The standard view seems to be the one expressed here:
Gene. 1985;40(1):67-78
Nucleotide sequence of the rpsU-dnaG-rpoD operon from Salmonella
typhimurium and a comparison of this sequence with the homologous
operon of Escherichia coli.
Erickson BD, Burton ZF, Watanabe KK, Burgess RR.
In Escherichia coli the genes encoding ribosomal protein S21
(rpsU), DNA primase (dnaG), and the 70-kDal sigma subunit of RNA
polymerase (rpoD) are contained in a single operon. These gene
products are involved in the initiation of translation, DNA
replication, and transcription, respectively. We have examined the
homologous region in the closely related bacterium Salmonella
typhimurium and have found that the same three genes are similarly
organized. We have sequenced the DNA for this operon in
S. typhimurium and have compared the (nt) nucleotide and amino
acid (aa) sequences with E. coli. In the coding regions, the
sequence conservation varies from extremely high for rpsU to
moderate for dnaG with respect to both nt and aa sequence. In the
noncoding regions, sequences thought to be important for the
regulation of transcription are conserved, while other sequences
are not conserved. aa differences in DNA primase and sigma are not
randomly distributed and suggest regions that may be important for
protein structure or function.
PMID: 3005129
and
Mol Microbiol. 1993 Apr;8(2):343-55.Links Conservation and evolution of the rpsU-dnaG-rpoD macromolecular synthesis operon in bacteria. Versalovic J, Koeuth T, Britton R, Geszvain K, Lupski JR. The macromolecular synthesis (MMS) operon contains three essential genes (rpsU, dnaG, rpoD) whose products (S21, primase, sigma-70) are necessary for the initiation of protein, DNA, and RNA synthesis respectively. PCR amplifications with primers complementary to conserved regions within these three genes, and subsequent DNA sequencing of rpsU-dnaG PCR products, demonstrate that the three genes appear to be contiguous in 11 different Gram-negative species. Within the Gram-negative enteric bacterial lineage, the S21 amino acid sequence is absolutely conserved in 10 species examined. The putative nuteq antiterminator sequence in rpsU consists of two motifs, boxA and boxB, conserved in primary sequence and secondary structure. The terminator sequence, T1, located between rpsU and dnaG is conserved at 31 positions in nine enterobacterial species, suggesting the importance of primary sequence in addition to secondary structure for transcription termination. The intergenic region between rpsU and dnaG varies in size owing to the presence or absence of the Enterobacterial Repetitive Intergenic Consensus (ERIC) DNA element. The rpoD gene contains rearrangements involving a divergent sequence, although two carboxy-terminal regions which encode functional domains are conserved in primary sequence and spacing. Our data suggest that primary sequence divergence and DNA rearrangements in both coding and non-coding sequences account for the interspecies variation in operon structure. However, MMS operon gene organization and cis-acting regulatory sequences appear to be conserved in diverse bacteria. PMID: 8316085
Before I comment further, let's talk briefly about the function of these three genes.
The DNA primase (EC 2.7.7.-) is well-known as a factor in DNA replication. There is a substantial amount of literature describing its role, crystal structures, etc.
The RNA polymerase sigma factor RpoD is the major sigma factor (which is the "read head" for the RNA polymerase in the normal growth condition).
What is the role of ribosomal protein S21p in this cluster? Consider this quote from a 1981 paper that S21 plays a role in binding the smal subunit of the ribosome to the ribosome binding site.
Eur. J. Biochem. 118, 615-619 (1981) The Funcion of Ribosomal Protein S21 in Protein Synthesis by Jan Van Duin and Robert Wijnands
These results indicate that the binding of natural templates differs from that of random RNA. More specifically it is implied that natural mRNA, in contrast to synthetic RNA, needs a base-pairing reaction with the 16-S RNA 3' terminus in order to bind to the ribosome. Recently we observed that 30-S subunits that miss S21 cannot bind oligonucleotides complementary to the 16-S RNA 3' end.
With these heretical thoughts emerging, I move to this second cluster. This diagram shows (as the red genes numbered 1) a gene that clusters with the three described above within the Proteobacteria. This hypothetical is worth studying for a bit. Under the standard interpretation it plays a central enough role to be added to this key regulatory operon. Under the heretical view, it would be implicated in the interface between transcription and translation.
Anyway, check it out.