YicC: the Connections to Ribonuclease PH and Guanylate kinase(?)
This discussion will relate to this cluster.
The graphical diagram is focused on the red genes numbered 1, which is the
yicC gene in E.coli. The clustering I want to discuss is with
- the green genes numbered 2 and annotated as Guanylate kinase (EC 2.7.4.8), and
- the purple genes numbered 4 and annotated as Ribonuclease PH (EC 2.7.7.56).
Let me begin by pointing out what little I found about yicC in E.coli:
Res Microbiol. 1991 Feb-Apr;142(2-3):283-8
Three genes preceding pyrE on the Escherichia coli chromosome are essential for survival and normal cell morphology in stationary culture and at high temperature.
Poulsen P, Jensen KF.
Previous studies of the upstream region of the pyrE gene in
Escherichia coli revealed three genes of unknown
function. Inactivation of these genes (designated orfE, orfX and
orfY) by crossing the KmR-cassette-disrupted orf into the
chromosome indicated that they were not required during
exponential growth (Poulsen et al., Mol., Microbiol., 1989
b). Here we report that the three genes are of importance in the
stationary phase. Thus, cultures of the mutants grown to a
stationary state in rich media contained bacterial filaments of
abnormal morphology. In addition, flow cytometric analyses showed
that outgrown cultures of the orf mutants have anomalous size
distribution and DNA content, and that rifampicin treatment of
exponentially growing mutants results in cell populations with
chromosome numbers in the range from about 1 to 10, compared with
wild type strains that end up with 4 and 8 full
chromosomes. Finally, it appeared that the three orf's are
indispensable at high temperatures since the insertion mutants
were unable to form colonies above 45 degrees C and since cultures
of exponentially growing mutants lysed upon a temperature shift
from 37 degrees C to 45 degrees C.
PMID: 1925027
or, as Swiss Prot puts it "Essential for E.coli under special growth condition".
Here is an abtsract relating to RNase PH:
Ribonuclease PH plays a major role in the exonucleolytic maturation of
CCA-containing tRNA precursors in Bacillus subtilis
by Tingyi Wen, Irina A. Oussenko, Olivier Pellegrini, David H. Bechhofer, and Ciaran Condon
In contrast to Escherichia coli, where all tRNAs have the CCA motif
encoded by their genes, two classes of tRNA precursors exist in the
Gram-positive bacterium Bacillus subtilis. Previous evidence had shown
that ribonuclease Z (RNase Z) was responsible for the endonucleolytic
maturation of the end of those tRNAs lacking an encoded CCA motif,
accounting for about one-third of its tRNAs. This suggested that a
second pathway of tRNA maturation must exist for those precursors with
an encoded CCA motif. In this paper, we examine the potential role of
the four known exoribonucleases of B.subtilis, PNPase, RNase R, RNase
PH and YhaM, in this alternative pathway. In the absence of RNase PH,
precursors of CCA-containing tRNAs accumulate that are a few
nucleotides longer than the mature tRNA species observed in wild-type
strains or in the other single exonuclease mutants. Thus, RNase PH
plays an important role in removing the last few nucleotides of the
tRNA precursor in vivo. The presence of three or four exonuclease
mutations in a single strain results in CCA-containing tRNA precursors
of increasing size, suggesting that, as in E.coli, the exonucleolytic
pathway consists of multiple redundant enzymes. Assays of purified
RNase PH using in vitro-synthesized tRNA precursor substrates suggest
that RNase PH is sensitive to the presence of a CCA motif. The
division of labor between the endonucleolytic and exonucleolytic
pathways observed in vivo can be explained by the inhibition of RNase
Z by the CCA motif in CCA-containing tRNA precursors and by the
inhibition of exonucleases by stable secondary structure in the
extensions of the majority of CCA-less tRNAs.
Thus, it appears to play a role in tRNA maturation.
The Guanylate kinase (EC 2.7.4.8) catalyzes the reaction
ATP + GMP = ADP + GDP
First, it should be noted that there appear to be multiple genes
annotated as guanylate kinase in a number of organisms. One has to suspect
that we may not be dealing with real guanylate kinase.
In any event, note that in the upper part of the pinned region, we see the red gene
coupled to the "guanylate kinase". In the bottom, the coupling is to ribonuclease PH.
Finaly, in just a few organisms, we see all three of the genes clustered.
So, I think that poses the question of "What does this mean?" quite nicely.
Is this a cluster relating to tRNA maturation? Does the occasional clustering
with the omega subunit of the RNA polymerase mean anything?