Table 1 Candidate genes possibly responsible for the anti-inflammatory properties of P. freudenreichii.

From: Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study

Gene locus tag

Gene name

Localisationa

Rankingb

Correlationc

Function/product

Inactivationd

G

T

P

PFCIRM121_10305

eno1

C

P1

  

(−) 0.4

Main glycolytic pathways/EC number 4.2.1.11, glycolysis enzyme, 2-Phospho-D-glycerate < = > Phosphoenolpyruvate + H2O

Yes

PFCIRM129_03920

merA

C

P2

(+) 0.079

 

(+) 0.245

Metabolism of coenzymes and prothetic groups/Pyridine nucleotide-disulphide oxidoreductase

No

PFCIRM129_05460

slpE

PSE

P3

(+) 0.030

(+) 0.148

(+) 0.205

Cell wall/surface protein containig 3 SLH domains predicted by HMM Pfam

Yes

PFCIRM129_01545

slpF

PSE

P4

  

(+) 0.205

Cell wall/surface layer protein containing 3 SLH domains predicted by HMM Pfam

Yes

PFCIRM129_10100

groL2

C

P5

(+) 0.052

 

(−) 0.205

Protein Folding/protein chaperon

Not tested

PFCIRM129_10785

pouf 10785

PSE

T1

 

(+) 0.761

 

No function/No homology found in the databases

No

PFCIRM121_08040

slpC1

PSE

T2

(−) 0.231

(−) 0.745

 

Cell wall/surface protein containing 1 SLH domain predicted by HMM Pfam

No

PFCIRM129_00525

hsdM3

C

T3

(+) 0.175

(+) 0.744

 

DNA restriction and modification/Type I site- specific DNA methylase

Yes

PFCIRM129_07765

lacl1

C

T4

 

(+) 0.693

 

Transcription regulation/transcriptional regulator, arabinose operon epressor

No

PFCIRM121_08300

acn

C

T5

 

(−) 0.683

 

TCA cycle/Aconitase

No

PFCIRM129_10930

pouf 10930

C

G1

(+) 0.263

(+) 0.518

 

No function/No homology found in the databases

No

PFCIRM129_10925

pep

C

G2

(+) 0.263

  

Metabolism of amino acids and related molecules/peptidase

Yes

PFCIRM129_04790

pouf 04790

C

G3

(+) 0.261

(+) 0.603

 

No function/No homology found in the databases

No

PFCIRM121_08235

pouf 08235

PSE

G4

(−) 0.245

  

No function/Highly conserved among bacteria

Yes

PFCIRM121_00805

dcuA

M

G5

(−) 0.232

  

Transport or binding of amino-acids/C4-dicarboxylates transport activity

No

PFCIRM129_00700

slpB

PSE

S1

(+) 0.014

(+) 0.624

(+) 0.122

Cell wall/surface protein containing 3 SLH domains predicted by HMM Pfam

Yes

PFCIRM121_07195

htrA4

SEC

S2

(−) 0.104

(−) 0.130

(−) 0.136

Trypsine-like serine protease

Yes

  1. The localisation corresponds to the category predicted in silico with SurfG + software, as described by Barinov et al.20. C cytoplasmic protein, PSE: Protein surface exposed, M: membrane protein, SEC: secreted protein. bGene [P/T/G]i corresponds to the I-th candidate gene according to proteomic, transcriptomic and genomic data analysis. S1 and S2 correspond to genes selected for external reasons. ccorrelation: G, T and P correspond to the R squared values (when available) of a regression of IL-10 production against a gene presence/absence pattern (G), expression levels (T) and protein presence/absence pattern at the bacterial surface (P). Pouf: Protein of Unknown Function. dMeans ‘genes successfully inactivated’. For details of the association study, see Methods section.
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