Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis

J Mol Biol. 2010 Jan 29;395(4):686-704. doi: 10.1016/j.jmb.2009.10.063. Epub 2009 Nov 3.

Abstract

Comprehensive multiple sequence alignments of the multisubunit DNA-dependent RNA polymerase (RNAP) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial RNAPs, eukaryotic RNAPs I-III, nuclear-cytoplasmic large double-stranded DNA virus RNAPs, and plant plastid RNAPs, were created [Lane, W. J. and Darst, S. A. (2009). Molecular evolution of multisubunit RNA polymerases: sequence analysis. In press]. The alignments were used to delineate sequence regions shared among all classes of multisubunit RNAPs, defining common, fundamental RNAP features as well as identifying highly conserved positions. Here, we present a systematic, detailed structural analysis of these shared regions and highly conserved positions in terms of the RNAP structure, as well as the RNAP structure/function relationship, when known.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Catalytic Domain
  • Conserved Sequence
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics*
  • Evolution, Molecular*
  • Genes, Bacterial
  • Glycine / chemistry
  • Models, Molecular
  • Phylogeny
  • Protein Multimerization
  • Protein Structure, Tertiary
  • Protein Subunits
  • Sequence Alignment
  • Structural Homology, Protein
  • Thermus thermophilus / enzymology
  • Thermus thermophilus / genetics

Substances

  • Bacterial Proteins
  • Protein Subunits
  • DNA-Directed RNA Polymerases
  • Glycine