In silico exploration of the fructose-6-phosphate phosphorylation step in glycolysis: genomic evidence of the coexistence of an atypical ATP-dependent along with a PPi-dependent phosphofructokinase in Propionibacterium freudenreichii subsp. shermanii.
We performed a detailed bioinformatic study of the catalytic step of fructose-6-phosphate phosphorylation in glycolysis based on the raw genomic draft of Propionibacterium freudenreichii subsp. shermanii (P. shermanii) ATCC9614 [Meurice et al., 2004]. Our results provide the first in silico evidence of the coexistence of genes coding for an ATP-dependent phosphofructokinase (ATP-PFK) and a PPi-dependent phosphofructokinase (PPi-PFK), whereas the fructose-1,6-bisphosphatase (FBP) and ADP-dependent phosphofructokinase (ADP-PFK) are absent. The deduced amino acid sequence corresponding to the PPi-PFK (AJ508922) shares 100% similarity with the already characterised propionibacterial protein (P29495; Ladror et al., 1991]. The unexpected ATP-PFK gene (AJ509827) encodes a protein of 373 aa which is highly similar (50% positive residues) along at least 95% of its sequence length to different well-characterised ATP-PFKs. The characteristic PROSITE pattern important for the enzyme function of ATP-PFKs (PS00433) was conserved in the putative ATP-PFK sequence: 8 out of 9 amino acid residues. According to the recent evolutionary study of PFK proteins with different phosphate donors [Bapteste et al., 2003], the propionibacterial ATP-PFK harbours a G104-K124 residue combination, which strongly suggested that this enzyme belongs to the group of atypical ATP-PFKs. According to our phylogenetic analyses the amino acid sequence of the ATP-PFK is clustered with the atypical ATP-PFKs from group III of the Siebers classification [Siebers et al., 1998], whereas the expected PPi-PFK protein is closer to the PPi-PFKs from clade P [Müller et al., 2001]. The possible significance of the co-existence of these two PFKs and their importance for the regulation of glycolytic pathway flux in P. shermanii is discussed.
Meurice
Guillaume
G
INRA-STLO, Rennes cedex, France. gmeurice@pasteur.fr
Deborde
Catherine
C
Jacob
Daniel
D
Falentin
Hélène
H
Boyaval
Patrick
P
Dimova
Diliana
D
D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D019295:Computational Biology; D019143:Evolution, Molecular; D005636:Fructosephosphates / Q000378:metabolism*; D016680:Genome, Bacterial; D023281:Genomics; D006019:Glycolysis / Q000235:genetics; D008969:Molecular Sequence Data; D010766:Phosphorylation; D010770:Phosphotransferases / Q000235:genetics* / Q000378:metabolism*; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D011424:Propionibacterium / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D005636:Fructosephosphates; C027618:fructose-6-phosphate; D000255:Adenosine Triphosphate; D010770:Phosphotransferases; D017853:Phosphotransferases (Alcohol Group Acceptor); C442129:ADP D-fructose-6-phosphate 1-phosphotransferase; C022502:pyrophosphate-fructose 6-phosphate 1-phosphotransferase