Bacterial RNA polymerase subunit ω and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly

Bacterial RNA polymerase subunit ω and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly

^*Waksman Institute, ^¶Department of Genetics, ^‡Department of Chemistry and ^§Howard Hughes Medical Institute, Rutgers, The State University, Piscataway, NJ 08854; and ^†The Rockefeller University, New York, NY 10021

Communicated by Jeffrey W. Roberts, Cornell University, Ithaca, NY (received for review October 6, 2000)

Abstract

Bacterial DNA-dependent RNA polymerase (RNAP) has subunit composition β′βα^Iα^IIω. The role of ω has been unclear. We show that ω is homologous in sequence and structure to RPB6, an essential subunit shared in eukaryotic RNAP I, II, and III. In Escherichia coli, overproduction of ω suppresses the assembly defect caused by substitution of residue 1362 of the largest subunit of RNAP, β′. In yeast, overproduction of RPB6 suppresses the assembly defect caused by the equivalent substitution in the largest subunit of RNAP II, RPB1. High-resolution structural analysis of the ω–β′ interface in bacterial RNAP, and comparison with the RPB6–RPB1 interface in yeast RNAP II, confirms the structural relationship and suggests a “latching” mechanism for the role of ω and RPB6 in promoting RNAP assembly.

Footnotes

↵ ‖ To whom reprint requests should be addressed. E-mail: severik{at}waksman.rutgers.edu.
Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. AJ295839).
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID code 1HQM).
Abbreviations:

RNAP,

RNA polymerase;

SeMet,

selenomethionine