Table 1 Frankia alni ACN14a genes up and down regulated in N-free condition supplemented with AgLTP24 versus N-free condition.

From: Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24

Label

Name

Log2 FoldChange

padj

Annotation

FRAAL1882

5.01

5.57E−03

Small heat shock protein

FRAAL4716

4.14

3.89E−02

Putative oxidoreductase

FRAAL6701

groL

4.10

4.24E−04

Chaperone Hsp60 (GroEL), part of GroE chaperone system

FRAAL4715

3.87

3.95E−02

Putative transcriptional regulator of the TetR family

FRAAL1884

ribD

3.55

1.10E−03

Putative riboflavin/cytosine deaminase (partial)

FRAAL0166

3.46

4.42E−03

Conserved hypothetical protein; putative membrane protein

FRAAL5655

sdhB

3.40

4.90E−03

Succinate dehydrogenase iron-sulfur protein

FRAAL1764

lon

3.29

2.11E−03

DNA-binding ATP-dependent protease La; heat shock K-protein

FRAAL2325

3.23

4.90E−03

putative 3-(3-hydroxy-phenyl)propionate hydroxylase, FAD/NAD(P)-binding

FRAAL5654

sdhA

3.10

5.06E−03

Succinate dehydrogenase flavoprotein subunit A

FRAAL6439

3.07

1.30E−02

Putative MoxR-like regulatory protein

FRAAL5653

sdhC

3.04

5.57E−03

Succinate dehydrogenase cytochrome B subunit

FRAAL6438

2.95

8.43E−03

Hypothetical protein

FRAAL6814

nifV

2.94

4.90E−03

Nitrogenase-associated homocitrate synthase

FRAAL5037

livG

2.88

7.01E−03

High-affinity branched-chain amino acid transport protein (ABC superfamily, atp_bind)

FRAAL6643

clpB

2.82

4.90E−03

ATP-dependent protease, Hsp 100, part of multi-chaperone system with DnaK, DnaJ, and GrpE

FRAAL0168

2.81

1.56E−02

Hypothetical protein; putative signal peptide; putative Dyp-type peroxidase domain

FRAAL6804

nifZ

2.79

5.06E−03

NifZ protein

FRAAL4308

copD

2.79

7.90E−03

Copper resistance membrane protein

FRAAL2326

2.76

2.55E−02

Hypothetical protein; putative serine-threonine protein kinase

FRAAL0988

2.69

5.06E−03

Putative regulator

FRAAL6807

2.62

4.62E−03

Conserved hypothetical protein

FRAAL6813

nifH

2.62

1.11E−02

Nitrogenase iron protein (NITROGENASE component II) (nitrogenase Fe protein) (nitrogenase reductase, dinitrogenase reductase)

FRAAL1134

groL

2.61

5.55E−03

Chaperone Hsp60 (GroEL), part of GroE chaperone system

FRAAL0989

2.61

1.16E−02

Cation-transporting P-type ATPase A

FRAAL6812

nifD

2.60

9.91E−03

Nitrogenase molybdenum-iron protein alpha chain (nitrogenase component I) (Dinitrogenase)

FRAAL6811

nifK

2.59

1.65E−02

Nitrogenase molybdenum-iron protein beta chain (nitrogenase component I) (dinitrogenase)

FRAAL1133

groS

2.58

6.17E−03

Chaperone Hsp10 (GroES), part of GroE chaperone system

FRAAL6638

2.57

1.41E−02

Hypothetical protein

FRAAL6640

grpE

2.56

1.52E−02

Heat shock protein (HSP-70 cofactor)

FRAAL4648

2.50

3.88E−02

(2,3-dihydroxybenzoyl)adenylate synthase (2,3-dihydroxybenzoate-AMP ligase; Dihydroxybenzoic acid-activating enzyme)

FRAAL4645

cetJ2

2.48

2.55E−02

Cupin domain-containing protein; fralnimycin synthesis

FRAAL6859

2.47

1.43E−02

Cupin domain-containing protein; fralnimycin synthesis

FRAAL4644

cetJ3

2.42

2.98E−02

Conserved hypothetical protein

FRAAL2286

2.42

1.16E−02

Putative WhiB-family transcriptional regulator; putative role in cell cycle control

FRAAL6639

dnaK

2.41

2.01E−02

Chaperone Hsp70 in DNA biosynthesis/cell division

FRAAL5036

2.38

1.21E−02

Putative high-affinity branched-chain amino acid transport protein (ABC superfamily, atp_bind)

FRAAL1506

2.36

4.90E−03

Hypothetical protein

FRAAL4245

2.35

7.01E−03

Hypothetical integral membrane protein

FRAAL1607

2.34

4.35E−02

Putative integral membrane protein

FRAAL6437

2.34

1.64E−02

Putative transglutaminase, putative cysteine proteases, putative membrane protein

FRAAL5911

2.33

1.63E−02

Hypothetical protein; putative signal peptide

FRAAL6335

2.32

2.91E−02

Hypothetical protein

FRAAL6641

dnaJ

2.32

1.98E−02

Heat shock protein (Hsp40), co-chaperone with DnaK

FRAAL6197

2.28

4.92E−02

Hypothetical protein; putative signal peptide

FRAAL6808

nifX

2.26

4.59E−02

NifX protein

FRAAL0596

2.20

4.24E−04

Putative regulator

FRAAL1002

2.13

3.31E−02

Putative cytochrome C biogenesis membrane protein

FRAAL6802

erpA

2.13

2.19E−02

Conserved hypothetical protein; Thioredoxin-like domain

FRAAL6860

2.13

3.70E−02

Putative 1L-myo-inositol-1-phosphate synthase

FRAAL0060

2.11

1.21E−02

Putative transcription regulator protein

FRAAL6803

nifB

2.08

2.09E−02

FeMo cofactor biosynthesis protein nifB

FRAAL1763

2.07

2.19E−02

Hypothetical protein

FRAAL6337

2.06

1.68E−02

Hypothetical protein

FRAAL5912

sigE

2.01

4.97E−02

Putative RNA polymerase ECF-subfamily sigma factor

FRAAL1001

1.98

2.55E−02

Thiol:disulfide interchange protein helX precursor (Cytochrome c biogenesis protein helX)

FRAAL4136

1.98

3.31E−02

Putative iron sulphur protein (Putative secreted protein)

FRAAL4747

1.97

2.80E−02

Putative stress-inducible protein; putative adenine nucleotide-binding domain

FRAAL6642

1.97

1.72E−02

Putative heat shock protein hspR

FRAAL6118

1.91

1.43E−02

Putative glycosyltransferase

FRAAL5016

1.91

4.59E−02

Hypothetical protein

FRAAL5461

1.82

2.25E−02

Putative Epoxide hydratase

FRAAL5462

1.80

5.06E−03

Putative TetR-family transcriptional regulator

FRAAL3287

1.76

2.20E−02

Glycine-rich cell wall structural protein

FRAAL1786

1.74

2.20E−02

Hypothetical protein

FRAAL4148

1.73

2.91E−02

Hypothetical protein

FRAAL3704

1.73

4.65E−02

Putative TetR-family transcriptional regulator

FRAAL5121

1.70

4.15E−02

Putative integral membrane protein

FRAAL4491

oxyR

1.69

5.06E−03

Transcriptional regulator of oxidative stress, regulates intracellular hydrogen peroxide (LysR family)

FRAAL4781

1.68

4.22E−02

Conserved hypothetical protein

FRAAL0075

1.67

2.98E−02

Conserved hypothetical protein

FRAAL3899

1.66

1.98E−02

Putative ATP/GTP binding protein; putative beta WD-40 repeat and TPR domains

FRAAL0863

1.66

1.21E−02

RicinB lectin

FRAAL0081

1.65

1.21E−02

Manganese transport system ATP-binding protein

FRAAL1576

1.63

4.22E−02

Hypothetical protein; putative signal peptide

FRAAL6408

1.63

5.06E−03

Conserved protein of unknown function

FRAAL6119

1.62

1.64E−02

Putative succinoglycan biosynthesis protein

FRAAL5109

qcrB

1.61

2.19E−02

Ubiquinol-cytochrome c reductase cytochrome b subunit

FRAAL1508

1.59

5.06E−03

Hypothetical protein; putative membrane protein

FRAAL5649

1.59

1.21E−02

Integral membrane protein with Succinyl-CoA ligase domain

FRAAL6227

1.52

1.86E−02

Putative NADH dehydrogenase

FRAAL5552

1.51

2.58E−02

Hypothetical protein; putative signal peptide

FRAAL4430

1.47

1.21E−02

Hypothetical protein; putative signal peptide

FRAAL1766

1.45

3.88E−02

Putative pirin-like protein

FRAAL1505

murI

1.43

2.98E−02

Glutamate racemase

FRAAL0938

1.43

3.56E−02

Putative molybdopterin converting factor

FRAAL1699

groL

1.39

1.56E−02

Chaperone Hsp60 (GroEL), part of GroE chaperone system

FRAAL4024

1.38

2.79E−02

Putative monooxygenase with luciferase-like ATPase activity

FRAAL1427

1.35

4.97E−02

Short-chain dehydrogenase/oxidoreductase with several Glucose/ribitol dehydrogenase and 17-Beta hydroxysteroid dehydrogenase domains

FRAAL6502

1.35

6.17E−03

conserved hypothetical protein

FRAAL1154

accD

1.33

2.55E−02

Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (ACCASE beta chain)

FRAAL0924

1.33

4.97E−02

Putative MarR-family transcriptional regulator; putative signal peptide

FRAAL2626

1.33

1.43E−02

Hypothetical protein

FRAAL5351

1.31

4.90E−02

Putative Na + /H + antiporter; putative membrane protein

FRAAL5685

1.29

4.45E−02

Membrane-bound Ribonuclease BN

FRAAL5137

1.29

1.88E−02

Hypothetical protein

FRAAL4890

1.25

2.19E−02

Putative transcriptional regulator (partial match)

FRAAL1577

1.24

3.56E−02

Short-chain dehydrogenase, NAD(P)-binding domain

FRAAL1016

1.23

1.65E−02

Hypothetical protein

FRAAL0229

1.22

4.57E−02

Hypothetical protein

FRAAL6260

1.22

2.55E−02

Secreted subtilisin-like serine protease

FRAAL2542

1.21

2.01E−02

Non-ribosomal peptide synthetase

FRAAL1157

sucD

1.13

3.88E−02

Succinyl-CoA synthetase, alpha subunit, NAD(P)-binding

FRAAL5156

lipB

1.11

4.85E−02

Lipoyltransferase (Lipoyl-[acyl-carrier protein]-protein -N-lipoyltransferase) (Lipoate-protein ligase B)

FRAAL5646

fecD

1.02

4.97E−02

Citrate-dependent iron (III) transport protein (ABC superfamily, membrane)

FRAAL4818

1.02

1.16E−02

Hypothetical protein

FRAAL6723

1.01

3.51E−02

Hypothetical protein; putative ATPase domain

FRAAL3352

− 1.02

1.63E−02

Putative phosphatidylinositol diacylglycerol-lyase

FRAAL0541

− 1.05

2.19E−02

Putative dehydrogenase/oxidoreductase

FRAAL0375

− 1.11

2.97E−02

Putative GntR-family transcriptional regulator

FRAAL0640

− 1.13

1.21E−02

Putative secreted cell wall peptidase

FRAAL2594

− 1.16

1.98E−02

Putative epoxide hydrolase

FRAAL1590

− 1.19

2.80E−03

Putative conserved protein; glyoxalase and dihydroxybiphenyl dioxygenase domain

FRAAL2705

− 1.19

2.98E−02

Hypothetical protein

FRAAL6479

− 1.20

3.47E−02

Short− chain dehydrogenase

FRAAL3995

− 1.22

3.58E−02

Putative hydrolase

FRAAL2484

− 1.32

2.19E−02

Conserved hypothetical protein

FRAAL3997

− 1.38

7.64E−03

Conserved hypothetical protein

FRAAL4133

− 1.42

3.45E−02

Putative glutathione S-transferase enzyme with thioredoxin-like domain

FRAAL2519

− 1.43

3.09E−02

Putative short-chain dehydrogenase

FRAAL2937

− 1.45

2.25E−02

Hypothetical protein

FRAAL3838

− 1.46

4.97E−02

Hypothetical protein; putative signal peptide

FRAAL3585

− 1.48

3.31E−02

Putative esterase

FRAAL3774

− 1.54

2.55E−02

hypothetical protein

FRAAL1571

− 1.57

1.64E−02

Putative acyl-CoA dehydrogenase

FRAAL0744

− 1.59

5.55E−03

Hypothetical protein; putative endonuclease domain

FRAAL2938

− 1.62

8.43E−03

Putative protein kinase

FRAAL3965

− 1.63

2.11E−02

Hypothetical protein; putative signal peptide

FRAAL2509

− 1.63

3.31E−02

Putative 3-ketoacyl-CoA thiolase

FRAAL0201

− 1.67

2.98E−02

Putative cytochrome P450 reductase

FRAAL3923

− 1.69

4.22E−02

Putative cytochrome P450

FRAAL0376

− 1.71

1.88E−02

Cytosine/purine/uracil/thiamine/allantoin permease family protein

FRAAL4527

− 1.71

5.57E−03

Putative Glycoside hydrolase

FRAAL2508

− 1.73

2.63E−02

Protein associated with acetyl-CoA C-acyltransferase

FRAAL0316

− 1.76

1.43E−02

Carveol dehydrogenase

FRAAL0200

− 1.87

6.87E−04

NAD+-dependent aldehyde dehydrogenase

FRAAL2706

− 1.89

1.98E−02

Hypothetical protein

FRAAL0348

− 1.90

1.30E−02

Putative 6-methylsalicylic acid synthase

FRAAL2076

narK

− 2.00

2.91E−02

Nitrite membrane extrusion protein

FRAAL2707

− 2.00

1.43E−02

Coenzyme PQQ synthesis protein

FRAAL2513

− 2.00

2.19E−02

Putative Acyl-CoA dehydrogenase

FRAAL3766

− 2.65

1.52E−02

Hypothetical protein

  1. p-value adjusted (padj) ≤ 0.05, up-regulated genes: Log2FoldChange ≥ 1, Down-regulated genes Log2FoldChange ≤  − 1. Gene label, name and annotation come from the Genoscope database.