A Model for Basic Eukaryotic Functions

A PLOS Biology research article titled Mutation of RNA Pol III Subunit rpc2/polr3b Leads to Deficiency of Subunit Rpc11 and Disrupts Zebrafish Digestive Development, which is authored by Nelson S. Yee, Weilong Gong, Ying Huang, Kristin Lorent, Amy C. Dolan, Richard J. Maraia and Michael Pack, cited data obtained through use of the zebrafish as a model for POL III function analysis. POL III is an RNA polymerase subunit. RNA polymerases are very large multi-subunit protein complexes. Three types of subunits found in eukaryotes are:

RNA polymerase I (Pol I). It transcribes the rRNA genes for the precursor of the 28S, 18S, and 5.8S molecules (and is the busiest of the RNA polymerases).

RNA polymerase II (Pol II; also known as RNAP II). It transcribes protein-encoding genes into mRNA (and also the snRNA genes).

RNA polymerase III (Pol III). It transcribes the 5S rRNA genes and all the tRNA genes.

The following is the summary of the authors of Mutation of RNA Pol III Subunit rpc2/polr3b Leads to Deficiency of Subunit Rpc11 and Disrupts Zebrafish Digestive Development (in blue):

The transmission of genetic information from DNA to messenger RNA to protein depends on the function of a large number of small noncoding RNA molecules. The genes encoding these RNAs are transcribed by RNA polymerase III (Pol III), a 17-subunit protein complex whose structure is closely related to that of RNA polymerases I and II. Here, we report the effect of a mutation in a gene encoding one Pol III subunit, Polr3b, which disrupts proliferation and growth of tissue progenitor cells in the zebrafish digestive system. Analyses of a nearly identical mutation in the yeast S. pombe gene encoding Polr3b, also known as Rpc2, suggested that the zebrafish mutation disrupted the mutant Polr3b protein's interaction with another Pol III subunit, Polr3k, also known as Rpc11. Overexpression of the gene encoding Polr3k in the Polr3b mutants partially rescued (reversed) the mutant phenotype. These findings extend our knowledge of the mechanism of Pol III function, which appears to have been highly conserved during eukaryotic evolution. Furthermore, these data also suggest that assembly of the 17-subunit Pol III enzyme is a dynamic process, since Polr3k overexpression can partially rescue the mutant phenotype. Understanding how Pol III is assembled has implications for human disease, since Pol III activity is markedly increased in most cancers.

Note that the function of the genetic code is dependent on the transcription function of RNA polymerase III (Pol III). In addition the structure of Pol III, a 17 subunit protein, is similar to RNA polymerases I and II. The translation function is made possible by Pol III. The first paragraph of the introduction is instructive. Quoting (in blue):

RNA Polymerase III (Pol III) is a 17-subunit complex that is responsible for the transcription of small noncoding RNAs such as transfer RNAs (tRNAs), 5S ribosomal RNA (rRNA), U6 small nuclear RNA (snRNA), 7SL RNA, and others in eukaryotes [1,2]. The two largest subunits, Rpc1 (160 kDa) and Rpc2 (130 kDa), are highly homologous to their counterparts in Pol I and Pol II, and together provide a large surface area for interaction with many of the other subunits [2]. Structural analyses of Pol III complexes [3,4], together with two-hybrid analysis [5], have identified multiple subunit interactions (reviewed in [1]). These, together with biochemical and genetic analyses, have led to a model that attributes some of the unique functions of Pol III, including its high processivity, efficient transcription termination and recycling activity, RNA 3′ cleavage activity, and interaction with diverse promoters, to specific individual subunits.

The model links unique and specified Pol III functions, including a capacity to interact with diverse promotors, to individual subunits. Quoting from the next paragraph (in blue):

Mutational analyses in yeast clearly show that an intact Pol III system is essential for cell growth. The effects of reduced Pol III function are predicted to be broad, including protein synthesis necessary for cell-cycle progression (tRNAs), ribosome biogenesis (5S rRNA), mRNA splicing (U6 snRNA), and membrane targeting of newly translated proteins (7SL RNA). Pol III transcription is tightly regulated during the cell cycle [6] and in response to cellular stress [7]. Recent studies in human cells have also highlighted the roles of oncogenes and tumor suppressors such as Rb [8,9], p53 [9–11], and cMyc [9,12] in controlling the interactions between the transcription factors that bring the Pol III complex to the promoters of its target genes (reviewed in [13,14]). Other proteins, such as Maf1 [15–18] and the oncogenic kinase CK2 [19–20], can regulate Pol III function through direct interactions with the Pol III complex. Thus, eukaryotic cells have evolved multiple independent mechanisms for regulating Pol III activity.

It would have been interesting if Michael Behe had focused on biosynthesis as an example of irreducible complexity. I would have enjoyed reading the responses of critics. A depiction of pathways to the evolution of "multiple independent mechanisms for regulating Pol III activity" would have been most interesting. So would a gradual, incremental model for cell-cycle progression.