A Conserved Cluster in the Gram-Positive Bacteria Containing a Phosphohydrolase and a Phosphate Starvation Induced Gene

This cluster contains nine genes, more-or-less:

  1. the red genes numbered 1 encode a metal dependent phosphohydrolase,
  2. the green genes numbered 2 encode a gene we annotated as Phosphate starvation-inducible protein PhoH, predicted ATPase,
  3. the blue genes numbered 3 encode a predicted metal-dependent hydrolase,
  4. the purple genes numbered 4 encode Diacylglycerol kinase (EC 2.7.1.107),
  5. the orange genes numbered 5 encode a gene we have annotated as GTP-binding protein Era,
  6. the dark purple genes numbered 6 encode DNA recombination and repair protein RecO,
  7. the light orange genes numbered 7 encode a gene that we have annotated as GatB Yqey domain protein,
  8. the blue-green genes numbered 8 encode Cytidine deaminase (EC 3.5.4.5), and
  9. the light green genes numbered 9 encode a gene we annotated as Sporulation protein.


First, let me mention a paper published in 1998 in which the genes numbered 2 and 9 were reported to occur in a 3-gene operon (with a third gene shown as 17) in B.megaterium.

The abstract of that paper is as follows: 
J Gen Appl Microbiol. 1998 Oct;44(5):317-326

Molecular characterization of the operon comprising the spoIV gene of
Bacillus megaterium DSM319 and generation of a deletion mutant.

Wittchen, Strey, and Bultmann

According to sequence analysis, the spoIV-locus of Bacillus megaterium
DSM 319 is 1,185 bp long; it is the second gene of a sporulation
operon, which altogether contains three open reading frames. The ORF
preceding spoIV encodes a putative polypeptide with 94 amino acids;
the 3rd ORF of the operon has 972 bp corresponding to 324 amino
acids. The operon is flanked on both sides by palindromic sequences,
probably representing Rho-independent terminators. A primer extension
analysis revealed that mRNA synthesis starts immediately downstream of
a promoter, which is similar to the consensus sequence of Bacillus
subtilis sigma(E) dependent promoters. Both the -35 and the -10 region
are within the terminator region of the preceding operon. Gene
knockout experiments and reporter gene assays with a newly developed
system based on the heterologous Paenibacillus macerans glucanase gene
(bgl) confirmed sigma(E)-dependent transcription. Two open reading
frames of a further upstream operon were also identified. Northern
analysis revealed that transcription of these ORFs comes about in late
sporulation phases. The genetic organization of the spoIV comprising
operon and adjacent loci clearly resembles that of the B. subtilis
yqfa-phoH gene cluster. Thus our findings are of general significance
for endospore-forming bacteria.


I have not checked all of the genomes in the shown in the pinned region, but many of them surely do form spores.

A paper written in 1999 describes a 3-gene operon in Pseudomonas that contains recO, engA, and rnc (encoding "a double-stranded endoribonuclease that assists in the maturation of stable RNAs". The authors wrote "there is growing evidence that RNase III and Era may share a common function in the maturation of rRNA and the assembly of the ribosome".

RNase III occurs in Bacillus but not clustered with the other two (it clusters with Chromosome partition protein smc).