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Table 4 List and dispatching of genes responsible for nitrate and sugar degradation in 21 strains of Propionibacterium freudenreichii

From: Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

 

Strains phenotype

Genes involved

Genetic support on chromosome

Glucose

degraded by the 21 strains

sglT, ppgk, pgi, pfk, X

dispatched genes

Glycerol

degraded by the 21 strains

glpF, glpK, glpA, glpB, glpC

dispatched genes and 1 genomic island glpABC (no tnp)

Mannose

degraded by the 21 strains

PFREUD_10820, PFREUD_18490

dispatched genes

Galactose

degraded by the 21 strains

galP, PFREUD_22330, galK1, galK2, galT, galE, galE2, galE3

1 genomic island galPE1encompassed by tnp

Inositol

degraded by the 21 strains

iolT1, iolT2, iolT3, iol, iolG1, iolG2, iolE1, iolE2, iolE3, iolB, iolC, iolD, iolA, iolE3, iolG2, iolH, iolA, iolD, iolB, iolC, iolG1, iolE, iolE2, iolG2, iolH

3 genomic islands: iolE3G2H, iolADBCG1E, iolE2G2H, several mutations introducing frameshift, functional redondancy and complementation

Nitrate

degraded by 6 strains in a qualitative manner

narK, narG, narH, narJ, narI

1genomic island: narKGHJI. Excision of narKG and 5’ part of narH in nitrate negative strains

Melibiose

degraded by 1 strain in a qualitative manner

rbsR, aga, msmE, amyD and amyC

1 genomic island rbsR, aga, msmE, amyDC (no tnp but GC skew)

Lactose

degraded by 17 strains in a qualitative manner

galP, lacZ, galE1

1 genomic island galP, lacZ, galE1 encompassed by tnp

Gluconate

degraded by 13 strains in a quantitative manner

gntP, gntU, gntK, ilvD, eda, gnd1, gnd2

dispatched genes, frameshifts could explained the inability

L-arabinose

degraded by 17 strains in a quantitative manner

rbsB, rbsA, rbsC, rbsH2, araA, araB, araD, araD1, araB, araM, araL

2 genomic islands: rbsBACH2araABDD1 and araBML

D-fructose

degraded by 18 strains in a quantitative manner

sacL, frk

dispatched genes

Ribose

degraded by 9 strains in a quantitative manner

rbsB, rbsA, rbsC, araH2, rbsK

1 genomic island rbsBAC (no tnp), frameshifts could explained the inability

  1. All pathways have been reconstructed in Propionibacterium freudenreichii, in this paper, glucose [15] and gluconate [8] pathways excepted. Reference pathways of other species are cited in the Results section. In the absence of a gene name, the locus-tag (PFREUD) of the reference strain CIRM BIA 1 was provided. A list of orthologous genes in the 21 strains is available in Additional file 1: Table S1.
  2. The annotations of all the strains studied are available in the EMBL database.