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Table 1 Induced genes with ≥ 2.0 fold change in expression level FDR (p-value ≤ 0.05)

From: Transcriptional profile of Pseudomonas syringae pv. phaseolicola NPS3121 in response to tissue extracts from a susceptible Phaseolus vulgarisL. cultivar

  

Fold change extract/control

Gene/ORF

Gene product

L

A

P

Cluster I Plant-bacteria interaction

pnlA

pectin lyase

3.0

  

PSPPH_A0072

Polygalacturonase

2.0

1.8

1.9

hopAK1

type III effector HopAK1

2.9

  

hopAT1

type III effector HopAT1

2.5

1.6

 

PSPPH_3107

type II and III secretion system family protein

3.7

2.6

1.8

PSPPH_2990

phytase domain protein

3.2

  

Cluster II Phaseolotoxin synthesis (Cluster Pht)

phtM

hypothetical protein

2.3

2.3

 

phtM-phtN

hypothetical protein (control)

2.1

2.1

 

phtO

hypothetical protein

2.1

2.1

 

amtA

L-arginine:lysine amidinotransferase, putative

2.9

2.5

 

phtQ

conserved hypothetical protein

2.7

2.1

 

phtS

adenylylsulfate kinase

2.7

3.2

 

phtT

membrane protein, putative

3.3

2.8

 

phtU

hypothetical protein

3.5

2.9

 

phtL

pyruvate phosphate dikinase, PEP/pyruvate binding domain protein

2.1

2.0

 

phtL

pyruvate phosphate dikinase, PEP/pyruvate binding domain protein(control)

2.6

2.3

 

Cluster III Bacterial metabolism

Ppc

phosphoenolpyruvate carboxylase

 

2.2

 

acsA

acetate-CoA ligase

 

3.0

 

PSPPH_1186

aldose 1-epimerase family protein

 

2.8

 

PSPPH_1256

transketolase, N-terminal subunit, putative

 

6.0

 

PSPPH_2070

nitrate reductase

 

2.2

 

PSPPH_3291

oxidoreductase, molybdopterin-binding

 

2.0

 

hutH2

histidine ammonia-lyase

2.0

1.5

 

nuoE

NADH-quinone oxidoreductase, E subunit

5.0

  

nuoF

NADH-quinone oxidoreductase, F subunit

2.4

  

nuoG

NADH-quinone oxidoreductase, G subunit

6.6

2.4

 

nuoH

NADH-quinone oxidoreductase, H subunit

4.3

1.7

 

PSPPH_2973

monooxygenase, NtaA/SnaA/SoxA family

2.3

  

PSPPH_2357

xylose operon regulatory protein

2.1

1.8

 

PSPPH_0756

glycosyl hydrolase, family 3

2.1

  

Cluster IV Adaptation responses

clpB2

clpB protein

2.2

1.5

 

groEL

chaperonin, 60 kDa

4.3

  

dnaK

dnaK protein

2.8

  

hslU

heat shock protein HslVU, ATPase subunit HslU

2.1

  

bfr2

Bacterioferritin

3.1

1.8

 

Cluster V Unknown function

PSPPH_3261

conserved hypothetical protein

4.4

  

PSPPH_3262

conserved hypothetical protein

4.4

  

PSPPH_1192

conserved hypothetical protein

2.8

  

PSPPH_2708

conserved hypothetical protein

2.5

  

PSPPH_1613

conserved hypothetical protein

2.3

  

PSPPH_1422

conserved hypothetical protein

2.2

  

PSPPH_4323

conserved hypothetical protein

2.0

  

PSPPH_3212

conserved hypothetical protein

4.9

2.3

 

PSPPH_3852

conserved hypothetical protein

2.5

1.6

 

PSPPH_3020

conserved hypothetical protein

 

2.1

 

PSPPH_1470

conserved hypothetical protein

 

2.2

1.9

Cluster VI None particular group

PSPPH_0804

methyl-accepting chemotaxis protein

3.2

  

PSPPH_2971

methyl-accepting chemotaxis transducer/sensory box protein

2.2

  

PSPPH_2994

transcriptional regulator, AraC family

2.3

  

PSPPH_1595

transcriptional regulator, GntR family

 

2.1

 

pbpC

penicillin-binding protein 1C

2.3

  

PSPPH_2053

membrane protein, putative

2.2

  

PSPPH_3868

ompA family protein

 

2.6

2.1

PSPPH_3993

acetyltransferase, GNAT family

3.0

  

PSPPH_0740

Ribosomal large subunit pseudouridine synthase D(Pseudouridine synthase) (Uracil hydrolyase)

2.6

1.6

 

PSPPH_2812

PAP2 superfamily protein

2.3

2.1

 

PSPPH_0920

S-type pyocin family protein

2.3

  

fadB

fatty oxidation complex, alpha subunit FadB

2.3

  

iucD

siderophore biosynthesis protein

2.0

  

PSPPH_2652

ABC transporter, ATP-binding protein

  

8.7

PSPPH_2653

lipopolysaccharide core biosynthesis domain protein

  

10.5

PSPPH_2654

lipoprotein, putative

  

6.4

  1. The table comprises all the genes that shown ≥ 2.0 fold change in expression level. L Bean leaf extract, A apoplastic fluid and P Bean pod extract. ORF nomenclature corresponding to 1448A reference sequenced strain. For a complete list of all statistically induced genes please consult Additional File 1.