Structure and function of CarD, an essential mycobacterial transcription factor

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12619-24. doi: 10.1073/pnas.1308270110. Epub 2013 Jul 15.

Abstract

CarD, an essential transcription regulator in Mycobacterium tuberculosis, directly interacts with the RNA polymerase (RNAP). We used a combination of in vivo and in vitro approaches to establish that CarD is a global regulator that stimulates the formation of RNAP-holoenzyme open promoter (RPo) complexes. We determined the X-ray crystal structure of Thermus thermophilus CarD, allowing us to generate a structural model of the CarD/RPo complex. On the basis of our structural and functional analyses, we propose that CarD functions by forming protein/protein and protein/DNA interactions that bridge the RNAP to the promoter DNA. CarD appears poised to interact with a DNA structure uniquely presented by the RPo: the splayed minor groove at the double-stranded/single-stranded DNA junction at the upstream edge of the transcription bubble. Thus, CarD uses an unusual mechanism for regulating transcription, sensing the DNA conformation where transcription bubble formation initiates.

Keywords: initiation; mycobacteria; ribosomal RNA (rRNA); transcription activator.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Mycobacterium smegmatis / chemistry
  • Mycobacterium smegmatis / genetics
  • Mycobacterium smegmatis / metabolism
  • Mycobacterium tuberculosis / chemistry*
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / metabolism
  • Promoter Regions, Genetic*
  • Structure-Activity Relationship
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic / physiology

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Transcription Factors

Associated data

  • GEO/GSE48164
  • PDB/4L5G