A Hypothetical Protein Coupled to PEP synthase
Check out this cluster.
The green genes numbered 2 are Phosphoenolpyruvate synthase (EC 2.7.9.2).
There are two things I think should be noted about this cluster:
- First, the red genes numbered 1 (often called ydiA)
are essentially
uncharacterized and probably play a role associated with the PEP
synthase or PEP.
- Second, note the coupling between the PEP synthase and the blue
genes numbered 3 with the function
Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54).
This couples PEP synthesis to chorismate synthesis (which takes PEP as
input).
The real issue is, of course, what do the red genes do? There are
clues, including some developed by Dmitry Rodionov:
Microbiology. 2004 Nov;150(Pt 11):3571-90.
Comparative genomics of the KdgR regulon in Erwinia chrysanthemi
3937 and other gamma-proteobacteria.
Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N.
In the plant-pathogenic enterobacterium Erwinia chrysanthemi,
almost all known genes involved in pectin catabolism are
controlled by the transcriptional regulator KdgR. In this study,
the comparative genomics approach was used to analyse the KdgR
regulon in completely sequenced genomes of eight enterobacteria,
including Erw. chrysanthemi, and two Vibrio species. Application
of a signal recognition procedure complemented by operon structure
and protein sequence analysis allowed identification of new
candidate genes of the KdgR regulon. Most of these genes were
found to be controlled by the cAMP-receptor protein, a global
regulator of catabolic genes. At the next step, regulation of
these genes in Erw. chrysanthemi was experimentally verified using
in vivo transcriptional fusions and an attempt was made to clarify
the functional role of the predicted genes in pectin
catabolism. Interestingly, it was found that the KdgR protein,
previously known as a repressor, positively regulates expression
of two new members of the regulon, phosphoenolpyruvate synthase
gene ppsA and an adjacent gene, ydiA, of unknown function. Other
predicted regulon members, namely chmX, dhfX, gntB, pykF, spiX,
sotA, tpfX, yeeO and yjgK, were found to be subject to classical
negative regulation by KdgR. Possible roles of newly identified
members of the Erw. chrysanthemi KdgR regulon, chmX, dhfX,
gntDBMNAC, spiX, tpfX, ydiA, yeeO, ygjV and yjgK, in pectin
catabolism are discussed. Finally, complete reconstruction of the
KdgR regulons in various gamma-proteobacteria yielded a metabolic
map reflecting a globally conserved pathway for the catabolism of
pectin and its derivatives with variability in transport and
enzymic capabilities among species. In particular, possible
non-orthologous substitutes of isomerase KduI and a new
oligogalacturonide transporter in the Vibrio species were
detected.
PMID: 15528647
As far as I can tell, I was the first one who annotated these genes
(the red ones) as ATP/GTP-binding protein, although I have no
recollection of doing so.