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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.