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

  1. the green genes numbered 2 and annotated as Guanylate kinase (EC 2.7.4.8), and
  2. 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?