title: Structure and function of CarD, an essential mycobacterial transcription factor.
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.
authors.affiliation: Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
authors.forename: Devendra B
authors.initials: DB
authors.lastname: Srivastava
authors.forename: Katherine
authors.initials: K
authors.lastname: Leon
authors.forename: Joseph
authors.initials: J
authors.lastname: Osmundson
authors.forename: Ashley L
authors.initials: AL
authors.lastname: Garner
authors.forename: Leslie A
authors.initials: LA
authors.lastname: Weiss
authors.forename: Lars F
authors.initials: LF
authors.lastname: Westblade
authors.forename: Michael S
authors.initials: MS
authors.lastname: Glickman
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.forename: Seth A
authors.initials: SA
authors.lastname: Darst
authors.forename: Christina L
authors.initials: CL
authors.lastname: Stallings
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Campbell
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020102:Mycobacterium smegmatis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009169:Mycobacterium tuberculosis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D014157:Transcription Factors
keywords: initiation; mycobacteria; ribosomal RNA (rRNA); transcription activator