umr 1136 inra/uhp tree-microbes interactions “physiology and functional genomic of transporters”...

UMR 1136 INRA/UHP

Tree-microbes Interactions “Physiology and functional genomic of transporters” team

Fungal pathogen : Melampsora larici-populina

Populus trichocarpa

Melampsora larici-populina Haustorium formation

Adapted from Mengden et al.,

Biotrophic interfaces Infected leaves

At a cytological level

Molecular and metabolic dialogue.

Entrainment of plant metabolism by phytopathogenic fungus

1. Sensing nitrogen or carbon availability

2. de-repression of specific metabolic pathways (transporters; enzymes)

3. Plant defence responses are taken up through AA permeases.

4. Plant invertase produce depolymerized sugars that both partners can use.

- Which role(s) transporters play in molecular dialogue, in exchange of nutrients ?

- Which transporteurs are key molecular markers for the interaction?

Divon and Fluhr, 2007

Toward an overview of Melamspora “transportome”……

© INRA

- TCDB: Transport Classification DataBase http://www.tcdb.org/ 550 families

-TransportDBhttp://www.membranetransport.org/

1. Retrieve proteins from DB

1. Analysis- Blastp - search for IPR, PFAM domains- search by KOG classification

And………manual curation (tblastn for some families)

http://www.tcdb.org/

http://www.membranetransport.org/

Plant pathogensSaprophytes

Plant Symbionts Animal pathogens

Increased genetic potential for transmembrane channel proteins

(water; solute as small carbohydrates (e.g. glycerol), urea, nitrate, CO2, H2O2, ions)

Family specific to plant-pathogen fungus (at least basidiomycetes). ascomycetes???

What makes a pathogen an obligate highly specialized pathogen?

1. Less ability to transport and likely utilize mineral nitrogen coumpounds.

2. an increased genetic potential for peptide uptake ...

Gene Family Number of Hits - Blastp (cut-off e-value=10-5) - Search using IPR number - Search using KOG nomenclature

Number of hits after curation

APC

-21 - 17 (IPR004841 aa associated permease) 10 (IPR004840aa permease) - 23 (aa transport)

- 20

OPT -25 -20 -19

-21

Eu

Ge

ne.

0005

0100

|Mel

lp1

: 93

456

EuG

ene.

0092

0002

Mel

lp1:

9605

1

estE

xt f

gen

esh

2 p

g.C

920

006|

Mel

lp1:

11...

PG

TG

170

16.2

|pre

dict

ed p

rote

in

EuG

ene.

0008

0166

|Mel

lp1:

959

42

EuGen

e.00

2701

25 M

ellp

1:88

574

EuGene.00710021|Mellp

1: 94692

estExt fgenesh2 pg.C 20111|M

ellp1:115025

EuGene.00020079|Mellp1: 88948

PGTG 03381.2|conserved hypothetical p...YPR194C (Opt2p)

Ca 87045975 (OPT6)

Ca 87045971 (OPT5)

Ca 87045969 (OPT4)

Ca 87045965 (OPT3)

Ca 87045961| (OPT2)

e gw1.10.26.1 Mellp1:34758

PGTG

06690.2|sexual differentiation p...

YJL212C (O

pt1p)C

a 68475288 (Opt1p)

Scpo 19112445 (Isp4p)

EuG

ene.00200025|Mellp1: 87295

EuG

ene.0

0120007| Mellp

1:84873

PG

TG

0284

1.2|con

served hypo

thetical p...

Ca

870

4597

9 (O

PT

7)

EuG

ene

.001

8012

1|M

ellp

1 8

6467

PG

TG

147

80.2

|pre

dict

ed p

rote

inE

uGen

e.00

2900

23| M

ellp

1:88

746

PG

TG 1

7677

.2|h

ypot

hetic

al p

rote

in

EuG

ene.

0023

0133

|Mel

lp1:

879

06

EuGen

e.00

1701

47|M

ellp

1: 8

6271

PGTG 15138.2|predict

ed protein

PGTG 15149.2|predicted protein

EuGene.00230137|Mellp1: 87910

fgenesh2 pg.23 156|Mellp1: 107483


estExt fgenesh2 pg.C 890028 Mellp1:11...

PGTG 07859.2|predicted proteinPGTG 20168.2|predicted protein

EuGene.00220005|Mellp1: 87588

PGTG 07855.2|conserved hypothetical p...



PGTG

02671.2|predicted protein

PG

TG


PG

TG


PG

TG

021

75.2

|predicte

d pro

tein

estExt fgenesh1 pg.C

150177 Mellp1:77...

PG

TG

10886.2|conserved hypothetical p...

ScY

gl114wp

Ca 87045983 (O

PT

8)E

uGene.00140070 M

ellp1:85440

PG

TG


Tetrapeptide signature

Mlp genes in tandem

Mlp genes

Phylogenetic analysis of the OPT family

NJ method, Poisson correction, 1000 bootstrap replicates (MEGA4)

Phc

hr1:

2592

9P

hch

r1 4

87

4

Phc

hr1:

108

Phc

hr1:

1027

6

Phc

hr1

1002

9

Lacb

i1:3

1290

6

Lacb

i1:3

0222

5

CC1G 12490.1

Phchr1:136917

Phchr1:9577

Lacbi1:300418CC1G 11245.1UM04347.1Ca 68475288 (Opt1p)

Scpo 19112445 (Isp4p)CNAG 01964.1

YJL212C (Opt1p)

YJL212C (Opt1p)(2)

CC1G 10984.1

CC1G 10290.1

Lacbi1:242631

Phchr1:135066

UM02387.1

e gw1.10.26.1 Mellp1:34758

PGTG 06690.2|sexual differentiation p...

CNAG 03013.1

Phchr1:134511

Lacbi1:255292

CC

1G 04679.1

CC

1G 04682.1

Ca 87045965 (OPT3)

Ca 87045961| (O

PT2)

Ca 87045969 (O

PT

4)

Ca 87045971 (O

PT

5)C

a 87045975 (OP

T6)

YP

R194C

(Opt2p)

YP

R1

94C

(Op

t2p

)(2)

CN

AG

04617.1

PG

TG

03

38

1.2

|con

serve

d h

ypo

the

tical p

...e

stExt fg

enesh

2 p

g.C

20

111

|Me

llp1:11

502

5E

uG

en

e.0

00

20

07

9|M

ellp

1: 88

94

8

Eu

Ge

ne

.00

27

01

25

Me

llp1

:88

57

4

EuG

en

e.00

710

02

1|Me

llp1: 9

469

2

PG

TG


EuG

ene.00080166|Mellp1: 95942


920006|Mellp1:11...

EuG

ene.00050100|Mellp1: 93456

EuG

ene.00920002 Mellp1:96051

CN

AG

057

90.1

UM

0457

4.1

EuG

ene.

0020

0025

|Mel

lp1:

872

95

EuG

ene.

0012

0007

| Mel

lp1:

8487

3

PGTG

028

41.2

|cons

erve

d hy

poth

etica

l p...

Ca

8704

5979

(OPT7

)

Lacb

i1:3

1091

3

Phchr

1:13

8073

CC1G 1

0862

.1

UM04028.1

Phchr1:132680

Phchr1:131282

UM05968.1

CC1G 02463.1

Lacbi1:190652

Phchr1:137519

Phchr1:127754Phchr1:130472

EuGene.00180121|Mellp1 86467


EuGene.00290023| Mellp1:88746PGTG 17677.2|hypothetical protein

EuGene.00230133|Mellp1: 87906EuGene.00170147|Mellp1: 86271



EuGene.00230137|Mellp1: 87910





PGTG


EuGene.00220005|M

ellp1: 87588

PG

TG 07855.2|conserved hypothetical p...

PG

TG 02060.2|predicted protein

PG


PG

TG


PG

TG


PG

TG

02025.2|pred

icted protein

PG

TG


Lacbi1: 250173

CC

1G 11084.1

UM

02763.1


150177 Mellp1:77...

PG

TG


ScY

gl114wp

ScY

gl1

14

wp

(2)

Ca 87045983 (O

PT

8)

Eu

Ge

ne

.00

14

00

70

Me

llp1

:85

44

0P

GT

G 1

35

61

.2|co

nse

rved

hyp

oth

etical p

...U

M02744.1

CN

AG

05737.1P

hchr1:36419Lacbi1:234936

CC1G 06323.1

0.2

Phc

hr1:

2592

9P

hchr

1 48

74

Phc

hr1:

108

Phc

hr1:

1027

6

Phc

hr1

1002

9

Lacb

i1:3

1290

6

Lacb

i1:3

0222

5

CC1G 12490.1

Phchr1:136917

Phchr1:9577

Lacbi1:300418CC1G 11245.1UM04347.1Ca 68475288 (Opt1p)Scpo 19112445 (Isp4p)

CNAG 01964.1

YJL212C (Opt1p)

YJL212C (Opt1p)(2)

CC1G 10984.1

CC1G 10290.1

Lacbi1:242631

Phchr1:135066

UM02387.1

e gw1.10.26.1 Mellp1:34758

PGTG 06690.2|sexual differentiation p...

CNAG 03013.1

Phchr1:134511

Lacbi1:255292

CC

1G 04679.1

CC

1G 04682.1

Ca 87045965 (OPT3)

Ca 87045961| (O

PT2)

Ca 87045969 (O

PT

4)

Ca 87045971 (O

PT

5)C

a 87045975 (OP

T6)

YP

R194C

(Opt2p)

YP

R194C

(Opt2p)(2)

CN

AG

04617.1P

GT

G 03381.2|conserved hypothetical p...


20111|Mellp1:115025

EuG

ene.00020079|Mellp1: 88948

EuG

ene.00270125 Mellp1:88574

EuG

ene.00710021|Mellp1: 94692

PG

TG


EuG

ene.00080166|Mellp1: 95942


920006|Mellp1:11...

EuG

ene.00050100|Mellp1: 93456

EuG

ene.00920002 Mellp1:96051

CN

AG

057

90.1

UM

0457

4.1

EuG

ene.

0020

0025

|Mel

lp1:

872

95

EuG

ene.

0012

0007

| Mel

lp1:

8487

3

PGTG 0

2841

.2|co

nser

ved

hypo

thet

ical p

...

Ca

8704

5979

(OPT7

)

Lacb

i1:3

1091

3

Phchr

1:13

8073

CC1G 1

0862

.1

UM04028.1

Phchr1:132680

Phchr1:131282

UM05968.1

CC1G 02463.1

Lacbi1:190652

Phchr1:137519

Phchr1:127754Phchr1:130472

EuGene.00180121|Mellp1 86467


EuGene.00290023| Mellp1:88746PGTG 17677.2|hypothetical protein

EuGene.00230133|Mellp1: 87906EuGene.00170147|Mellp1: 86271



EuGene.00230137|Mellp1: 87910





PGTG


EuGene.00220005|M

ellp1: 87588

PGTG


PG


PG


PG

TG


PG

TG


PG

TG


PG

TG


Lacbi1: 250173

CC

1G 11084.1

UM

02763.1


150177 Mellp1:77...

PG

TG


ScY

gl114wp

ScY

gl114wp(2)

Ca 87045983 (O

PT

8)

EuG

ene.00140070 Mellp1:85440

PG

TG

13561.2|conserved hypothetical p...U

M02744.1

CN

AG

05737.1P

hchr1:36419Lacbi1:234936

CC1G 06323.1

0.2

L. bicolor :2P. chrysosporium:6C. cinerea: 2C. neoformans: 0

U. maydis: 2P.graminis: 14M.larici populina: 8

Phylogenetic analysis of the APC family

Lacb

i1:1

4300

7

CC

1G 0

1034

.1

Af2

93 6

6849

835

Agp

2

YB

R13

2C A

GP

2

CN

AG

053

45.1

CN

AG

009

12.1

NC

U07

129.

1

YO

R34

8C P

UT4

En

6303

83 P

utXN

CU

0072

1.1

Phc

hr1:

1277

17

Lacb

i1:2

4532

9

Lacb

i1:3

0859

5

Lacb

i1:3

0859

7

Lacbi1:18801

5

Hc 74663954 G

AP1UM03325.1

CNAG 06070.1

CNAG 02539.1

estExt Genewise1Plus.C 350029 Mellp1:...

Ufa 15485607 AAT1p

e gw1.6.48.1 Mellp1:34045

Ufa 1764097 AAT2

e gw1.26.16.1 Mellp1:37139

estExt Genewise1Plus.C 880007 Mellp1:...fgenesh1 pg.C scaffold 136000006 Mell...UM05269.1

NCU04468.1PENCH 74638092 Mtr

UM04186.1

Lacbi1:300838CC1G 03688.1

Am 4468097 AAT1

Phchr1:135376

CNAG 01118.1

UM06012.1

e gw1.19.49.1 Mellp1:36162

e gw1.19.48.1 Mellp1:36184 Homology P...

estExt fgenesh1 kg.C 250027 Mellp1:72...

Ufa 44682842 AAT3p

EuGene.00360058 Mellp1:90273 Homology...

e gw1.36.25.1 Mellp1:38039

e gw1.97.7.1 Mellp1:41039

Lacbi1:182249

CC1G 04288.1

Phchr1:133012

YPL265W DIP5

UM03700.1

CNAG 00552.1

CN

AG

00597.1

NCU

05168.1

YNL268W

LYP1

YN

L270C A

PL1

YE

L063C C

AN

1

Lacbi1:157448

CC

1G 02032.1

Phchr1:4184

Af 21627813 LY

P

Lacbi1:301980P

hchr1:135277

YF

L055W A

GP

3

UM

05035.1A

f293 66846710 Gap1

PE

NC

H 41745538 G

AP

NC

U05830.1

NC

U02783.1

UM

00343.1

NC

U03509 N

aap1

CC

1G 07764.1

Lacbi1:143243 Lacbi1:296817

Gm

62361830

YLL061W

MM

P1

YP

L274W S

AM

3

YG

R191W

HIP

1

YK

R039W

GA

P1

YO

L020W TA

T2

YB

R069C

TAT1

YC

L025C A

GP1

YDR

508C GN

P1

YBR068C BAP2

YDR046C BAP3

NC

U00

648.

1 UM

0340

0.1

Phc

hr1:

4672

UM

0469

5.1

fgen

esh2

pg.

76 3

8 M

ellp

1:11

3062

fgen

esh2

pg.

76 4

4 M

ellp

1:11

3068

CC

1G 1

1390

.1P

hchr

1:13

9236

Lacb

i1:1

8555

7C

NA

G 0

5952

.1

Lacb

i1:1

8551

5

Lacb

i1:2

5228

0SC

HPO

152

1439

6

CN

AG

051

19.1

UM

0214

6.1

NCU

0577

6.1

CNAG 0

5017

.1

CNAG 0

2455

.1

En 746

6583

5 Gab

A

UM02791.1 YNR056C BIO

5

YGL077C HNM1

Lacb

i1:2

3428

9

CC1G 09113.1

Phchr1:122343

Phchr1:27552

CNAG 01535.1

UM02154.1

estExt Genewise1Plus.C 90054 Mellp1:4...

NCU00765 AAP2

Lacbi1:191715

Lacbi1:311288

CC1G 02731.1

Phchr1:125336

NCU07175.1

e gw1.68.5.1 Mellp1:40209e gw1.32.15.1 Mellp1:37702Lacbi1:244309

Phchr1:133143YDL210W UGA4

UM03522.1Phchr1:135275Phchr1:5862

Phchr1:26909Lacbi1:142738

Lacbi1:254728


YHL036W MUP3Lacbi1:229402

CC1G 04186.1Phchr1:37473

UM01762.1CNAGJEC21 57223589

CNAG 03955.1


Af293 66844481 MUPNCU02195.1CC1G 07574.1

CNAG 05950.1

Lacbi1:249579

Lacbi1:298603

Lacbi1:298666

Phchr1:126209NCU07754.1

NCU04942.1YGR055W M

UP1

Lacbi1:166470C

C1G

04074.1

CC

1G 08094.1

Phchr1:38005

Lacbi1:250926

CC

1G 09573.1

EuGene.00120043 M

ellp1:84909

Phchr1:134349NCU08880.1

UM

03258.1

CN

AG 06541.1

UM

02459.1

Phchr:185U

M00056.1

NC

U06619.1 A

AP

1

CN

AG

01074.1

CN

AG

05685.1

Lacbi1:141811

CC

1G 07103.1P

hchr:45006

CN

AG

06828.1

estExt G

enewise1.C

40004 Mellp1:41988

NC

U03783.1

YK

L146W A

VT

3

UM

02946.1

YN

L101W A

VT

4

Ph

chr1:677

4

CC

1G 03673.1

UM

02159.1gw

1.6.234.1 Mellp1:30092

CN

AG

05996.1

Lacbi1:247252

CC

1G 01897.1

UM

02253.1gw

1.87.12.1 Mellp1:24482

CN

AG

03988.1N

CU

01481.1Y

EL064C

AV

T2Y

BL089W

AV

T5

YE

R119C

AV

T6

YIL088C

AV

T7estExt fgenesh2 pg.C

120046 Mellp1:11...

UM

02221.1

CNAG 01904.1

Phchr:137449

Lacbi1:187989

CC1G 00905.1

0.2

YAT

ACT

LAT

AAAP

NJ method, Poisson correction, 1000 bootstrap replicates (MEGA4)

Lacb

i1:1

4300

7

CC

1G 0

1034

.1

Af2

93 6

6849

835

Agp

2

YB

R13

2C A

GP

2

CN

AG

053

45.1

CN

AG

009

12.1

NC

U07

129.

1

YO

R34

8C P

UT

4

En

6303

83 P

utX

NC

U00

721.

1

Phc

hr1:

1277

17

Lacb

i1:2

4532

9

Lacb

i1:3

0859

5

Lacb

i1:3

0859

7

Lacb

i1:188

015

Hc 74663954 GAP1

UM03325.1

CNAG 06070.1

CNAG 02539.1

estExt Genewise1Plus.C 350029 M

ellp1:...

Ufa 15485607 AAT1p

e gw1.6.48.1 Mellp1:34045

Ufa 1764097 AAT2

e gw1.26.16.1 Mellp1:37139

estExt Genewise1Plus.C 880007 Mellp1:...fgenesh1 pg.C scaffold 136000006 Mell...UM05269.1

NCU04468.1PENCH 74638092 Mtr

UM04186.1

Lacbi1:300838CC1G 03688.1

Am 4468097 AAT1

Phchr1:135376

CNAG 01118.1

UM06012.1

e gw1.19.49.1 Mellp1:36162

e gw1.19.48.1 Mellp1:36184 Homology P...

estExt fgenesh1 kg.C 250027 Mellp1:72...

Ufa 44682842 AAT3p

EuGene.00360058 Mellp1:90273 Homology...

e gw1.36.25.1 Mellp1:38039

e gw1.97.7.1 Mellp1:41039

Lacbi1:182249

CC1G 04288.1

Phchr1:133012

YPL265W DIP5

UM03700.1

CNAG 00552.1

CN

AG

00597.1

NC

U05168.1

YNL268W

LYP1

YN

L270C A

PL1

YE

L063C C

AN

1 Lacbi1:157448

CC

1G 02032.1

Phchr1:4184

Af 21627813 LY

P

Lacbi1:301980P

hchr1:135277

YF

L055W A

GP

3

UM

05035.1A

f293 66846710 Gap1

PE

NC

H 41745538 G

AP

NC

U05830.1

NC

U02783.1

UM

00343.1

NC

U03509 N

aap1

CC

1G 07764.1

Lacbi1:143243 Lacbi1:296817

Gm

62361830

YLL061W

MM

P1

YP

L274W S

AM

3

YG

R191W

HIP

1

YK

R039W

GA

P1

YO

L020W TA

T2

YB

R069C

TAT1

YC

L025C A

GP

1

YDR

508C G

NP1

YBR068C

BAP2

YDR046C BAP3

NC

U00

648.

1 UM

0340

0.1

Phc

hr1:

4672

UM

0469

5.1

fgen

esh2

pg.

76 3

8 M

ellp

1:11

3062

Uromyces fabae genes (PIG, permeases)

Mlp genes

tandem

- OPT : example of how evolution has shaped Mlp genome to suit specialized pathogenic lifestyle.

- Role of nutrition in the host-pathogen relationship with respect to host restriction and evolution towards obligate pathogenesis

Conclusion

Small number of transporter-encoding gene models EST support

umr 1136 inra/uhp tree-microbes interactions “physiology and functional genomic of transporters”...

Documents

predicted proteinpgtg

predicted proteineugene

hypothetical proteineugene

aa transport

plantpathogen fungus

c 20111mellp1

c 920006mellp1

specialized pathogen