A Cluster on the Boundary of Transcription and Translation (or is it Replication?)

Let us begin with this cluster which I use to illustrate the widespread co-occurrence of the three genes:

  1. the red genes numbered 1 (dnaG) encode DNA primase (EC 2.7.7.-),
  2. the green genes numbered 2 (rpoD) encode RNA polymerase sigma factor RpoD, and
  3. the blue genes numbered 3 (rpsU) encode SSU ribosomal protein S21p.


It has been shown in at least E.coli and Rickettsia prowazekii that the three genes make up an operon.

Why should these three genes make up an operon?

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
The common wisdom is that this operon should be called to mcromolecular synthesis operon, and that it is a major switch used to regulate the cell from growth to non-growth situation. This one switch can shutdown macromolecular synthesis (of RNA, DNA and proteins).

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.


Now, given all that, I wish to make the completely irresponsible conjecture that the three genes may not be just representatives of three disparate systems that occasionally need to be shutdown simultaneously. What if they were actually related components of the same process? The link between the sigma factor and ribosomal protein S1p is clear: shortly after the sigma factor binds and the RNA polymerase starts producing mRNA, the S1p protein acts as the link between transciption and the start of translation. The sticky issue is DnaG. If it really only plays a role in replication, then there is nothing more to say. However, I must ask "Is there any possibility it plays a role in transcription?"

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.