1

GS (1,1,1)

Asparaginase 3,0,1

GDH à NAD 2,1,1

Asparagine synthase

1,1,1Aspartate Amino Transférase

(2,3,3)

Alanine Amino Transférase (1,1,1)

Laccaria laccataPhanerochaete chrysosporiumCryptococcus neoformans

2-nitropropane

dioxygenase (1,1,1)

Cystathionine gamma-lyase

4,1,5

Phenylalanine ammonia-lyase

2,1,2

D-amino-acid dehydrogenase1,2,1

Aminomethyltransferase 2,1,1

Carbamoyl-phosphate synthase 1,0,1

Carbonate dehydratase

9,3,0

Nitrate reductase1,1,1

Nitrite reductase 1,1,1

Cycle de l’urée

1

1

2

2

Arginase (1,1,1)

Argininosuccinate lyase (2,1,1)

Argininosuccinate synthase (2,1,1)

Ornithine carbamoyle transferase (2,1,1)

Carbamoyl-phosphate synthase (1,1,1)

Aminoacylase (1,1)

Acetylornithine aminotransferase

(2,2,2)

Glutamate N-acetyltranferase (1,1,1)

Amino-acid N-acetyltransferase (2,2,2)

Glutamate 5-kinase (1,1,1)

Ornithine decarboxyase

(1,1,1)

Urease (1,1,1)

Guanidinoacetate N-methyltransferase

(1,1,1)

Glutamate-5-semialdehyde

dehydrogenase(1,1,1)

Ornithine-oxo-acid aminotransferase

(1,1)

Pyrroline-5-carboxylate reductase (1,1)

Protein ARG5,6 (1,1)

Spermidine Synthase (1,1,1)

Chimeric Spermidine Synthase/ Saccharopine Dehydrogenase (1,2,1)

Laccaria laccataPhanerochaete chrysosporiumCryptococcus neoformans

Comparison of relative gene numbers for each amino acid pathway

0,00

0,50

1,00

1,50

2,00

Alanine andAspartate

metabolism

Arginine andproline

metabolism

Cysteinmetabolism

Glutamatemetabolism

Nitrogenmetabolism

Ureametabolism

Ratio of number of genes

Lac/CopLac/PhaLac/UstLac/AspLac/CryLac/Neu

Read, D. J. & Perez-Moreno, J.(2003)


Gene annotation: Nitrogen transporter families and N metabolism Annick Brun, Eva Lucic, Marc Buée,...

Documents

Transcript of Gene annotation: Nitrogen transporter families and N metabolism Annick Brun, Eva Lucic, Marc Buée,...